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April 2006 Vol. LXXXIV, No. 8

MonthlyMeetingEsselen Award to Prof. Richard D. DiMarchi

Book ReviewThe Physics of Superheroes by Dennis Sardella

Summerthing2006 - Red Sox

SummerResearchScholar“Efforts Towards the StructuralDetermination of LnmQ, a NovelAdenylation Domain”

The Nucleus is distributed to the members of the Northeastern Section of the American Chemical Society, to the secretaries of the Local Sections, and to editors of all local A.C.S. Section publications.Forms close for advertising on the 1st of the month of the preceding issue. Text must be received by theeditor six weeks before the date of issue.Editor: Michael P. Filosa, Ph.D., ZINK Imaging Incorporated, 1265 Main Street,

Waltham, MA 02451 Email: Michael.Filosa(at)zink.com; Tel: 781-386-8479.Associate Editors: Myron S. Simon, 20 Somerset Rd., W. Newton, MA 02465, Tel: 617-332-5273

Nancy Simons, Analytical Chemist, Corporate R&D, Boston Scientific Corp., 1 Boston Scientific Place A4, Natick, MA 01760-1537. Email: Nancy.Simons(at)bsci.com; Tel. 508-650-8603; Fax 508-647-2329Sheila E Rodman, Malden, MA. Email:serodman(at)hotmail.com Tel: 781-771-4116.

Board of Publications: Mary Mahaney (Chair), Martin Idelson, Vivian K. Walworth Business Manager: Karen Piper, 19 Mill Rd., Harvard, MA 01451, Tel: 978-456-8622Advertising Manager: Vincent J. Gale, P.O. Box 1150, Marshfield, MA 02050,

Tel: 781-837-0424; FAX: 781-837-1453Contributing Editors: Morton Hoffman, Feature Editor; Dennis Sardella, Book Reviews; Calendar Coordinator: Sheila Rodman, email: serodman(at)hotmail.comPhotographers: Morton Z. Hoffman, Ying Wei and James PhillipsProofreaders: Donald O. Rickter, Myron S. Simon, Vivian K. WalworthWebpage: Webmaster: Sathish Rangarajan, sathish.rangan2(at)gmail.comCopyright 2006, Northeastern Section of the American Chemical Society, Inc.

The Nucleus April 2006 3

The Northeastern Section of the AmericanChemical Society, Inc.Office: Marilou Cashman, 23 Cottage St., Natick, MA 01760. 1-800-872-2054 (Voice or FAX) or 508-653-6329. e-mail: mcash0953(at)aol.comAny Section business may be conducted via the business office above.NESACS Homepage:http://www.NESACS.orgSathish Rangarajan, WebmasterACS Hotline, Washington, D.C.: 1-800-227-5558Officers 2005Chair:Patricia MabroukChemistry Department, Northeastern UniversityBoston, MA 02115617 373 2845; p.mabrouk(at)neu.eduChair-Elect:Mukund Chorghade14 Carlson Circle, Natick, MA 01760-4205508-651-7809 and 508-308-3891Chorghade(at)comcast.netImmediate Past Chair:Amy TapperPeptimmune64 Sidney Street, Suite 380, Cambridge, MA 02139617-715-8005; amy.tapper(at)peptimmune.comSecretary:Michael SingerSigma RBI3 Strathmore Rd. Natick, MA 01760-2447508-651-8151x291 msinger(at)sial.comTreasurer:James Piper19 Mill Rd., Harvard, MA 01451978-456-3155 piper28(at)attglobal.netAuditor:Anthony RosnerArchivist:Myron S. Simon20 Somerset Rd. Newton, MA 02465; 617-332-5273romysimon(at)mindspring.comTrustees:Joseph A. Lima, Esther A.H. Hopkins, Michael E. Strem, Councilors Alternate CouncilorsTerm Ends 12/31/2006Michaeline F. Chen Wallace J. GleekmanCatherine E. Costello Howard R. MaynePatricia A. Mabrouk Alfred ViolaJulia H. Miwa Barbara G. WoodDorothy J. Phillips David WarrTerm Ends 12/31/2007Thomas R. Gilbert Arlene W. LightMichael J. Hearn Timothy B. FrigoMichael Singer Mary MahaneyPamela Nagafuji Mark FroimowitzTerm Ends 12/31/2008Doris I. Lewis Patrick M. GordonMorton Z. Hoffman Michael P. FilosaChristine Jaworek-Lopes Lawrence ScottMary Burgess Liming ShaoDonald O. Rickter S. B. Rajur

All Chairs of standingCommittees, the editor of THE NUCLEUS, and the Trustees of SectionFunds are members of theBoard of Directors. AnyCouncilor of the American Chemical Societyresiding within the section area is an ex officiomember of the Board of Directors.

ContentsAnnouncements________________________________________4Candidates for Election 2006, 68th Annual NEACT Summer Conference,Speaker's Bureau

April Meeting__________________________________________5Esselen Award Meeting: Dr. Richard D. DiMarchi, Indiana University andChairman, Ambrx, Inc. “Chemical Biotechnology as a Means to Optimal Protein Therapeutics,”

Announcements________________________________________6Lyman C. Newell Grants, NERM 2006, Summerthing 2006 - Red Sox, 2ndAnnual NESACS Golf Tournament

Book Review __________________________________________7“The Physics of Superheroes” by James Kakalios, reviewed by Dennis Sardella

Summer Research Scholar _______________________________9“Efforts Towards the Structural Determination of LnmQ, a Novel AdenylationDomain”, by William Hillmann and Steven D. Bruner, Department of Chemistry,Boston College

Announcements ______________________________________12Call for Papers: The 8th Annual Northeast Student Chemistry Research Confer-ence, 3rd Annual Student Chemistry Career Fair sponsored by NSYCC

Pictures from Recent Meetings __________________________13Pictures from December, January and February Meetings by Ms. Ying Wei

Cover: Professor Richard D. DiMarchi (Photo: Courtesy of Indiana University)

Deadlines: Summer 2006 Issue: June 16, 2006September 2006 Issue: July 14, 2006

Chair-Elect Marietta Schwartz

TreasurerJim Piper

AuditorTony Rosner

Trustee Joe Lima

Nominating Committee Tom Gilbert Patrick GordonMark FroimowitzArthur GreenbergRobert Grubbs

Councilor / Alternate CouncilorAmy TapperMichaeline ChenCatherine CostelloPam MabroukJulia MiwaDorothy Phillips

(Councilor/Alternate continued)Wallace GleekmanAl ViolaMukund ChorghadeJerry JasinskiEva BinnunMarietta SchwartzMick HurreyDenyce WichtEd BrushPeter JacobiAngeles Dios

Norris Award Committee Mort HoffmanDean Wilcox Mary Schultz Todd Wimpfheimer

Director-at-Large Harry MandevilleGary WeismanCassandra CelatkaIvan Korendovich ◆◆

Candidates for Election2006

4 The Nucleus April 2006

Golf Tournament - Osmium Level DonorIRIXCorporate Patrons and Golf PlatinumAstraZeneca R&D BostonCardinal HealthDSMGenzyme Drug Discovery & Dev.HovioneIBMLyophilization Service of New Eng-

landPhasex CorporationStrem Chemicals Inc.Zone EnterprisesCorporate Sponsors and Golf GoldAerodyne Research Inc.Cambridge Isotope LaboratoriesNew England BioLabs, Inc.PfizerRhodia Pharma SolutionsSigma-RBITeledyne ISCODonors and Golf SilverConsulting Resources Corp.Dishman Pharmaceuticals and Chem-

icals LimitedHoughton Chemical CompanyOrganix Inc.PeptimmuneVertex

Speak Up &Speak OutThe Northeastern Section of the Amer-ican Chemical Society (NESACS) islooking for good speakers. In a neweffort to build awareness about thebenefits of Chemistry in our schools,towns and other industries we are seek-ing willing and able speakers.

The James Flack Norris Speaker’sBureau of the NESACS is in the midstof a recruitment drive. Qualified vol-unteers will be asked to appear in frontof audiences around the New Englandarea and present a wide variety of sub-jects ranging from bioterrorism to bub-ble gum – whatever your area of

New England Associationof Chemistry Teachers

The 68th Annual NEACT Summer ConferenceAugust 7-10, 2006

Bridgewater State College, Bridgewater, MATopic: Green Chemistry

Workshops; “Hands on” Teaching Materials; Informal discussion timewith participants and speakers; modern, air-conditioned accommodations.

Continuing Education Credits available for Massachusetts, Connecticut and Rhode Island teachers.

Keynote Speaker: Dr. John Warner, UMass LowellNEACT and NEACS Scholarships available

Program details will be posted at: www.neact.orgRegistration information will be available soon.

Approximate cost for entire conference is about $300 per participant. Contact Kathy Siok, Registrar-Treasurer at neactks(at)cox.net

Continued on page 12

BiographyRichard DiMarchi is the Linda & JackGill Chair in Biomolecular Sciencesand Professor of Chemistry at IndianaUniversity. He is a retired Group VicePresident at Eli Lilly & Companywhere for more than two decades heprovided leadership in biotechnology,endocrine research and product devel-opment. He currently serves as a co-founder and Board Chairman ofAmbrx Inc. He previously served as a

board member to the biotechnologytrade group BIO and the AmericanPeptide Society, as well as such com-panies as Millennium Biotherapeuticsand Inproteo. He currently serves asBoard member to Isis Pharmaceuticals,and scientific advisor to Alba Inc.,Epitome Biosciences, Kai Pharmaceu-ticals, Semafore Biotechnologies,SAM Ventures, and Twilight Ventures.Professor DiMarchi is readily recog-nized for discovery and developmentof rDNA-derived Humalog® (LisPro-

human insulin). This designer insulinrepresents the first demonstration thatstructurally altered rDNA-derivedbiosynthetic proteins can improvepharmacological performance withoutincreasing the risk of an abnormalimmunological response. As scientistand administrator Dr. DiMarchi partic-ipated in the commercial developmentof Humulin, Humatrope, Xigris®, andForteo®. The goal of his currentresearch and commercial endeavors isto develop proteins with enhancedtherapeutic properties through bio-chemical optimization with non-natu-ral amino acids, an approach he hastermed chemical-biotechnology ◆◆


Abstract The scientific work from this labora-tory was central to the discovery andthe commercial development of a num-ber of prominent protein-based medi-cines, such as Humulin, HumalogHumatrope, rGlucagon, Xigris, andForteo. Humalog represents the firstbiosynthetic hormone optimized byrDNA technology approved as a humanmedicine. It established the precedentthat endogenous hormones were notoptimized for use as drugs, and thatthrough insightful structural modifica-tion a more efficacious and safer pro-tein could be developed. The structuralbasis for the design of Humalog wasderived from our previous work on thestructure and function study of IGF-1.

The recent emergence of new tech-nologies in protein biosynthesis is dra-matically enlarging the structural spacethat can be utilized by protein medici-nal chemists. This period in proteinchemistry is quite analogous to theadvent of rDNA-based synthesis whenthe first natural sequenced proteinswere produced and the foundation forthe delivery of optimized proteins wasestablished. The integration of newsynthetic tools with more conventionalmethodologies is dramatically enhanc-ing the academic and commercialopportunities in protein chemistry. Ourcurrent scientific activities are focusedon novel methods of drug delivery with

Monthly MeetingThe 869th Meeting of the Northeastern Section of the AmericanChemical SocietyEsselen Award MeetingThursday, April 6, 2006Harvard University, Cambridge, MAHarvard Faculty Club, 20 Quincy St.5:30 pm Social Hour6:30 pm Dinner8:15 pm Award Meeting, Mallinckrodt Building, 12 Oxford St.

Pfizer Lecture Hall (MB23), ground floor. Dr. Patricia Mabrouk, NESACS Chair, presidingWelcome - Dr. William Klemperer, Chair, Esselen Award CommitteeThe Esselen Award - Dr. Myron S. Simon, Founding Member of theEsselen Award CommitteeIntroduction of the Award Recipient - Dr. David E. Clemmer, Indi-ana UniversityPresentation of the Award - Gustavus J. Esselen, III“Chemical Biotechnology as a Means to Optimal Protein Therapeu-tics,” Dr. Richard D. DiMarchi, Gill Chair of Biomolecular Sci-ences, Indiana University and Chairman, Ambrx, Inc.

Dinner reservations should be made no later than noon, Friday, March 31.Please call or fax Marilou Cashman at (800) 872-2054 or e-mail atMCash0953(at)aol.com. Reservations not cancelled at least 24 hours inadvance must be paid. Members, $30.00; Non-members, $35; Retirees, $20;Students, $10.THE PUBLIC IS INVITEDAnyone who needs special services or transportation, please call Marilou Cash-man a few days in advance so that suitable arrangements can be made.Free Parking in the Broadway Street garage (3rd level or higher), enter fromCambridge St. via Felton St.Next Meeting: The May Meeting is Education Night. The meeting will be heldat Northeastern University on Thursday, May 11, 2006. The evening speakerwill be Michael Gilbert of EIC Laboratories.

Continued on page 7

Please check our website(www.nesacs.org) for details on theSecond Annual NESACS Golf Tourna-ment. NESACS is looking for play-ers, sponsors, and volunteers. ◆◆

2nd AnnualNESACS GolfTournament

The bearer of bad tidings is hardly evercheered as a hero and so we come toyou all with a heavy heart to report thechange in the Red Sox group ticketsales distribution has devastated theNortheastern Section. The Red Soxhave now limited groups to only 110tickets per game for a maximum ofthree games. That’s the bad news, butnot the worst news.

The worst news turns out to bethat our account executive who han-dled our reservations has left the RedSox organization and, more impor-tantly, did not pass along the list oforganizations he handled. So when itcame time to send out the new policyinformation and notification, no wordwas relayed to the Northeastern Sec-tion. E-mails we had sent in Decemberin anticipation of group ticket avail-ability went unanswered. Phone num-bers did not seem to work. Finally, inJanuary, we managed to get through toan answering machine and that’s whenwe discovered that our executive wasno longer with the Sox. We contactedsomeone who seemed to be in chargeand was informed that all tickets weregone. We did manage to convince thepowers that be, however, to give usfifty tickets to the May 14th game withTexas and we know that will not satisfythe voracious appetite of NESACS

Summerthing2006 – RedSox

Lyman C.NewellGrantsThe Northeastern Section of the Amer-ican Chemical Society is again offeringthe Lyman C. Newell Grants for theNEACT 68th Annual Summer Confer-ence on Green Chemistry at Bridgewa-ter State College, in Bridgewater, MA,August 7-10, 2006. (http://www.neact.org/sumconf.htm)

The Lyman C. Newell Grantscommemorate a former chair of theNortheastern Section who was a distin-guished chemist, teacher, and historianof chemistry. For many years LymanNewell was chair of the ChemistryDepartment at Boston University. Heserved as the first president of NEACTfrom 1889 to 1900 and expressed acontinuing interest in training chem-istry students throughout his longcareer. His efforts are continued bygrants that bear his name.

This year we will be awardingfour grants. The total fees for Mondayevening through Thursday morning,including registration, room and board,banquets and socials are expected to befrom about $300 to $325. EachNewell Grant will be for $225, paid tothe NEACT Summer Conference Reg-istrar/Treasurer.

While preference will be given toteachers who are new to teaching orreturning to teaching, the awards areopen to all secondary school teachers.Applicants need not be members of theNortheastern Section of the AmericanChemical Society or of NEACT. Theapplication for the Newell Grants isavailable on the website of the North-eastern Section at http://www.nesacs.org. Applications for the grantsare due by April 14, 2006, and allapplicants will be notified of theresults by e-mail on April 25, 2006.Mail your completed application to thefollowing address.Dr. Ruth TannerTelephone: (978) 934-3662Education Committee Chair, NESACS

e-mail:Ruth Tanner(at)uml.eduUniversity of Massachusetts-LowellChemistry Department, Olney Hall1 University AvenueLowell, MA 01854ATTN: Newell Grant Committee ◆◆


NERM 200634th NORTHEASTREGIONAL ACS MEETING October 5-7, 2006Best Western Regency Hotel and Conference Center, Binghamton, NYHosted by the Binghamton ACS LocalSection and sponsored by the NortheastRegion, Inc.The Materials Research Society, theWatson School of Engineering andApplied Science, and the IntegratedElectronics Engineering Center (IEEC)at Binghamton University join the ACSto present NERM 2006, “EmergingTechnologies and the Chemical Sci-ences.” The program of the meetingwill highlight topics such as sensorsand small scale systems integration,lithography, environmentally benignmaterials and processes, nanomaterials,and electronics packaging. In addition,there will be symposia in analytical,inorganic, organic, and physical chem-istry, biochemistry, and chemical edu-cation, the display of undergraduateresearch posters, and an open publicsession on environmental issues impor-tant to the local region. Tobin Marksof Northwestern University will pres-ent a keynote lecture on his research inthe area of molecular electronics andphotonics.Important dates:May 1 – abstract submission and

advance registration beginsAugust 21 – abstract deadlineSeptember 11 – advance registration

endsOctober 5-7 – NERM 2006See www.nerm2006.org for details. ◆◆

Continued on page 7


In an often-quoted essay, New YorkTimes columnist Russell Baker wroteabout the difference between being“serious” and being “solemn,” observ-ing that “The transition from serious-ness to solemnity occurs inadolescence, a period in which nature,for reasons of her own, plunges peopleinto foolish frivolity. During thisperiod the organism struggles to regaindignity by recovering childhood’sgenius for seriousness. It is usually ahopeless cause.” The contrast betweenseriousness and solemnity can unfortu-

nately often be seen in introductoryscience courses, where serious subjectsare presented in solemn ways, theresult being that students who are notalready committed to science end upbeing bored by them, see them as meremathematical manipulations to be mas-tered, conclude that they lack “the sci-ence gene,” and vote with their feet.

In contrast, in the spirit of Heisen-berg, who once observed that there arethings that are so serious that one canonly joke about them, James Kakalioshas written The Physics ofSuperheroes, a book that tackles thetask of presenting to non-scientists thebasic ideas of physics – a serious sub-ject if ever there was one – in arefreshing way that lacks all solemnity.

The book grew out of a freshmanseminar entitled “All I Know AboutPhysics I Learned From the Comics,”

in which Kakalios, a physics professorat the University of Minnesota reachedback to his lifelong love of comicbooks, using the exploits of super-heroes to illustrate the application (or,in some misapplication) of the princi-ples of physics to such momentousquestions as:• Does the fact that Superman can leap

tall buildings at a single bound tell usanything about the gravity on Kryp-ton? (Newton’s first law)

• What really killed Spiderman’s girl-friend? (momentum)

• How much food does The Flash haveto eat in order to run so fast? (conser-vation of energy)

• How can Electro run up the side of asteel-frame building? (Faraday’slaws)

Book ReviewThe Physics of Superheroes, by James Kakalios (Gotham Press, 2004) 292 pp., ISBN 1-592-40146-5; $26.00 hardcover)Reviewed by Dennis J. SardellaDepartment of Chemistry, Merkert Chemistry Center, Boston College, Chestnut Hill, MA 02467

particular emphasis in endocrinology.We are in the midst of exploring thesechemical approaches in collaborationwith academic, biotechnology, andpharmaceutical company collaborators.◆◆

AbstractContinued from page 5

members. We pleaded, cajoled andbegged, to no avail. We apologize pro-fusely.

The tickets we have are right fieldgrandstand seats with a base price of$27 plus a $6 contribution to the edu-cation fund plus $2 for handling,postage and insurance for a total of$35 per ticket. I checked the internetfor ticket agency prices and discoveredthat they are charging $60-80 for thesame seats!!

To reserve your tickets (maximum4) until the supply is exhausted, pleasecontact Wally Gleekman at 617-527-1192 or gleekman(at)msn.com. Afteryou reserve your tickets you can mail acheck made out to the Brookline Edu-cators Association to Wally at 35Rangely Road, West Newton, MA02465-1218. ◆◆

Summerthing – SOXContinued from page 6

Continued on page 8


• Why can’t Superman change historyby traveling into the past and alteringevents? (quantum mechanics and themany-world interpretation)

Kakalios writes with a clear style,incorporating plenty of humor, as illus-trated both in the chapter headings(“Deconstructing Krypton,” “DoesSize Matter?,” “The Central City DietPlan. Conservation of Energy,”“Through A Wall Lightly. TunnelingPhenomena”), and in some of hisnumerous (but mostly serious) paren-thetical remarks. Using examples takenfrom comics (of which he clearly hasan encyclopedic knowledge) as ajumping-off point, he manages tocover all the basic topics in a physicssurvey course, including mechanics,thermodynamics relativity and quan-tum mechanics. Aiming at non-scien-tists, he eschews mathematics almostentirely, relying instead on verbalexposition and the use of imaginativeparallels that suggest he would be anenjoyable and effective classroominstructor.

In addition to principles ofphysics, The Physics of Superheroesconveys considerable informationabout the history and production ofcomic books. It also includes numer-ous illustrations from classic comics.Though it would have been more visu-ally appealing had they been repro-duced in color, I imagine this wouldhave increased the price of the bookconsiderably (though still keeping itfar below the near-astronomical cost ofthe average contemporary sciencetext).

I found no obvious mistakes andfew typos (though manganese wasaccidentally transmuted typographi-cally to magnesium at the top of page275). One point that did seem poten-tially confusing, though, was the dis-cussion of uncertainty, using as anexample a hypothetical attempt todetermine the frequency of a vibratingstring by touching it gently and feelingits vibrations (p. 239). “ … [O]nce wehave touched the string, it will nolonger be oscillating at the same fre-quency as before. It will either havestopped shaking altogether or bevibrating at a different frequency.”

Kakalios had already pointed out ear-lier that the frequency of a vibratingstring, like that of a pendulum,depends only on its length. Thus, if oneonly touched the string lightly enoughto feel it beating against one’s finger(as opposed to pressing it firmlyagainst a fret), one would logicallyexpect its amplitude to be changed, butnot its frequency (unless the touch cre-ates a node, thereby producing anovertone or two frequencies beatingagainst one another).

On p. 307, in his discussion ofadamantium, the defect-free “cova-lently-bonded metal,” composingWolverine’s claws, Kakalios writes,“In order to break these bonds, onemust remove the electrons from all ofthe bonds connecting an atom to all ofits neighbors.” To a chemist’s ear thissounds more like multiple ionizationthan bond cleavage, but is probablymore a matter of unfortunate phrasing.

One amusing point: Kakalios’ ownalter ego. The photo on the back fly-leaf of a smiling, benevolent teacher-author bursting with humor, contrastsstrongly to the rather stern photo of theresearcher in his University of Min-nesota website, evoking an echo of the“serious-solemn” distinction!

For the reader who gets bitten bythe physics bug after finishing ThePhysics of Superheroes and wants toscratch it, Kakalios includes plenty ofsuggestions for further reading in theback – mostly semi-popular books,biographies, histories, and occasionaltexts. This is still a good-sized jump(though not one of superhero dimen-sions), and, given people’s propensityfor brief reading, I would have likedhim to have included some articles ofthe Scientific American genre, thoughthis is at best a minor criticism.

Overall, Kakalios has done a greatjob of presenting the principles ofphysics to non-scientists in an effectiveand enjoyable way. By sensitizingthem to look for the basic principles ofphysics at work in the everyday worldof superheroes, Kakalios may succeedin getting them to apply a similarapproach to their own daily experi-ences, thus helping them develop into

Book ReviewContinued from page 7

Continued on page 9


IntroductionA considerable number of the mostpotent anticancer and antibiotic naturalproducts are produced by large, multi-functional proteins termed non-riboso-mal peptide synthetases (NRPSs) andpolyketide synthases (PKSs). Themodular structure of these megasyn-thases suggests great potential forcombinatorial manipulation of discreetmodules to generate “unnatural” prod-ucts using the existing enzymaticmachinery. Before this may beattempted, a thorough understanding ofthe structure and function of individualdomains must be obtained. In order tomeet this end, it is necessary to solvethe structure of NRPS/PKS domainsand gain a mechanistic understandingof how these domains perform chem-istry. Thus, the structure of LnmQ, anovel adenylation domain from theleinamycin biosynthetic pathway, willbe determined by X-ray crystallogra-phy, and its structure refined throughthe use of synthetic inhibitors.

Leinamycin is an antitumor,antibiotic compound containing anovel 1,2-dithiolan-3-one 1-oxide hete-

rocycle which has been shown to pro-mote oxidative damage of DNA aswell as alkylating DNA at the N7 posi-tion of guanine.1 Leinamycin is ahybrid polyketide/non-ribosomal pep-tide natural product: its biosyntheticmachinery of which contains severalunique features.2 One of the unusualaspects of the leinamycin syntheticmachinery is that there are three stand-alone enzyme domains not covalentlyembedded in the PKS/NRPS hybridmachinery. Two of these domains areLnmQ, an adenylation domain, andLnmP, the peptidyl carrier protein(PCP) domain associated with LnmQ.This unique system presents manyopportunities for studying NRPSmachinery. