Comparison of the Protein Crystal Structure between Wild-Type...

38
Comparison of the Protein Crystal Structure between Wild-Type and Per-acetylated Bovine Carbonic Anhydrase Christine Cuddemi Senior Thesis Emmanuel College Chemistry and Chemical Biology Department at Harvard University April 22, 2013 © Christine Cuddemi

Transcript of Comparison of the Protein Crystal Structure between Wild-Type...

Page 1: Comparison of the Protein Crystal Structure between Wild-Type …library.emmanuel.edu/archive/sites/default/files/Cuddemi... · 2015. 3. 25. · Figure 1: BCA crystal structure [3].

Comparison of the Protein Crystal Structure between Wild-Type and Per-acetylated

Bovine Carbonic Anhydrase

Christine Cuddemi

Senior Thesis

Emmanuel College

Chemistry and Chemical Biology Department at Harvard University

April 22, 2013

© Christine Cuddemi

Page 2: Comparison of the Protein Crystal Structure between Wild-Type …library.emmanuel.edu/archive/sites/default/files/Cuddemi... · 2015. 3. 25. · Figure 1: BCA crystal structure [3].

Abstract

Understanding how proteins crystalize is a fundamental question in biochemistry,

and has important implications in molecular recognition. Carbonic anhydrase,

specifically bovine carbonic anhydrase (SCA) is a good model system to study

crystallization because SCA is structurally rigid, easily produced in large quantities, and

well-studied. SCA contains 18 lysine amino groups, each of which is on the surface of

the protein. When the lysine amino groups are acetylated with acetic anhydride, the

overall negative charge of the protein increases substantially. We explored three

physical properties of SCA and per-acetylated SCA: protein crystallization

thermostability of the proteins and the binding affinity of each protein to a given ligand.

We successfully labeled the lysine amino groups ((SCA-(NHAc)18), as well as obtained

a crystallized structure. With differential scanning calorimetry we were able to gather

stability data of both proteins. Further studies will look into the binding affinity of

arylsulfonamide ligands to per-acetylated SCA using isothermal titration calorimetry.

Overall, this research will aid pharmaceutical studies with the understanding of protein­

ligand interactions and protein stability in regards to the functionality of drugs.

Cuddemi 1

Page 3: Comparison of the Protein Crystal Structure between Wild-Type …library.emmanuel.edu/archive/sites/default/files/Cuddemi... · 2015. 3. 25. · Figure 1: BCA crystal structure [3].

Table of Contents

ABSTRACT . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1

TABLE OF CONTENTS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2

LIST OF FIGURES . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3

1. INTRODUCTION . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4 -11

PROTEIN CRYSTALLIZATION . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4 -5

BOVINE CARBOINC ANHYDRASE . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5 -7

THESIS HyPOTHESiS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7 -8

METHODS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8 -10

FUTURE OF RESEARCH . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10 -11

SUMMARY OF RESULTS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11

2. MATERIALS AND METHODS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12 -15

2.1 ACETYLATION . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12 -13

2.2 CRYSTALLIZATION . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14 -15

2.2.1 BCA CRYSTALLIZATION . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14

2.2.2 BCA-(Ac)18 CRYSTALLIZATION . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14

2.3 THERMOSTABILITY . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15

3 RESULTS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16 -28

ACETYLATION . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16 -17

CRySTALLIZATION . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18 -19

PROTEIN - PROTEIN INTERACTIONS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19 -26

THERMOSTABILITY . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26 -28

4 DiSCUSSiON ................................................................................ 29 -32

SUMMARY OF RESULTS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29 -30

FUTURE DIRECTIONS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32

5 REFERENCES .............................................................................. 33 -34

6 ApPENDiX ................................................................................... 35 -37

Cuddemi 2

Page 4: Comparison of the Protein Crystal Structure between Wild-Type …library.emmanuel.edu/archive/sites/default/files/Cuddemi... · 2015. 3. 25. · Figure 1: BCA crystal structure [3].

2. List of Figures

[1] BCA CRYSTAL STRUCTURE . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6

[2] CAPILLARY ELECTROPHORESIS SCHEMATIC ................................ 9

[3] DIFFERENTIAL SCANNING CALORIMETRY SCHEMATIC ................... 10

[4]lsOTHERMIAL TITRATION CALORIMETRY SCHEMATIC .................... 10

[5] CAPILLARY ELECTROPHEROGRAM .............................................. 1 7

[6] BCA CAPILLARY ELECTROPHEROGRAM COMPARISON ................. 1 7

[7] COMPARISON OF CRYSTAL STRUCTURES .................................... 19

[8] DSC COMPARISON DATA . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27

[9] BTA & TA liGAND STRUCTURES . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28

[10] NMR OF HCA DATA . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31

2. List of Tables

[1] ACETYLATION VOLUMES ............................................................ 1 2

[2] PROTEIN-PROTEIN INTERACTIONS KEY . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20 - 22

[3] BCA CRYSTAL INTERACTIONS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22

[4] BCA-(Ac)18 CRYSTAL INTERACTIONS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23 - 25

[5] INTERACTIONS SUMMARY TABLE . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25 - 26

Cuddemi 3

Page 5: Comparison of the Protein Crystal Structure between Wild-Type …library.emmanuel.edu/archive/sites/default/files/Cuddemi... · 2015. 3. 25. · Figure 1: BCA crystal structure [3].

1 Introduction

Crystallization is one of the fundamental processes that allow a three­

dimensional structure of proteins and nucleic acids to be observed. The first published

observation of a crystallized protein was in the year 1840 by Hunefel [1]. Hemoglobin

from an earthworm was obtained as a flat plate-like crystal when the worm's blood was

pressed between two slides of glass. It was then noted that in a controlled environment

of evaporation, a protein solution can be crystallized, also known as slow dehydration

[1]. Fast forward about eighty years to when the first enzyme, urease, was crystallized

by Sumner in the year 1925. This was around the same time that insulin, a hormone,

was successfully crystallized. With the advantages of protein crystal observations, more

questions began to be asked about the processes of crystallization; how exactly

different molecules crystallized and under what conditions this occurred.

Protein growth and crystallization have many applications, especially in the

pharmaceutical industry. The first published observation of crystallized proteins dates

back about 160 years [1]. In relation to pharmaceutical implications, the understanding

of protein crystals can be helpful in the development of novel drugs. Knowledge of the

three-dimensional structure of a target protein can be used to design compounds that

selectively bind to sites of this protein and thereby inhibit or stimulate its activities [1].

Proteins are composed of different amino acid residues, some of which have polar side

chains, specifically the amino groups on ends of molecules may be charged. There are

four amino acids with "charged" side chains at the physiological pH; arginine and lysine

are positively charged; aspartic acid and glutamic acid are negatively charged. When a

protein is in solution, these charged groups interact extensively with water and help to

Cuddemi 4

Page 6: Comparison of the Protein Crystal Structure between Wild-Type …library.emmanuel.edu/archive/sites/default/files/Cuddemi... · 2015. 3. 25. · Figure 1: BCA crystal structure [3].

solvate the protein [1]. The net charge of a protein depends on both the amino acid

sequence and environmental factors (ie. the pH of the solution, the ionic strength of the

solution and the presence of other co-solutes).

