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r 2011 American Chemical Society 334 DOI: 10.1021/jz101619f |J. Phys. Chem. Lett. 2011, 2, 334344
Elucidating Peptide and Protein Structure and Dynamics:UV Resonance Raman SpectroscopySulayman A. Oladepo, Kan Xiong, Zhenmin Hong, and Sanford A. Asher*
Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
ABSTRACT UV resonance Raman spectroscopy (UVRR) is a powerful methodthat has the requisite selectivity and sensitivity to incisively monitor biomolecularstructure and dynamics in solution. In this Perspective, we highlight applications ofUVRR for studying peptide and protein structure and the dynamics of protein andpeptide folding. UVRR spectral monitors of protein secondary structure, such asthe amide III3 band and the CR;H band frequencies and intensities, can be used todetermine Ramachandran angle distributions for peptide bonds. These incisive,quantitative glimpses into conformation can be combined with kinetic T-jumpmethodologies to monitor the dynamics of biomolecular conformational transi-tions. The resulting UVRR structural insight is impressive in that it allows differ-entiation of, for example, different R-helix-like states that enable differentiating and 310 states frompure R-helices. These approaches can be used to determine theGibbs free-energy landscape of individual peptide bonds along themost importantprotein (un)folding coordinate. Future work will find spectral monitors that probepeptide bond activation barriers that control protein (un)folding mechanisms. Inaddition, UVRR studies of side chain vibrations will probe the role of side chains indetermining protein secondary, tertiary, and quaternary structures.
P rotein Folding Problem. An understanding of themecha-nism(s) of protein folding, whereby the ribosome-synthesized biopolymer folds into its native protein,is arguably one of the most important unsolved problems inbiology.1-7 The primary sequence of many or most proteinsencodes both the native structure as well as the foldingmechanism pathway to the native structure.8-10 An under-standing of the encoded protein folding rules would dra-matically speed insight into protein structure and function.
A number of mechanisms have been proposed that differin the order of folding events. The frameworkmodel11 and thediffusion-collision model12 propose that the initial step infolding involves formation of native-like secondary structuralunits, while the hydrophobic collapse model and the nucle-ation-condensation model13 suggest that hydrophobic ornucleating domains fold first and that these structures drivethe subsequent formation of secondary structure. Recentenergy landscape models14 propose the occurrence of funnel-shaped folding energy landscapes, where the native stateis accessed via a strategically sloped energy landscape that
funnels myriads of partially folded conformations towardthe native folded state.15
Techniques for Studying Protein Folding. Numerous experi-mental techniques are being applied to study protein folding.In addition, various theoretical approaches are also beingutilized with empirically developed parameters to try to getinsight into the foldingmechanisms.16 UV-visible absorptionspectroscopy was the first technique used to monitor the UVabsorption of the peptide backbone. This method was able todetect protein backbone conformational changes because ofthe hypo- and hyperchromic interactions that, for example,result from peptide bond excitonic interactions in the R-helixconformation.17,18 Thedevelopmentof circular dichroismspec-troscopy enabled more direct monitoring of protein second-ary structural content, especially the occurrence of R-helicalconformations.19
X-ray Crystallography is the gold standard technique fordetermining static protein structures (from protein crystals),andmuch of the insight into protein science has resulted fromthe many incisive stationary X-ray structures. However, thesestatic X-ray structures do not give the dynamic structuralinformation essential to determine enzymatic mechanisms,for example.
Nuclear magnetic resonance spectroscopy (NMR) is anextraordinarily powerful tool for studying protein folding.20
An understanding of the encodedprotein folding rules would dra-matically speed insight into protein
structure and function.
Received Date: December 1, 2010Accepted Date: January 20, 2011
r 2011 American Chemical Society 335 DOI: 10.1021/jz101619f |J. Phys. Chem. Lett. 2011, 2, 334344
The technique is also capable of elucidating detailed aspectsof the structure and dynamics of large proteins. However, theatomic distances and dihedral angles measured by thistechnique are generally time averages.21
Laser spectroscopy techniques enable highly incisive struc-tural investigations that can be utilized to study dynamics inthe femtosecond to static time scales. IR and Raman vibra-tional spectroscopies can monitor small changes in proteinstructure resulting from tiny0.001nmbond length changes.Unfortunately, the use of IR absorption spectroscopy is chal-lenging for biological samples because it is generally limited toD2O solution samples due to the overwhelming IR absorptionof H2O.
Raman spectroscopymonitors the vibrations of gas, liquid,and solid samples.23-25 H2O is a relatively weak Ramanscatterer. This enables Raman studies of biological moleculesin H2O. Raman spectroscopy is an inelastic light-scatteringphenomenon where the incident electromagnetic field inter-acts with a molecule such that there is an exchange of aquantumof vibrational energy between the two, resulting in avibrational frequency difference between the incident andscattered light.26-35 In normal or off-resonance Raman scat-tering, the incident photon at a frequency outside of anyelectronic absorption band is inelastically scattered, leavingthe molecule in an excited vibrational level of the electronicground state (for Stokes scattering). A similar vibrationaltransition occurs for resonance Raman scattering, whereexcitation occurs at a frequency within an electronic absorp-tion band. In this case, the vibrational modes observed areparticular vibrations whose motions couple to the drivenelectronic motion occurring in the electronic transition. Thevibrational modes enhanced are those localized in the chro-mophoric segments.
The additional resonance Raman enhancement can be anadditional 106-108-fold. This results in a crucial ultrahighresonance Raman selectivity and sensitivity that makes it avery powerful technique for studying macromolecules; in-steadof all of the samplevibrations contributingwith compar-able intensities, only a small subset of resonance Raman-enhanced vibrations localized around the chromophoricgroup dominate the spectra. By judiciously tuning the excita-tion wavelength, we can selectively enhance particular vibra-tions in particular regions of themacromolecule.36,37 Figure 1demonstrates the UVRR selectivity available, for example, forstudying the protein myoglobin (Mb).38,39 The visible wave-length absorptionbands ofMbresult fromthe in-planef*electronic transitions of its heme group. Resonance Raman(RR) excitation of Mb at 415 nm in the strong heme Soretabsorption band results in an intense RR spectra whichcontains only the in-plane heme ring vibrations.40 In contrast,excitation at 229 nm within the absorption bands of the Tyrand Trp aromatic side chains shows RR spectra completelydominated by Tyr and Trp aromatic ring side chain vibra-tions.39,41 Deeper UV excitation at 206.5 nm, within the f* transitions of the amide peptide bonds, shows UVRRspectra dominated by the peptide bond amide vibrations.39
Thus, tuning the UVRR excitation wavelengths allows theprobing of different chromophoric segments of a macromo-lecule. Another advantage of deep UV Ramanmeasurements
is that there is no interference from molecular relaxed fluo-rescence.42 In addition, UVRR can also be used in pump-probe measurements to give kinetic information on fast bio-logical processes.43
UVRR Instrumentation. The rapid development of UVRRhas been aided by recent advances in lasers, optics, anddetectors. For temperature-jump (T-jump) measurements,an IR pump pulse at 1.9 m excites the overtone absorptionband of water and heats a small sample volume. A time-delayed UV probe pulse excites the UVRR of the IR-pulse-heated volume. TheUVRR light is collected anddispersed by aspectrograph, and the spectrum is detected by a CCD detec-tor. Non-kinetic Raman measurements of static structure arebestmeasuredby usingCW lasers that avoid nonlinear opticaland thermal processes that can induce sample degradation.44
However, high repetition rate (1-5 kHz) pulsed (10-50 ns)Nd:YLF pumped Ti:Sapphire lasers43,45 are very convenientUVRR laser sources because their output can be easily andcontinuously tuned between 193 and 240 nm. These deep-UV excitation beams are generated by frequency quadruplingor tripling and mixing the Ti:Sapphire laser fundamentals.Liquid-nitrogen-cooled CCDcameras are the optimumUVRRdetector because of their low noise.
Protein and Peptide Bond Studies. UV excitation involvesthe HOMO and LUMOmolecular orbitals of the peptide bond(secondary amides, except for proline). The lowest-energynf * transition at220 nm is electronically forbidden andweak. It gives rise to the strong CD signature of the R-helixconformation but gives rise to negligible resonance Ramanenhancement.19,46 The 190 nm f * transition isstrongly allowed, with a strong absorption band that givesrise to strong UVRR intensities.47 Excitation within this ab-sorption band gives rise to the strong UVRR enhancement ofvibrations that have large components of C;N stretching. Asomewhat smaller enhancement occurs for vibrations withstrong CdO stretching.48
Figure 1. Selectivity of resonance Raman spectral measurementsof myoglobin showing the protein absorption spectrum and thedifferent resonance Raman spectra obtainedwith different excita-tion wavelengths.
r 2011 American Chemical Society 336 DOI: 10.1021/jz101619f |J. Phys. Chem. Lett. 2011, 2, 334344
Excitation at 200 nm gives rise to strong UVRR spectrathat show particular peptide bond vibrations,49 that includethe amide I (AmI) vibration (1660 cm-1) that consistsmainly of CdO stretching and a small amount of out-of-phaseC;N stretching, the amide II (AmII) vibration (1550 cm-1)that consists of anout-of-phase combinationofC;NstretchingandN;Hbendingmotions, and the amide III (AmIII) vibration(between1200and1340 cm-1),which is a complex vibrationinvolving C;N stretching and N;H bending. A vibration thatcontains significant CR;H bending (1390 cm-1) is alsoenhanced if the peptide bond conformation causes the couplingof CR;H bending to C;N stretching and N;H bending.
TheseUVRR-enhancedpeptidebondvibrations (except forthe AmI) derive from local modes within individual peptidebonds. The AmI vibrations show small couplings betweenadjacent peptide bonds.50,51 The local mode character of theAmII, AmIII, and CR;H bending peptide bond vibrationsallows the measured UVRR spectrum to be modeled as thelinear sum of contributions of the individual peptide bondUVRR spectra.52
This enabled Asher and co-workers to develop a quantita-tive methodology to determine protein secondary structuredirectly from the measured UVRR spectra.53 They measuredthe UVRR spectra of a set of proteins with known X-raystructures and determined the basis spectra of the threemajor secondary structure motifs, the R-helix, -sheet, andunfolded conformations. These basis spectra represent theaverage pure secondary structure Raman spectra (PSSRS) ofR-helix, -sheet, and unfolded conformations.53 The frac-tional secondary structure composition of a protein with anunknown secondary structure can be uniquely determined bylinearly fitting the PSSRS to the protein UVRR spectra. Thefitted weighting fractions are the fractional amounts of eachsecondary structure motif.53
Correlation between Spectral Features and Protein Sec-ondary Structure. The UVRR spectra of proteins and peptidesare conformationally sensitive, as shown in the Figure 2UVRRstudy of R-helix melting of poly-L-glutamic acid (PGA) at pH4.3. PGA isR-helical at low temperaturesbutmelts to unfoldedstructures at high temperatures.54 The R-helix low-tempera-ture UVRR spectrum shows an AmI band at1660 cm-1, anAmII band at 1560 cm-1, and an AmIII band centeredaround 1300 cm-1. As the temperature increases, the AmI
band upshifts from 1660 to 1670 cm-1 and becomesbroader, while the AmII band downshifts from 1560 to1555 cm-1. These results indicate weakened hydrogenbonding (HB) with increasing temperature. Previous workshowed thatwater HB to the peptide bond CdO site increasesthe CdO bond length and, thus, downshifts the AmI band,while water HB to the peptide bond N-H upshifts the AmIIband. Thus, the extent of HB partially determines the UVRRband frequencies. The CR;H intensity increase with tem-perature indicates R-helix melting.53,55 The R-helix conforma-tion shows a negligible CR;H bending band intensity, incontrast to the unfolded extended conformation that has ahigh CR;H bending intensity.
The AmIII region contains three sub-bands, AmIII1, AmIII2,and AmIII3. However, only two of these sub-bands areclearly resolved in the AmIII region of PGA, the AmIII2 band(1303 cm-1) and the AmIII3 band (1250 cm-1). TheAmIII3 band, which ismost sensitive to conformation, derivesfrommotions that involve couplingofN;Hbending toCR;Hbending and C;N stretching.56,57 As the temperature in-creases, the concentration of melted polyproline II (PPII)-likeconformation increases, and the corresponding unfolded PPIIAmIII3 band (1247 cm-1) in PGA becomes more promi-nent, overshadowing the low-temperature R-helical AmIII3band. This clearly signals melting of the R-helix conformationto a PPII conformation.
The large AmIII3 band frequency conformational depen-dence derives from the fact that coupling between CR;Hbending and N;H bending peptide bond motion dependssensitively on the peptide bond Ramachandran dihedralangle that, in part, defines the peptide bond secondarystructure conformation.57
Determination of Psi () Angle Distribution. The Ashergroup discovered a sinusoidal dependence of the AmIII3frequencyon thisRamachandranangle.54Conveniently, theyalso found little dependence of the AmIII3 frequency on theother dihedral angle, the Ramachandran angle (for stericallyallowed angles).56 The origin of this angle frequency dif-ference between the R-helix and extended conformationsresults from the fact that the R-helix peptide bond conforma-tions have trans N;H and CR;H bonds that prevent coupling(Figure 3). Thus, the R-helix AmIII3 frequency occurs at 1258cm-1, and the CR;Hband contains negligible C;N andN;Hbending motion and is, thus, not resonance-enhanced.
In contrast, peptide bonds adopting an extended PPII-likeconformation have cis N;H and CR;H bonds whosemotionscouplewell.TheAmIII3bandfrequencydownshifts to1245cm
-1,and the CR;H bending vibration contains C;N stretchingandN;Hbendingmotions, resulting in resonance enhance-ment.54 Quantitative relations were developed to relate theAmIII3 band frequencies to Ramachandran angles fordifferent peptide bond HB states,57 for example, for peptidebonds fully hydrogen bonded to water, such as in PPII, 2.51-helix, and extended -strand conformations
EXTAmIII3, T 1256 cm- 1 -54 cm- 1 3 sin 26-0:11 cm-1=CT 1
where T is the temperature.
Figure 2. The temperature dependence of the UVRR spectra andresulting R-helix fractions of poly-L-glutamic acid at pH 4.3 cal-culated from the UVRR spectra. Adapted from ref 54.
r 2011 American Chemical Society 337 DOI: 10.1021/jz101619f |J. Phys. Chem. Lett. 2011, 2, 334344
The family of quantitative relationships determining theAmIII3 frequencies ignore the more modest Ramachandran angle dependencies.56 Equations have been proposed toallow estimation of the angle for the different possiblepeptide bond HB states. The estimated error of this determi-nation is suggested to bee(14.57 Figure 4 shows the familyof theoretical curves that correlate the AmIII3 frequencies tothe Ramachandran angles for the different HB states.57 Asshown below, correlating the inhomogeneously broadenedAmIII3 band shape to the underlying Ramachandran angledistribution enables the determination of the peptide bondconformational distribution in peptides and proteins. Mostimportantly, this conformational distribution can be used tocalculate the Gibbs free-energy landscape along the anglecoordinate, which is the most important (un)folding reactioncoordinate.
The UVRR spectra show inhomogeneously broadenedRaman bands that reflect the distribution of conformationsexperienced by the protein. In the case of the AmIII3 band,the inhomogeneous distribution reflects mainly the distribu-tion of peptide bond angles and HB states.
We assume that the experimentally measured, inhomo-geneously broadened AmIII3 band, A(), derives from thesum of M Lorentzian bands which result from the differentpeptide bond conformations with different band frequencies,ei. The AmIII3 band homogeneous linewidth, =7.5 cm
was determined from UVRR measurements of small peptidecrystals in defined secondary structure states58
v- vei2 22
where Li is the probability for the contributing band to occur atfrequency ei.
We can deconvolute out the homogeneous linewidth fromthe peptide bond UVRR spectra to calculate the underlyinginhomogeneously broadenedAmIII3 band shape,
58 leading tothe calculation of the frequency distribution of the AmIII3 band.We can then use eq 1, relating the AmIII3 band frequency tothe Ramachandran angle, to convert the frequency dis-tributions to angle distributions (Figure 5). Figure 5Ashows histogram plots of the calculated underlying AmIII3band frequency distributions for a set of peptides and proteins.The XAO peptide of sequence Ac-XXAAAAAAAOO-NH2 (A isalanine, O is ornithine, X is diaminobutyric acid) is known tobe primarily in a PPII conformation.59 As shown in Figure 5A,the XAO frequency distribution is similar to that of Ala5-Ala3(the difference UVRR between Ala5 and Ala3 that modelsthe spectrum of the interior Ala5 peptide bonds). This resultindicates that these peptide bonds predominantly populatethe PPII conformation, as do the peptide bonds of a 21-residuemainly alanine peptide (AP) of sequence AAAAA(AAARA)3Aat elevated temperature. Acid-denatured apomyoglobin showsa broad frequency distribution, as expected, from its broad
Figure 3. Relative orientations of N;H and CR;H bonds in thepolyproline II and R-helix conformations.
Figure 4. Correlation betweenAmIII3 frequency, peptide bondHBpattern, and Ramachandran angle; (0) measured AmIII3 fre-quencies of R-helix, antiparallel -sheet, PPII, and 2.51-helix inaqueous solution; ()) measured AmIII3 frequencies of peptidecrystals, plotted against their angles (1) Ala-Asp, (2) Gly-Ala-Leu 3 3H2O, (3) Val-Glu, (4) Ala-Ser, (5) Val-Lys, (6) Ser-Ala, and(7) Ala-Ala. The blue curve is the predicted correlation (eq 1) forfull HB towater (PPII, 2.51-helix, and extended -strand); the greencurve is a theoretically predicted correlation (eq 1) for two end-onpeptide bond-peptide bond HBs (R-helix-like conformation andinterior strands of -sheet); the magenta curve is the predictedcorrelation (eq 1) for the peptide bond where only the CdO grouphas a peptide bond-peptide bond HB (three R-helix N-terminalpeptide bonds and half of the peptide bonds of the exterior strandsof the -sheet); the black curve is the predicted correlation (eq 1)for the peptide bondwith just theN;Hgroup peptide bond-peptidebondHB (threeR-helix C-terminal peptide bond and the other halfof the peptide bond of the exterior strand of the -sheet). Repro-duced from ref 57.
The UVRR spectra show inhomo-geneously broadened
Raman bands that reflect the dis-tribution of conformations experi-
enced by the protein.
r 2011 American Chemical Society 338 DOI: 10.1021/jz101619f |J. Phys. Chem. Lett. 2011, 2, 334344
distribution of conformations. The protein library, of course,shows the broadest frequency distribution. Figure 5B showsthe calculated Ramachandran angle distributions for thesamples. These plots are obtained by converting the frequencydistributions of Figure 5A into Ramachandran angle distri-butions using eq 1.
Further, by applying the Boltzmann relation to the angledistributions, we can calculate the relative Gibbs free energyalong the Ramachandran angle coordinate because thepopulation at any particular angle is determined by itsrelative Gibbs free energy.58
For example, this approachwas used to determine theGibbsfree-energy landscape for poly-L-lysine (PLL). At neutral and lowpH values, PLL adopts extended conformations that includesthe PPII and 2.51-helix conformations. The 2.51-helix confor-mation results from the PLL charged side chains' electrostaticrepulsions.60Maet al.55 usedUVRR tomonitor the temperatureand NaClO4 concentration dependence of the PLL Gibbs free-energy landscape (Figure 6). They observed an R-helix-likebasin containing R-helix and -bulge conformations and abasin containingPPII and2.51-helical extendedconformations.
As indicated in Figure 6, adding NaClO4 induces a changefrom a solution equilibrium between extended PPII and 2.51-helical conformations to an equilibrium involving R-helix-likeconformations. This conformational change results fromcharge screening due to strong ion-pair formation betweenClO4
- and the lysine side chain ;NH3 that reduces the
repulsion between charged side chains. Figure 6 also showsthat increasing temperatures cause theR-helix-like conforma-tions to melt to extended conformations.
T-Jump Kinetic Studies of Protein Folding. Dynamic UVRRmeasurements canbeused toelucidatebiomolecular structural
dynamics.61,62 UVRR T-jump measurements can elucidate theevolution of peptide and protein secondary structure.61-70
These studies probe the evolution between different second-ary structural motifs such as R-helix, 310-helix, -bulge, andPPII conformations.71 The rates of these transitions occur inthe 100 ns to 2 s time regime.
Recentnanosecond tomicrosecondprotein foldingdynamicsstudies find complex unfolding behaviors. For example,recent studies of the mainly alanine peptide (AP) meltingdemonstrate a complex pathway that involves melting ofmultiple R-helix-like structures, which include the 310-helix,-bulge, and pure R-helix conformations that have differentmelting curves than the PPII-like unfolded conformation.63
To gain insight into the dynamics of protein (un)folding,the Asher group constructed the first T-jump UVRR spectrom-eter that they used to examine conformational relaxationsubsequent to nanosecond T-jumps.61-63 The peptide andprotein relaxation after the T-jump utilizes folding and unfold-ing conformational change coordinates that are easily studiedwith UVRR. These T-jumps used 5 ns excitation pulses at1.9 m that occur within awater vibrational overtone absorp-tion band. Thermalization of the absorbed energy occurswithin 70 ps.72,73 It is easy to achieve 20 C T-jumps fromthe 5 ns IR laser pulses.
In their first kinetic studies, the Asher group examined thekinetics of melting of the AP that is mainly R-helical at lowtemperature.63 Steady-state measurements showed that theR-helix melts to a PPII conformation. Figure 7A shows theT-jump relaxation transient difference UVRR spectra of AP inH2O and D2O. The transient difference spectra measured atdelay times as long as 1 s were modeled using a linearcombination of R-helix and the PPII equilibrium UVRR basis
Figure 5. (A) Frequency distribution of the AmIII3 band calculated by deconvolution of homogenously broadened AmIII3 band profiles ofXAO of the sequence Ac-XXAAAAAAAOO-NH2 (A is alanine, O is ornithine, X is diaminobutyric acid), A5-A3 (Ala5-Ala3), non-R-helical APofthe sequence AAAAA-(AAARA)3A, acid-denatured apomyoglobin, and disordered protein conformations. The resulting histogram showsthe population distribution underlying the measured AmIII3 band. (B) Estimated Ramachandran angle distribution of XAO, A5-A3, non-R-helical AP, acid-denatured apomyoglobin, and disordered protein conformations. Reproduced from ref 58.
r 2011 American Chemical Society 339 DOI: 10.1021/jz101619f |J. Phys. Chem. Lett. 2011, 2, 334344
spectra. The first spectral changes evident at
r 2011 American Chemical Society 340 DOI: 10.1021/jz101619f |J. Phys. Chem. Lett. 2011, 2, 334344
Figure 8B shows the melting curves determined for thesedifferent R-helix-like conformations by assuming identicalRaman cross sections for the pure R-helix, the 310-helix, andthe-bulge conformations.Tmwasdetermined tobe45,20and10 C for the R-helix, 310-helices, and -bulges, respectively.
The anti-Arrhenius behavior observed by Lednev et al.'sT-jump measurements directly results from these differentTm for the 310-helix, -bulge, and pureR-helix conformations.75
As the temperature increases, the pureR-helix conformationincreasingly dominates the equilibrium conformational dis-tribution. Apparently, the folding rate of the pure R-helixconformation is slowest. These studies clearly show theutility of UVRR to gain crucial insight into the complex natureof peptide folding dynamics.
These types ofT-jump studies can give important biologicalinsight. For example, in a recent protein T-jump study, Spiroet al.70 examined the early events in the unfolding of apomyo-globin using both 197 and 229 nm excitation. These excita-tions allowed themtoprobeboth the aromatic side chains andthe peptide backbone conformations. Aromatic amino acid
side chain UVRR bands can monitor the solvent exposure,while the peptide bond UVRR bands report on backboneRamachandran angles, as discussedabove.Measuringbothspectral bands can answer the question of whether a changingsolvent exposureof theprotein coreprecedesor follows second-ary structure changes. The authors were able to clearly differ-entiate the order of these events. They found that the Trp14bands respond twice as fast as does the peptide bond R-helixmelting. Thus, Trp14 that is originally buried in the protein corebecomes exposed to solvent prior tomelting of the protein core.
Kinetic IR T-jump experiments have also been carriedout on R-helical peptides.22,76 For instance, in their IR studies,the Dyer group found that suc-Fs 21-peptide (a peptide verysimilar to AP) shows fast unfolding kinetics with a timeconstant of160 ns.22 This result is consistent with theUVRRstudies of Lednev et al.63 In another IR T-jump kinetic study,the Gai group examined the helix-coil transition of anR-helicalpeptide and its deuterated analogue, Ac-YGSPEA3KA4KA4-CO-D-Arg-CONH2andAc-YGSPEA3KAAAAKA4-CO-D-Arg-CONH2,where the underlined residues are 13C-labeled. Thisdesign was meant to use the 13CdOAmI band of the centralAla residues to probe conformational changes associatedwith only the middle of the peptide sequence and to dis-criminate it from signals due to end-fraying. They reporteda complex helix-coil transition that does show single-exponential relaxation.76 Their multiexponential relaxationkinetics based on 13CdOAmI band changes show a compo-nent with a time constant of 230 ns similar to ours that doesnot arise from end-fraying.22,63 The IR peptide foldingdynamic studies show less information content becausethey only monitor the AmI band,22,76 whereas UVRR moni-tors the CR;H, AmII and AmIII bands, in addition to the AmIband. Thus, UVRR can give a more informative picture ofpeptide folding dynamics. Further, as shown in Figure 2, thespectral dependence of the AmI band is less than that for theAmIII3 and the CR;H bending bands.
Other UVRR Insights. A number of other recent UVRRstudies havealso illustrated the important protein informationavailable. Forexample, Ianoul etal. usedUVRR to examine thepeptide backbone spatial dependence of R-helix melting ofdeuterium-labeled AP (AdP).71 In AdP, all of the Ala residuesexcept the four central oneswere selectively deuterated. Theyfound that melting of the isotopically labeled exterior pep-tide bonds could be spectrally resolved from the central ones,thus allowing the spatial resolution of the peptide bondconformational changes. The results show that the centralresidues are essentially 100% R-helix-like at 0 C with a Tmof 32 C, while the exterior residues are60% R-helix-like at0 C with a Tm of 5 C.
More recently, Lednev's group reported the application ofUVRR for studying amyloid fibrils,77,78which arewell-organizedprotein aggregates associatedwithmanyneurodegenerativediseases. Amyloid fibrils are not soluble and do not formcrystals, limiting the application of conventional NMR spec-troscopy and X-ray crystallography, two major biophysicaltools of structural biology. UVRR spectroscopy is uniquelysuitable for characterizing the protein structure at all stagesof fibrillation. Chemometric79 and 2D correlation80 analysisofUVRR spectra allowed fordirectmonitoring of the fibrillation
Figure 8. (A) Calculated Ramachandran probability distribu-tions in AP at (A) 0, (B) 10, (C) 20, and (D) 30 C. Reproduced fromref 74. (B) Melting curves for AP R-helix-like conformations. ()Original R-helix melting curve as reported by Lednev et al. (refs 61and 62), which is a sumof individualR-,-, and 310-helicalmeltingcurves; (red () pure R-helix melting; (green 9) 310-helix (type IIIturn) melting; (blue b) -bulge (-helix) melting. Adapted fromref 74.
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nucleus,81 establishing the sequential order of changes inthe protein secondary structure and the kinetic mecha-nism of lysozyme fibrillation.82
Their combinationof hydrogen-deuteriumexchangewithUVRRand advanced statistics enabled them to determine thespectroscopic signature of the fibril core.83 They then utilizedour method described above to determine the Ramachandran angle distribution in the fibril core.84,85 This informationis a powerful constraint for determining the conformationof -strands in the fibril core. This approach is the onlyexperimental tool available at the moment to directly char-acterize the cross- core structure in fibrils prepared from thefull-length proteins. X-ray crystallography of small peptidemicrocrystalsmimicking the fibril core and solid-state NMRoffibrils, prepared from isotope-labeled peptides, can providethe atomic-resolution structure of the fibril core. UVRR-hydrogen-deuterium exchange indicated a significant varia-bility in the core structure of fibrils prepared from differentproteins.84,85 In addition, it allowed differentiation of paralleland antiparallel -sheets in the cross- core of amyloid fibrils.84 Moreover, the conformation of the parallel -sheet inthe A1-40 fibril corewas atypical for globular proteins, while,in contrast, the antiparallel -sheet in A32-42 fibrils was acommon structure in globular proteins.84 Consistent with thelatter observation, the Raman signature of the fibrillar-type-sheet was required in addition to the globular protein-sheet to satisfactorily fit the UVRR spectra of the aggregatedprion protein.86
Future Direction and Outlook. The UVRR methodologiesdiscussed in thisPerspectiveenable incisive investigations into themechanism of protein folding. Future studies will include singlepeptide bond conformational changes and studies of the con-formation of side chains such as Phe, Tyr, Trp, Arg, Asn, and Gln.
Resolution of Individual Peptide Bond ConformationalChanges. The current state-of-the-art UVRR measurementslack sufficient S/N to monitor conformational changes at thesingle peptide bond level of a100 residue protein. However,UVRR instrumentation continues to advance due to improve-ments in laser technology and the development of UVRamanspectrometers with dramatically improved spectral disper-sion that enable dramatically increased throughput. We areconstructing a spectrometer which utilizes very high disper-sion gratings with optics specially coated for deep UV effi-ciencies. The increased S/N will enable the monitoring of theGibbs free-energy landscape of individual peptide bonds in apeptide or protein. CR deuteration silences the angledependence of the AmIII3 band frequency. Thus, the differ-ence UVRR between a CR deuterium-labeled and the naturalabundance protein reveals the AmIII3 band of the labeledpeptide bond; the frequencies and band shapes reveal its
Ramachandran angle distribution, which reveals its Gibbs free-energy landscape. T-jump kinetic measurements of the isotope-labeleddifference spectrawill reveal the individual peptidebonds'activation barriers that control (un)folding mechanisms.
Amino Acid Side Chain Conformations. There are numerousaminoacidsidechainchromophores that showUVRR-enhancedbands with 200 nm UVRR excitation. These UVRR bandscan be used to monitor amino acid side chain conforma-tions and their interactions with other side chains and thebackbone peptide bonds. There is now a deep under-standing of the conformational dependence of the Trp, Tyr,and Phe aromatic amino acid UVRR spectra.87,88 In contrast,there are few studies of the UVRR bands of these residues89
and no published studies, to our knowledge, of Arg, Asn, andGln residues. The Asn and Gln side chains give rise to UVRR-enhanced primary amide UVRR bands that partially overlapthe peptide bond amide bands. These can be selectivelymonitored by comparing very deep UV,195 nmUVRR, forexample, to UVRR spectra excited at 204 nm; primaryamides show their f * transition at shorter wavelengthsthan the peptide bond f * transition.90 Thus, appro-priately scaled 195-204 nm difference spectra will displaythe side chain primary amide bands.
We are now characterizing the UVRR spectra of Asn andGln side chain vibrations in order to determine their HBdependence. This will ultimately enable UVRR to detect HBof side chains in peptides and proteins. The Arg side chainshows an isolated band at 1178 cm-1, which is easily observedin AP, for example.46Ourwork is also investigating the role ofArg residues in R-helix stabilization.
The uniqueutility ofUVRR for the studyof protein folding isdiscussed in this Perspective. Specifically, we have shownhowpeptide bond resonance Raman enhancement permits thestudy of protein secondary structure by using 200 nm UVexcitation. It now is clear that UVRR is the most useful dilutesolution method to quickly determine protein and peptidesecondary structure. The sinusoidal dependence of the AmIII3Raman band frequency on the Ramachandran angleenables the determination of solution peptide bond angledistributions. The measurement of this distribution reveals theGibbs free-energy landscape along the angle protein(un)folding coordinate. Kinetic T-jump studies allow theexamination of the kinetics of protein folding and revealaspects of the activation barriers between equilibrium con-formations. The application of UVRR to the study of theformation mechanism of amyloid fibrils is an importantillustration of the power of the technique to probe structureand dynamics. The development of statistical methods forthe analysis of UVRR spectra dramatically increases theinformation content of the spectroscopy.
The increased S/N will enable themonitoring of the Gibbs free-energylandscape of individual peptidebonds in a peptide or protein.
UVRR is the most useful dilute so-lutionmethod to quickly determine
protein and peptide secondarystructure.
r 2011 American Chemical Society 342 DOI: 10.1021/jz101619f |J. Phys. Chem. Lett. 2011, 2, 334344
Corresponding Author:*To whom correspondence should be addressed. E-mail: [email protected] Phone: 412-624-8570. Fax: 412-624-0588.
BiographiesSulayman Oladepo received his Ph.D. from the University of
Alberta, under the supervision of Prof. Glen Loppnow. He iscurrently doing his postdoctoral work in the laboratory of Prof.Sanford Asher at the University of Pittsburgh. His current researchinvolves the use of UV resonance Raman spectroscopy to study themelting dynamics of -sheet structures and the effects of citrullina-tion on protein folding dynamics.
Kan Xiong received his Bachelor's Degree in Chemistry from theUniversityof ScienceandTechnologyofChina in2006.He is currentlyasenior graduate student under the direction of Prof. Sanford A. Asher atthe University of Pittsburgh and is working on using UV resonanceRaman spectroscopy to study protein and peptide folding.
ZhenminHong is currently a graduate student in theDepartmentof Chemistry, University of Pittsburgh. He received B.S. and M.S.degrees from Tsinghua University, China. His research interestincludes using UV resonance Raman spectroscopy to study proteinand peptide structure and folding. He is nowexamining the effect ofside chain interactions on determining peptide conformations.
Sanford Asher is Distinguished Professor of Chemistry at theUniversity of Pittsburgh. He received his Bachelor's degree from theUniversity of Missouri at St. Louis in 1971 and his Ph.D. in 1977fromUCBerkeley. Followingpostdoctoralwork inApplied Physics atHarvard, he joined the department of Chemistry of the University ofPittsburgh in 1980. His current research concentrates on develop-ing UV resonance Raman spectroscopy for probing protein struc-ture and dynamics. His research group also investigates anddevelops photonic crystal materials and sensors. See http://www.pitt.edu/~asher/homepage/index.html
ACKNOWLEDGMENT The authors gratefully thank Igor Lednevfor helping us describe his groups fibrillation studies. We alsogratefully acknowledge NIH Grant 1R01EB009089 for funding.
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