Model systems have been used to hundreds of years and many of the common

scientific techniques have been brought about by these systems. Common model

systems used today are; E.coli, C.elegans, Zebrafish and mice. For this research, we

focused on carbonic anhydrase (CA), which is a well-developed model system for

studies in biophysics, bioanalysis, physical-organic chemistry and medicinal chemistry

[2]. Carbonic anhydrase catalyzes the hydration of COz and the dehydration of

bicarbonate: COz + 2HzO;='o HC03 - + H30+ Scientists believe that carbonic

anhydrase is present in all living organisms, because the ability to maintain a (near)

constant cellular pH is important for all living organisms. In eukaryotes, the enzyme

plays a role in various physiological functions; including the inter-conversion between

COz and HC03 - in intermediary metabolism, facilitated diffusion of COz, pH homeostasis

and io n tra nspo rt [3].

There are a number of isozymes of carbonic anhydrase, ranging from human to

bovine carbonic anhydrase. Bovine carbonic anhydrase II (BCA) is well characterized

and a model protein because it can be obtained in large quantities, BCA is derived from

the erythrocytes of Bos taurus, more simply, cow's red blood cells. BCA is a monomeric

protein that is 86% identical in its amino acid sequence to that of human carbonic

anhydrase [4]. Native BCA contains eighteen positively charged lysine residues each of

which are on its surface, as well as a binding cavity surrounded by catalytic Znll ions

[4]. The structure of BCA makes it a convenient protein to study the role of charged

Cuddemi 5

Page 7: Comparison of the Protein Crystal Structure between Wild-Type …library.emmanuel.edu/archive/sites/default/files/Cuddemi... · 2015. 3. 25. · Figure 1: BCA crystal structure [3].

amino acids on protein-protein interactions, protein-ligand interactions and

thermostability. We removed the positively charged lysine residues from the surface of

SCA, with an acetylation reaction, to better understand the relationship between the net

charge of a protein and protein interactions.

SCA is an ideal model protein for studying the crystallization of proteins because

it is structurally rigid and stable under a large number

of pH and salt conditions. SCA does not undergo a

change in the secondary or tertiary structure when the

eighteen lysine residues on the surface are

acetylated; the conditions needed to crystallize SCA

are known and crystal structures of wild-type SCA are

available (Figure 1). The structural rigidity of SCA is

not a common feature among proteins, because gross

changes in the surface of a protein may typically result in

changes of the secondary or tertiary structure. Changes

Figure 1: BCA crystal structure

[3].

in the secondary structure of a protein are less dramatic than tertiary effects and often

result from distortions in the beta sheets or alpha helices of a protein. On the other

hand, changes in the tertiary structure of a protein will cause the protein to appear

sufficiently different.

There are three main reasons that SCA is widely used in physical-organic studies.

SCA is a relatively easy protein to handle and purify because of its stability under

standard experimental conditions [2]. Secondly, changes in the overall net charge of

SCA protein can be monitored with a capillary electrophoresis machine using charge

Cuddemi 6

Page 8: Comparison of the Protein Crystal Structure between Wild-Type …library.emmanuel.edu/archive/sites/default/files/Cuddemi... · 2015. 3. 25. · Figure 1: BCA crystal structure [3].

ladders for reference. A charge ladder is a family of derivatives for a protein that differ in

integral units of charge [5]. The final reason for its model stature is that it is readily

available and sufficiently cheap to acquire (as crystallography and calorimetry

experiments require milligram levels of protein for each experiment) [2]. Model systems

are important in studies of protein structure because the more that is known about a

particular protein the easier it is to make accurate predictions about relationships

between structure and function. Once the model system (BCA) is understood, it is

simpler to test predictions made on less characterized proteins. Using BCA as a model

protein system for our research will aid in further research of the functionality of drugs

and their targets.

Crystal structures of wild-type BCA (BCA) are available in the Protein Database. We

recently solved the structure of per-acetylated BCA (BCA-(Ac)18) in which each amino

group on the side chain lysine was acetylated. A comparison of the crystal structures of

BCA and BCA-(Ac)18 show that the secondary or tertiary structure of the protein is

conserved after acetylation. Given these findings, we hypothesized that the overall

charge of BCA (1) decreased its ability to crystalize, (2) decreased its stability in

solution, and (3) increased the binding affinity of a ligand to BCA. We were interested to

see if a change in the net charge of BCA affected its ability to crystallize, and in

particular if removing the positively-charged residues would decrease the stability of the

protein crystal because the number of ion-ion interactions that could form between two

proteins in the crystal may be decreased. We crystallized the acetylated BCA, obtained

their X-ray crystal structure of the protein with the help of the staff at National

Synchrotron Light Source at Brookhaven National Laboratory, and compared the

Cuddemi 7

Page 9: Comparison of the Protein Crystal Structure between Wild-Type …library.emmanuel.edu/archive/sites/default/files/Cuddemi... · 2015. 3. 25. · Figure 1: BCA crystal structure [3].

regions of contact between molecules of SCA and SCA-(Ac)18. As previously

mentioned, the change in the protein's charge does not affect the secondary or tertiary

structure, which is important for a comparison of protein-protein interactions as only a

single amino acid residue is altered upon acetylation. The second question asked if a

change in surface chemistry by increasing the net negative charge of SCA reduced its

thermostability in solution (i.e. the temperature at which the protein could be

successfully unfolded in solution). We measured the overall stability of SCA and SCA­

(Ac)18 with differential scanning calorimetry (DSC), which monitors the heat generated

from the protein (as it unfolds) as a function of temperature. We found that SCA-(Ac)18 is

less stable in solution than wild-type SCA. The third question asked if a change in the

surface chemistry by increasing the net negative charge of SCA maintain the binding on

an arylsulfonamide ligand (i.e. thiazolesulfonamide and benzothiazolesulfonamide) to

the protein. If the structure of a protein does not change when the net charge of the

protein is increased, then does the affinity of the interaction between a ligand a protein

remain unchanged?

The approach of our research was to successfully acetylate the eighteen lysine

residues on the surface of SCA, to determine at which temperature the newly acetylated

protein would denature and what the binding affinity of a ligand to the acetylated SCA

was. There were three methods used in this research to complete the above objectives.

(1) Capillary electrophoresis (CE), which is commonly used to separate ionic species by

their charge and frictional forces [5]. A CE machine was used to determine how many of

the eighteen lysine residues were acetylated on the SCA molecules (because each

acetylation increases the overall net negative charge of the protein by about 0.9).

Cuddemi 8

Page 10: Comparison of the Protein Crystal Structure between Wild-Type …library.emmanuel.edu/archive/sites/default/files/Cuddemi... · 2015. 3. 25. · Figure 1: BCA crystal structure [3].

Separations in CE are similar to the separations that occur in gel electrophoresis, where

electrically charged particles move in a conductive buffer medium under the influence of

an electric field. As shown in Figure 2, the setup

Deled"" 1190.600 rom)

""'., (10-100,.ml.d._

--

-� 2O-100cm,""gIh)

<'/---

of the CE machine is relatively simple. The main

components are a sample vial, a glass capillary, ""

ANODE v tl"",wm (02-W) CATHODE

�V

Eledrode -

-

electrodes, a high-voltage power supply, and a

detector combined with a computer for data r- I-, EIec:trrMyle cootairw

(5-150mM)

output. The separated chemical compounds '-- '--

I: n HighvcMrnge SOIXoe appear as peaks monitored from a UV absorptio

(o.30 kV)

measurement with different migration times in Figure 2: CE schematic.

an electropherogram CE has been established http://www.doping.chuv.chlenilad-schema-ec-eng.jpg

as an independent and reliable analytical technique in separating protein samples in

which the physical or chemical properties are altered [6].

We altered the surface of bovine carbonic anhydrase by acetylating the lysine

amino groups and produced a protein with an equivalent likelihood of crystallizing as

wild-type SCA. We modified the surface of SCA by introducing the proteins to a solution

of acetic anhydride (to acetylate the Iysines) or an N-hydroxysuccinimide (NHS)-

activated formic acid (to formylate the Iysines). This chemical modification increases the

overall negative charge of SCA (Z = -3.4 at pH = 8.0) by I'lZ = -15.6 to yield a protein

with an overall negative charge of I'lZ = -19.

(2) Differential scanning calorimetry (DSC) is used to measure thermostability of

the acetylated SCA protein crystals. DSC is the most direct experimental technique that

measures the heat capacity of a solution of a molecule as a function of temperature [7].

Cuddemi 9

Page 11: Comparison of the Protein Crystal Structure between Wild-Type …library.emmanuel.edu/archive/sites/default/files/Cuddemi... · 2015. 3. 25. · Figure 1: BCA crystal structure [3].

DSC gives the immediate access to the

thermodynamic stability of molecules in

solution, and there are many examples in the

sample polymer sample reference

p

\ I pan

;" I

literature of using DSC to monitor the unfolding \� u I C�I I I

I of proteins and other polymers in solution [7].

Our research used this method on the basis of

I I • �" / ,

heaters I computer to morutor temperature

monitoring the thermal unfolding of BCA and and re gulate he at flow

Figure 3: DSC schematic. BCA-(Ac)1s. The schematic of the DSC machine is http://pslc.ws/macrog/images/dscOl.gif

shown in Figure 3.

(3) Isothermal titration calorimetry (ITC) is used

to study the binding affinity of ligands to proteins. ITC is

important in drug discovery studies as this method

determines the affinity of a ligand for a protein, and

provides information about the binding constant

(L'.GObind), the enthalpy of binding (L'.Hobind), and the

entropy of binding (-TL'.Sobind) [7]. Figure 4

shows the basic setup of an ITC machine.

Pr<>l�h in

�amplucell

Figure 4: ITC schematic. http://www.nature.cominprotijoumal/v6/n2iimages/n prot.20 10. 187-F2.jp g

For the future of this research we hope to accomplish three real-life applications;

the first involving protein-protein interactions. There is no way to currently predict what

set of reaction conditions will cause a protein to crystallize. Crystal structures offer a

large amount of insight into the active site of a protein -- the areas of a protein that are

exposed to solvent -- the way complicated molecules interact in the solid state.

Understanding the interactions between proteins will help scientists in numerous fields

Cuddemi 10

Page 12: Comparison of the Protein Crystal Structure between Wild-Type …library.emmanuel.edu/archive/sites/default/files/Cuddemi... · 2015. 3. 25. · Figure 1: BCA crystal structure [3].

of chemistry and biology. The second application entails protein-ligand interactions. The

majorities of drugs bind to a protein (active site, exterior, etc) and inhibit a structure or a

function. We are incapable of predicting how tightly a molecule will bind to a protein

(even if we know what the protein and molecule look like). Understanding these

interactions will allow us to better rationalize what and how a drug should look. The third

application involves protein stability in solution when changes are introduced, which is

important for protein-based therapeutics. Masking the charge of a molecule allows it to

more easily cross the membrane of a cell, or it also could allow the protein to last longer

in the body without denaturing or succumbing to enzymatic breakdown. Helping

medicinal chemistry and pharmaceuticals research is the target for the future

implications of our research.

We were interested in determining if the overall charge of SCA affects its (1)

ability to crystalize, (2) its stability in solution, and (3) the binding affinity of a ligand to

SCA. We successfully labeled the eighteen lysine amino groups ((SCA-(NHAc)18) on a

SCA protein with acetic anhydride. We were then able to obtain a crystallized structure

of SCA-(Ac)18 to compare to a wild-type SCA protein crystal. With differential scanning

calorimetry we were able to gather stability data of both wild-type SCA and per­

acetylated SCA proteins, to answer the second question of our research. Further

studies will look into the binding affinity of arylsulfonamide ligands to per-acetylated

SCA using isothermal titration calorimetry. Overall, this research will aid pharmaceutical

studies with the understanding of protein-ligand interactions and protein stability in

regards to the functionality of drugs.

Cuddemi 11

Page 13: Comparison of the Protein Crystal Structure between Wild-Type …library.emmanuel.edu/archive/sites/default/files/Cuddemi... · 2015. 3. 25. · Figure 1: BCA crystal structure [3].

2 Materials and Methods

2.1 Acetylation of BCA

Ten different acetylation reactions were run before testing the extent of

acetylation with capillary electrophoresis. We chose those reaction conditions to

determine the appropriate amounts of reagents needed to acetylate all eighteen lysine

residues on BCA. These ten test tubes were prepared with varying volumes of acetic

anhydride (Sigma-Aldrich) and 100mM NaOH (VWR International). The following

Table 1 depicts the amount of each reagent added into each of the ten tubes:

Tube # Amount of Amount of Amount of BCA (mL) AA (mL) NaOH (!.IL)

BCA = bovine carbonic

anhydrase

AA = acetic anhydride

NaOH = sodium hydroxide

(100mM)

1A 0.5 0.5 1B 0.5 0.5

1C 0.5 0.5 10 0.5 0.5 1E 0.5 0.5

2A 0.5 2.0 2B 0.5 2.0

2C 0.5 2.0 20 0.5 2.0

2E 0.5 2.0

Table 1: Volumes of reagents added to the reaction tubes for the acetylation of BCA.

0 43

86

172 344

0

43

86

172 344

The ten reactions were prepared into 100mM HEPBS (pH 9.0), incubated at 4°C

for two hours, and the reaction was then quenched with 0.5mL of 1 OOmM NaOH and

added to each tube to stop the reaction. The products of the reaction were exchanged

into 1 X TrisGly buffer in anion exchange spin columns following a standard protocol

prepared by the manufacturer (Thermo Scientific).

Cuddemi 12

Page 14: Comparison of the Protein Crystal Structure between Wild-Type …library.emmanuel.edu/archive/sites/default/files/Cuddemi... · 2015. 3. 25. · Figure 1: BCA crystal structure [3].

A fraction of each reaction (1 OOI-lL) was added into sample vials, loaded into the

capillary electrophoresis machine (CE), and separated with a standard program

07feb2013_BCA. This program included: a ten minute wash cycle in which the column

was rinsed with 1 M HCl, 1 M NaOH and 1 X TrisGly buffer; a sample injection of 5nL of

solution onto the column; a ten minute separation at 1 O.OV; and a ten minutes wash

cycle with deionized water. The CE instrument contained freshly prepared vials of H20,

MeOH, NaOH, HCl, and 1X TrisGlybuffer.

We used the results from the above procedure to design a second set of

experiments, in which the amount of acetic anhydride was decreased, in the attempt to

acetylate the entire eighteen lysine residues on the BCA protein. Nine reaction tubes

were prepared before running the solutions on the CE machine for results.

The acetylation reactions were carried out in 1.5mL centrifuge tubes with the

following amounts of reagents: 200l-iL of a stock solution of BCA (1 mg/mL solution of

BCA in HEPBS, pH = 9.0); 40l-lL of neat acetic anhydride; 60l-lL of 1 M NaOH, which was

added to each tube after a five minute incubation at 4°C. The reaction mixture was

incubated for thirty minutes at 4°C, and then another 40l-lL of acetic anhydride was

added, five minutes in the cold room and 60l-lL of NaOH.

As mentioned previously, the products of the reaction were exchanged into 1X

TrisGly buffer in anion exchange spin columns following a standard protocol prepared

by the manufacturer (Thermo Scientific). The amount of 1 00 1-1 L of each reaction solution

was added into a separate sample vial and loaded into the capillary electrophoresis

instrument and separated with the method discussed above (14march2013_BCA).

Cuddemi 13

Page 15: Comparison of the Protein Crystal Structure between Wild-Type …library.emmanuel.edu/archive/sites/default/files/Cuddemi... · 2015. 3. 25. · Figure 1: BCA crystal structure [3].

2.2 Crystallization

After the successful completion of acetylation to form BCA-(Ac)18, we crystallized

both wild-type BCA (unmodified) and per-acetylated BCA-(Ac)18. The following

procedures were carried out to crystalize the proteins.

2.2.1 BCA CRYSTALLIZATION

Wild-type BCA was crystallized in small tubes (2 mL) with round bottom, with a

protocol published by Saito, Saito and Ikai. A concentrated solution of BCA (200 IJM) in

50 mM Tris-HCI (with 2.4 M ammonium sulfate at pH 7.5) was placed in the small tube

(-100 IJL) and stored at 40C until crystallized.

2.2.2 BCA-(Ac)18 CRYSTALLIZATION

We screened a number of values of pH, and a number of concentrations of

ammonium sulfate, to determine the conditions needed to crystalize [BCA-(Ac)18]; thin

plates of [BCA-(Ac)18r19 formed at pH = 7.0 and [(NH4hS04] = 1.6 M over a two-month

period. We prepared solutions of protein by combining 2 IJL of protein (200 IJM) with 2

IJL of the precipitant solution; a droplet of solution was placed on a glass slide, and was

sealed over 1 mL of precipitant solution in a well of a 24-well plate. Amorphous

precipitates of BCA-(Ac)18 formed, in less than one day, in droplets containing

concentrations of ammonium sulfate greater than 1.6 M.

Cuddemi 14

Page 16: Comparison of the Protein Crystal Structure between Wild-Type …library.emmanuel.edu/archive/sites/default/files/Cuddemi... · 2015. 3. 25. · Figure 1: BCA crystal structure [3].

2.2.3 COLLECTION AND SOLVING X-RAY

We captured a crystal of wild-type BCA or BCA-(Ac)1B (thin plates approximately 200

!-1m x 200 !-1m x 25 !-1m in size) in a nylon loop, transferred the crystal to a reservoir

containing a solution of 17.5 % glycerol / 82.5% cryoprotectant, and soaked it briefly

before rapidly freezing the crystal in liquid nitrogen. We collected the X-ray diffraction

data at 77 K on an RAXIS IV instrument equipped with a rotating copper anode.

To solve the X-ray crystal structure, we indexed, scaled, and integrated the X-ray

diffraction data with the HLK2000 software package. The structure of [BCA-(Ac)1Br

19 was refined with the CCP4i suite of programs; molecules of water were added

automatically to regions of density greater or equal to 1 cr.

2.3 Thermostability

We measured the thermostability of the BCA and BCA-(Ac)1B with a differential

scanning calorimeter (nano-DSC, TA Instruments). A 25 uM solution of protein in 10

mM sodium phosphate buffer (pH = 7.4) was placed in the calorimeter, degassed, and

then scanned at a rate of 1 DC / minute. We fit the DSC data with DSC-fit software

provided by TA instruments.

Cuddemi 15

Page 17: Comparison of the Protein Crystal Structure between Wild-Type …library.emmanuel.edu/archive/sites/default/files/Cuddemi... · 2015. 3. 25. · Figure 1: BCA crystal structure [3].

3 Results

3.1 Acetylation

To acetylate all eighteen lysine groups that are present on a structure of SCA, we

used acetic anhydride and analyzed the results on a CE machine. A CE machine

separates molecules by their charge and by the absorption. The machine itself, referring

back to Figure 2, contains a wire that is negative on one end and positive on the other.

As the SCA protein becomes more negative, it will move towards to positive end (right

side of the figure). Therefore, we can interpret that the data as a protein containing

more acetylated lysine groups. The capillary electropherogram, shown in Figure 5,

depicts the separation of charge and absorption of SCA; wild-type and per-acetylated.

In Figure 5, the lines are representative of SCA with different numbers of lysine

residues labeled with acetyl groups. Each peak in the electropherogram is a protein of a

different charge. Since the overall charge of SCA is typically positive (charged lysine

groups), the top line shows SCA that was only contained one acetylated lysine group.

The bottom line shows a SCA protein that contained all eighteen acetylated lysine

groups. The left-most line is that of N-N dimethylformamide (OM F), which serves as a

neutral marker in the results. This allows us to compare each run to one another.

In Figure 6, the same information is shown, expect in simpler terms. The top line

is a SCA protein with all eighteen labeled lysine residues, while the bottom line is wild­

type SCA (zero acetylated lysine residues). The middle line is a charge ladder, serving

as a marker to understand the previous Figure 6. Each peak represents a protein with a

different number of labeled lysine residues. The SCA charge ladder helps to emphasize

the movement of protein within the CE machine.

Cuddemi 16

Page 18: Comparison of the Protein Crystal Structure between Wild-Type …library.emmanuel.edu/archive/sites/default/files/Cuddemi... · 2015. 3. 25. · Figure 1: BCA crystal structure [3].

N e!'ative ( ) I I Positive (+)

E c

'<t

0.16

0.14

0.12

0.10

0."

0.06

0.04

"

W-214nm W-214nm W-214nm W-214nm W-214nm w- 214nm W-214nm

1.9.001.dlt 1.9.003 .dll 1.S.002.d;1t 1.S.oo3.dll 1.9.004.dat 1.9.00�.dM 1.9.006.dat 1.9.001.dlt U.OO8.cbt

I DMF I 0.18

I 1 Ivsine I ./\ , 0.14

LA 0.12

�A

� 0.10

'"'--' �

"'" � ,..

"'"

0"

I Hllvsines I on,

13 14 " " 17 " " " 21 n " 24 " " 27 " 29 :lO 31

MnUles

Figure 5: Capillary electropherogram, the final product of complete lysine acetylation of a SCA

protein. All eighteen lysine residues were acetylated (overall charged changed). DMF (far left

peaks) are markers. Each peak represents the number of Iysines acetylated. Conditions for

acetylation were; 40l-lM SCA, 20mM acetic anhydride, NaOH, pH = 8.

[BCA-(NH, +),,]-H

DMF

[BCA-(NHCOCH,),l"

i • i • • Iii i • I •• i. i": (NHCOCH1)n o 5 10 15 1.8

Figure 6: Electropherograms of wild-type [SCA-(NH3 +)18r

3.4

(bottom), a charge ladder of wild-type SCA (middle) in

which each peak in the ladder represents the number of

acetylated lysine groups, and [SCA-(NHCOCH3)18r19

(top). Conditions for electrophoresis were: unmodified

capillary, 25 mM Tris-192 mM Gly buffer, pH = 8.4, with

electrophoretic mobilities estimated relative to a neutral

marker, N,N-dimethy/formamide.

-2 0 2 4 6 8 10 12 14 16 18 20 22 24

mobility (em' kV-' min-')

Cuddemi 17

Page 19: Comparison of the Protein Crystal Structure between Wild-Type …library.emmanuel.edu/archive/sites/default/files/Cuddemi... · 2015. 3. 25. · Figure 1: BCA crystal structure [3].

3.2 Crystallization

After acetylating wild-type SCA, understanding how the crystal structure changed

was a crucial part in our research. We know that the change in charge of a protein does

not affect the secondary or tertiary structure, therefore we were able to obtain a crystal

structure of SCA, as well as SCA-(Ac)18. Figure 7 shows the difference in the crystal

structure of SCA and SCA-Ac. The crystal structures were obtained from x-ray

diffraction. The pictures in Figure 7 were gathered from a computer representation of

SCA and SCA-(Ac)18 for the purposes of illustrating the crystal structures.

The results allowed us to understand the different protein-protein interactions that

are happening inside of the SCA and SCA-(Ac)18 crystal structures. The different

colored folded structures represent different SCA or SCA-(Ac)18 proteins in the crystal,

indicating that there are five core proteins present in protein-protein interactions inside

the crystals. The core SCA protein is able to interact with each protein to form bonds to

produce the crystal. In Figure 7, each arrow indicates a unique lysine residue

interaction taking place. We were able to conclude that there are eight lysine

interactions that happen in the wild-type SCA protein crystal. An interesting result was

that the per-acetylated SCA-(Ac)18 protein crystal involved twenty-nine lysine

interactions. We determined this by zooming in on each lysine residue in the core SCA

protein and measuring the length of the chemical bonds between the Iysines. If the

length of the bond measure greater than or equal to 3.oA (angstroms), the bond was

considered a protein-protein interaction.

Cuddemi 18

Page 20: Comparison of the Protein Crystal Structure between Wild-Type …library.emmanuel.edu/archive/sites/default/files/Cuddemi... · 2015. 3. 25. · Figure 1: BCA crystal structure [3].

[BCA-(NH +) ]-34 3 18 [BCA-(NHCOCH3)

Figur. 7: Comparison of packing in crystals of wild-type SCA

[SCA-(NH3+)18] and per-acetylated SCA [SCA-(NHCOCH3)18].

The labEJed regions (A - G) represent unique contacts between

the neighboring molerules in each crystal.

3.3 Protein-protein Interactions

To aid in the comparison of the crystal structures of SCA and SCA(Ac)18, we

measured all of the protein-protein contacts within the crystal lattices with the MOE

program suite (http://www.chemcomp.com). We chose those dimensions (2x2x2 unit

cells) so that the crystal lattices would contain all possible inter- and intra-unit-cell

protein-protein contacts. We wrote software using the OESpicoli toolkit provided by

OpenEye Scientific Software (http://www.eyesopen.com) to calculate the solvent-

19

accessible surface area (SASA) of a crystal lattice, and to measure how much surface

area is contributed by each residue of each protein monomer in the lattice. The

software developed was specific for our research project. For each protein monomer in

the crystal lattice, our program also calrolated the per-residue SASA contributions for

Cuddemi 19

Page 21: Comparison of the Protein Crystal Structure between Wild-Type …library.emmanuel.edu/archive/sites/default/files/Cuddemi... · 2015. 3. 25. · Figure 1: BCA crystal structure [3].

that monomer independently of the crystal lattice (by removing all other protein

monomers and recalculating the SASA). By computing the difference between the

SASA of a residue in the crystal lattice with the SASA of the same residue outside of the

crystal lattice, we determined how much of the SASA of that residue is buried by

protein-protein contacts in the crystal lattice. Our program produced a model of a single

unit cell, in which each residue was labeled with the amount of SASA buried by crystal

contacts [8].

Part A: Protein-Protein Interactions Key

Classification Example

charge-charge

charge-dipole

ydrogen bond

Cuddemi 20

Page 22: Comparison of the Protein Crystal Structure between Wild-Type …library.emmanuel.edu/archive/sites/default/files/Cuddemi... · 2015. 3. 25. · Figure 1: BCA crystal structure [3].

dipole-dipole

igher-order

alkyl group - alkyl

group

alkyl group - carbonyl

oxygen atom

alkyl group - oxygen

atom or nitrogen atom

alkyl group - aromatic

carbon

Cuddemi 21

Page 23: Comparison of the Protein Crystal Structure between Wild-Type …library.emmanuel.edu/archive/sites/default/files/Cuddemi... · 2015. 3. 25. · Figure 1: BCA crystal structure [3].

alkyl group - carbonyl

carbon

Table 2: computerized depictions of the types of interactions shown in the corresponding tables. These reactions exist in the crystal structures of BCA and BCA­(Ac)1s. This table serves to act as a key to understanding the reactions presented.

Part B: Interactions Present In A BCA Crystal

Wild-type BCA

charge-charge

alkyl C-carbonyl 0

Table 3: computerized images of the lysine interactions between wild-type BCA proteins within the crystal structure. The type of reactions are labeled according to the key in Figure_.

Cuddemi 22

Page 24: Comparison of the Protein Crystal Structure between Wild-Type …library.emmanuel.edu/archive/sites/default/files/Cuddemi... · 2015. 3. 25. · Figure 1: BCA crystal structure [3].

Pari C: Interactions Present In A BCA-(Ac)18 Crystal

BCA-(Ac)18

GlU·212

char�e-dipole

carbonyl-carbonyl

GLN-1.35

A

carbonyl-carbonyl carbonyl N-O

Cuddemi 23

Page 25: Comparison of the Protein Crystal Structure between Wild-Type …library.emmanuel.edu/archive/sites/default/files/Cuddemi... · 2015. 3. 25. · Figure 1: BCA crystal structure [3].

carbonyl N-O high order

alkyl-alkyl C

alkyl-alkyl C

THR·Bl

alkyl-alkyl C

alkyl-alkyl C

(1 )- AtY-44 3� ...... ,,,-...

Cuddemi 24

Page 26: Comparison of the Protein Crystal Structure between Wild-Type …library.emmanuel.edu/archive/sites/default/files/Cuddemi... · 2015. 3. 25. · Figure 1: BCA crystal structure [3].

alkyl C-carbonyl 0

Table 4: computerized images of the lysine interactions between per-acetylated BCA-(Ac)1s proteins within the crystal structure. The types of reactions are labeled

according to the key in Figure_.

Part D: Summary Table of the Interactions

Interaction Types BCA BCA-(Ac)18

charge-charge 2 --

ch arge-d i pole 1 3

hydrogen bond -- 3

dipole-dipole -- --

higher-order -- 2

alkyl group - alkyl group 1 6

alkyl group - carbonyl

oxygen atom 1 6

Cuddemi25

Page 27: Comparison of the Protein Crystal Structure between Wild-Type …library.emmanuel.edu/archive/sites/default/files/Cuddemi... · 2015. 3. 25. · Figure 1: BCA crystal structure [3].

alkyl group - oxygen atom or

nitrogen atom 1 5

alkyl group - aromatic

carbon -- 2

alkyl group - carbonyl

carbon -- 1

TOTAL INTERACTIONS 6 28

Table 5: summary of the interactions between proteins within the crystals of

SCA and SCA-(Ac)18. As shown, there are about 6-8 interactions present in wild-type SCA and 28-29 interactions present in SCA-(Ac)18.

As seen in the comparison Table 5 above, the interactions present in the crystals

of SCA and SCA-(Ac)18 immensely differ. In wild-type SCA, there are about six to eight

lysine protein-protein interactions within the crystal. An interesting finding was the ability

of acetylated SCA-(Ac)18 to interact significantly more within its crystal. Noted in the

table above, there are anywhere from twenty-seven to twenty-nine lysine protein-protein

interactions in the acetylated SCA-(Ac)18 crystal.

3.4 Thermostability

The comparison of melting points between wild-type SCA (SCA) and per-

acetylated SCA was completed by using differential scanning calorimetry (DSC). DSC

measures the amount of heat (kJ) that it takes to denature a protein crystal in solution.

Figure 8 depicts the temperature at which SCA and SCA-Ac crystal structures melted,

either with or without a ligand present. Each point on the graph denotes the kJ of heat

that was required to denature the protein crystals. The y-axis is the measurement of the

heat that was applied and the x-axis represents the protein that was being tested.

Cuddemi 26

Page 28: Comparison of the Protein Crystal Structure between Wild-Type …library.emmanuel.edu/archive/sites/default/files/Cuddemi... · 2015. 3. 25. · Figure 1: BCA crystal structure [3].

Examining the first column on the len, SCA Vv'ithout a ligand present is shown.

The results show that wild-type SCA (red boxllop) required a higher amount of heat

(900 kJ) to denature the crystal structure. Per-acetylated SCA-(Ac)18 (green

trianglelbollom) required only 300kJ of heat to denature the crystal. The nexl two

columns compared the presence oftvvo different ligands (STA or TA) in the SCA or

SCA-(Ac)18 crystals. Figure _ shoVv"S the molecular structure of the TA and STA

ligands. In the data presented, we are able to note that the SCA-Ac crystal structure is

less stable than SCA, Vv'here the SCA-Ac unravels at a lower melting temperature. The

presence of the ligands stabilizes acetylated SCA (melting temp increases), but

destabilizes the wild-type SCA. This phenomenon is still unexplained.

6H of Unfolding ,�

� •

� •

• '00

- • SCA <; � E

-� .. SCA-Ac ;2 .. -

% � ..

..

� ..

'00

'00

" BCA BCA+ TA BCA+ BTA

Figure 8: DSC data comparing the thermostability of Vv'ild-type SCA

(SCA) and per-aceyllated SCA (SCA-Ac). The difference of melting

temperature is compared with respect to ligand presence. The x-

axis depicts the presence of a ligand; TA or STA.

Cuddcmi 27

Page 29: Comparison of the Protein Crystal Structure between Wild-Type …library.emmanuel.edu/archive/sites/default/files/Cuddemi... · 2015. 3. 25. · Figure 1: BCA crystal structure [3].

In Figure 9, the molecular structure of the ligands used in DSC are depicted.

BTA is the bulkier ligand, resulting in the decreased thermostability of wild-type BCA

when bound. TA shows a slightly increased thermostability in BCA than the BTA ligand.

But when examining the results of acetylated BCA-(Ac)18, the results are opposite.

When the ligands are bound, there seems to be an increase in protein thermostability,

shown by the higher temperature that it takes to denature the crystal. As mentioned

above, this is still not well understood.

o N II

}-S-NH2 S II

o

o eN II I }-S-NH2

S II o

Figure 9: Molecular structure of ligands

used; BTA (top), TA (bottom).

Cuddemi 28

Page 30: Comparison of the Protein Crystal Structure between Wild-Type …library.emmanuel.edu/archive/sites/default/files/Cuddemi... · 2015. 3. 25. · Figure 1: BCA crystal structure [3].

4 Discussion

4.1 Summary of Results

4.1.1 Acetylation of BCA and Crystallization

In this study, we were able to successfully acetylate the eighteen lysine residues

on BCA (as shown in Figure 5 and Figure 6). The acetylation of the lysine residues

resulted in an overall negative charge to the BCA-(Ac)18 protein. When a protein is not in

solution, we found that acetylation does not affect the secondary or tertiary structures of

the protein, but it does affect the protein-protein interactions within the crystal structure.

As previously mentioned, a BCA crystal consists of eight lysine interactions, while a

BCA-(Ac)18 crystal consists of twenty-nine lysine interactions. I t seems that the presence

of a negative charge in the per-acetylated crystal structure helps the overall stability of

the solid crystal, when not in solution. A wild-type BCA crystal is more likely to denature

because there are less interactions between protein structures. This causes the crystal

to become less mechanically and less thermo stable (dissolving at a lower

temperature). The wild-type BCA crystal is also less dense and less favorable. But all of

this is only possible when the crystal structures are not in solution.

4.1.2 Thermostability

We determined that the thermostability in solution of wild-type BCA is high than

that of per-acetylated BCA-(Ac)18. I t seems that the positive charge of the Iysines

present on the wild-type BCA crystal stabilize the protein when in a solution of water.

The charge-charge interactions with other groups on the BCA (such as COO- groups)

that are present will interact with the positively charged lysine groups (N H3 +) , causing

Cuddemi 29

Page 31: Comparison of the Protein Crystal Structure between Wild-Type …library.emmanuel.edu/archive/sites/default/files/Cuddemi... · 2015. 3. 25. · Figure 1: BCA crystal structure [3].

stronger bonds in the crystal. There are also lysine-water interactions that occur, which

also stabilize the crystal. These interactions are unable to occur in the per-acetylated

BCA-(Ac)18 crystals because of the presence of a negative charge.

We were able to disprove our hypothesis regarding the idea that altering the

overall charge of BCA would alter the secondary or tertiary structure of the protein. But

we were able to show that BCA-(Ac)18 is a more stable, interactive crystal when not in

solution, though wild-type BCA is the more stable crystal in solution. But as mentioned

previously in the thermostability results section, we are still unable to explain how the

presence of either the TA or BTA ligand in the acetylated BCA-(Ac)18 crystal increases

the thermostability. To test this, we could perform experiments that used different

ligands for interaction. This may allow insight into the binding of a ligand to acetylated

BCA-(Ac)18.

During the acetylation procedure, we ran into a few problems. The first few times

that we attempted to acetylate BCA, we were unsuccessful. Troubleshooting allowed us

to realize that our amount of reagents used was too large. In the small scale of our

research, we needed to avoid denaturing the protein during the reaction. But we learned

that the heat given off during the acetylation reaction was able to denature the proteins.

Therefore, we decreased the amount of acetic anhydride from 2mL to 200l-iL in the

reaction tubes. This allowed the acetylation to occur without disruption from the natural

heat given off.

Cuddemi 30

Page 32: Comparison of the Protein Crystal Structure between Wild-Type …library.emmanuel.edu/archive/sites/default/files/Cuddemi... · 2015. 3. 25. · Figure 1: BCA crystal structure [3].

Crystallizing the structures of SCA and SCA-(Ac)18 was completed by X-ray

crystallography, which allows us to obtain a picture of the solid-state, lowest energy

conformation of the protein. An alternative method to evaluate the structure of SCA

would be to use nuclear magnetic resonance (NMR). NMR give a picture of the protein

in solution, however there is no automated method for converting the peaks produced

by NMR into a 3D structure. In X-ray crystallography, there are software programs that

use the diffraction pattern and standardized methods to evaluate the patterns,

producing a 3D structure. Though we would have the ability to look at the structures of

SCA and SCA-(Ac)18 in solution with NMR, it would require us taking that average of

many time snapshots during the process. The final picture would be at a lower

resolution than X-ray crystallography provides. Figure 10 shown below, depicts an

NMR spectrum of human carbonic anhydrase (HCA). The dots represent the separate

points at which one would have to record the average. A 3D structure is difficult to

retrieve from the information provided by NMR.

12 11 10 9 8 7 6

10

11

.........

E 11 0..

0.. �

Z Lf) �

?: 12

13

13

12 11 10 9 8 7 6

Figure 10: NMR of human carbonic anhydrase. The dots are the average points that

are recorded during the NMR process. A 3D structure is extremely difficult to interpret frnfn th ic ri <>t<>

Cuddemi 31

Page 33: Comparison of the Protein Crystal Structure between Wild-Type …library.emmanuel.edu/archive/sites/default/files/Cuddemi... · 2015. 3. 25. · Figure 1: BCA crystal structure [3].

4.2 Future Directions

The next step of our research is to test the binding affinity of arylsulfonamide

ligands to wild-type SCA and per-acetylated SCA using isothermal titration calorimetry.

We want to compare the difference in stability of the SCA and SCA-(Ac)18 protein crystal

structures in solution. It is noted that a SCA crystal is stable in solution, while SCA­

(Ac)18 is less stable. When a ligand binds to a protein, heat is released. The question

asked in our research is if the heat released in the binding of a ligand is enough to

denature the crystal structure.

The long-term goals of our research are to aid in medicinal chemistry and

pharmaceuticals research. Since SCA is a model protein system, once we understand

the implications of protein-protein interactions, protein-ligand interactions and its

stability, we will be able to apply the knowledge to something more specific. In the area

of pharmaceuticals, protein-ligand interactions are a large part of research. Insight into

this phenomenon will guide research in diseases such as cancer. An important target in

cancer research is matrix metalloproteinases (MMPs), which degrade extracellular

matrices in the body. If we are aware of how a ligand interacts with a protein through

our SCA model, the knowledge may be applied to MMPs and their interactions.

Identifying the capability of molecules that can make proteins less stable could be used

to degrade a cancer cell in the body. This ability to apply our system to pharmaceutical

drugs in crucial in fostering the process of drug discovery. Though the long-term goals

of our research are far advanced, the relevance of less complex knowledge is largely

needed.

Cuddemi 32

Page 34: Comparison of the Protein Crystal Structure between Wild-Type …library.emmanuel.edu/archive/sites/default/files/Cuddemi... · 2015. 3. 25. · Figure 1: BCA crystal structure [3].

5 References

[1] Leunissen, Mirjam. "Protein Crystallization." An essay on several aspects of protein

crystallization research. United Kingdom: Department of Solid State Chemistry, October

2001. http://people.ds.cam.ac. uk/ml527 Ipublications/assets/le unissen-

literature research .pdf.

[2] Krishnamurthy, Vijay M., et al. "Carbonic Anhydrase as a Model for Biophysical and

Physical-Organic Studies of Proteins and Protein-Ligand Binding." Chemistry

Review (September 2009): 946-1051.

http://www.ncbi.nlm.nih.gov/pmclarticles/PMC27407301.

[3] Saito, Ryuta, et al. "Structure of bovine carbnic anhydrase II at 1.95 A resolution."

Acta Crystal/ographica (February 2004): 792-795.

[4] Sarraf, B. S., et al. "Structural and functional changes of bovine carbonic anhydrase

as a consequence of temperature." Acta Biochimica Polonica (November 2003):

665-671.

[5] Carbeck, Jeffrey D., et al. "Protein Charge Ladders, Capillary Electrophoresis, and

the Role of Electrostatics in Biomolecular Recognition." Accounts of Chemical

Research (1998): 343-350.

[6] Tagliaro, F., et al. "A Brief Introduction to Capillary Electrophoresis." Forensic

Science International (1997): 75-88.

[7] Jelesarov, lIian and Hans Rudolf Bosshard. "Isothermal Titration Calorimetry and

Differential Scanning Calorimetry as Complementary Tools to Investigate the

Energetics of Biomolecular Recognition." Journal of Molecular Recognition

(1999): 3-18.

[8] Lockett, Matthew R. and George M. Whitesides. "The Surface Chemistry, and not

Shape Determines Differences in the Crystal Structures of Bovine Carbonic

Anhydrase and Per-acetylated Bovine Carbonic Anhydrase." (2011).

[9] Anderson, Janelle R., et al. "Analysis by Capillary Electrophoresis of the Kinetics of

Charge Ladder Formation for Bovine Carbonic Anhydrase." Analytical Chemistry (April

15, 2002): 1870-1878.

[10] Durbin, S. D. and G. Feher. "Protein Crystallization." Annual Review Physical

Chemistry (1996): 171-204.

Cuddemi 33

Page 35: Comparison of the Protein Crystal Structure between Wild-Type …library.emmanuel.edu/archive/sites/default/files/Cuddemi... · 2015. 3. 25. · Figure 1: BCA crystal structure [3].

[11] Gudiksen, Katherine L., et al. "Eliminating Positively Charged Lysine E-NH3+

Groups on the Surface of Carbonic Anhydrase Has No Significant Influence on

Its Folding from Sodium Dodecyl Sulfate." Journal of the American Chemical

Society (October 11,2004): 4707-4714.

[12] Gitlin, Irina, Katherine L. Gudiksen and George M. Whitesides. " Effects of Surface

Charge on Denaturation of Bovine Carbonic Anhydrase." ChemBioChem (2006):

1241-1250.

[13] Matulis, Daumantas, et al. "Thermodynamic Stability of Carbonic Anhydrase:

Measurements of Binding Affinity and Stoichiometry Using ThermoFluor."

Biochemistry (2005): 5258-5266.

[14] Mack, Eric T., et al. "Using Covalent Dimers of Human Carbonic Anhydrase II to

Model Bivalency in Immunoglobulins." Journal of the American Chemical Society

(2011).

[15] Shaw, Bryan F., et al. "Neutralizing Positive Charges at the Surface of a Protein

Lowers Its Rate of Amide Hydrogen Excahnge without Altering Its Structure or

Increasing Its Thermostability." Journal of the American Chemical Society (2010):

17411-17425.

Cuddemi 34

Page 36: Comparison of the Protein Crystal Structure between Wild-Type …library.emmanuel.edu/archive/sites/default/files/Cuddemi... · 2015. 3. 25. · Figure 1: BCA crystal structure [3].

6 APPENDIX

The following is the procedure and results from the first acetylation method

described on page 12. These results helped us to determine which volume of BCA and

NaOH to use. As shown in the results below, Tube 2D, gave us the best results at that

time. From these volumes of reagents was how we carried out the preceding

experiments, until we determined that a smaller volume of acetic anhydride was

needed.

6.1 BCA CE Run

1. Things to note

a. we are using the CE machine to separate the BCA proteins based on their

charge.

b. should help us determine if the acetylation process worked correctly and at

which ratio of BCAacetic anhydride should be used.

2. Solutions

'Look at the procedure on February 1 for the calculations'

a. 5mL of 20l-lM BCA in HEPBS

b. 15mL of 200l-iM Acetic Anhydride in H20

3. BCA acetylation reactions

- we will prepare tubes will varying volumes of acetic anhydride with a constant volume

of BCA.

- this was done to check if the concentration of AA and NaOH were the cause for the

poor labeling with the last experiment.

- ten tubes were prepared with the following:

Tube 1A: O.5mL BCA

O.5mL AA

OI-iL NaOH

Tube 1B: O.5mL BCA

O.5mL AA

431-1L NaOH

Tube 2A: O.5mL BCA

2.0mL AA

OI-iL NaOH

Tube 2B: O.5mL BCA

2.0mL AA

431-1L NaOH

Cuddemi 35

Page 37: Comparison of the Protein Crystal Structure between Wild-Type …library.emmanuel.edu/archive/sites/default/files/Cuddemi... · 2015. 3. 25. · Figure 1: BCA crystal structure [3].

Tube 1C: O.5mL SCA

O.5mL AA

86IJL NaOH

Tube 10: O.5mL SCA

O.5mL AA

172IJL NaOH

Tube 1E: O.5mL SCA

O.5mL AA

344IJL NaOH

Tube 2C: O.5mL SCA

2.0mL AA

86IJL NaOH

Tube 20: O.5mL SCA

2.0mL AA

172IJL NaOH

Tube 2E: O.5mL SCA

2.0mL AA

344IJL NaOH

- each of the tubes was then incubated in the cold room for 2 hours on the rocker.

- after 2 hours -7 O.5mL of NaOH was added to each tube to stop the reactions.

4. Spin column

- each of the solutions in Tubes 1A-2E needs to be placed into the correct buffer for the

CE run.

- this process will allow a buffer exchange.

A. Protein Desalting Spin Column Preparation and Sample Loading

*Look at the procedure described in the February 1 protocol.

*Run 07feb2013_SCA sequence on the CE machine*

- this was run with both a glycerol + H20 buffer and a 15% glycerol buffer (refer to the

previous experiment for buffer concentrations).

Cuddemi 36

Page 38: Comparison of the Protein Crystal Structure between Wild-Type …library.emmanuel.edu/archive/sites/default/files/Cuddemi... · 2015. 3. 25. · Figure 1: BCA crystal structure [3].

6.1 CE Electropherogram Results

UV _ 21<1nm " _ 2Unm UV _ 214nm UV _ 214nm UV __ 2Unm

01fob2013 BCro01E.doi , eb2013 bcaOOI .'" 011002013 bcaOOI a.dlll 011002013 bcaOOlb.dat 01feb201J bcaOOlc.d"i

0_0015 0 0015

0 0010 {) 0010

0.0005 {) 0005

Tube IE

0 0000 0 0000

I Tube ID " " < <

-0 0005 -0 0005

Tube Ie -0 0010 - 0 0010

-00015 Tube tB - 0 0015

-0.0020 -0.0010

I Tube IA

-0.0025 -0 0025

" " ;0 " " " " " " " 70 " " "' " " ",

Minute.

UV - 214nm UV - 214nm UV - 214nm UV - 214nm UV - 214nm IJ7feb2013 Be 02E.dat 07feb2013 bcaQ()2d.dat ()71'eb2013 bcaOO2a.dat 07feb2013 bcaOO2b.dat 07'feb2013 �c.d;;Jt

0.00125 "''"'"

0 00100 0 00100

0_00015 "'''''

0""'" Tube2E

0000"'

"

0.00025 Tube 2D 0 00025 «

0= 0 00000

.0""'" .0""'"

.0""'" .0""'"

Tube2A

-000075 ,� -000075

" " " " .. , '.0 " " ., 70 " " " " " 10.0 10.5 '"

Minutes

Cuddemi 37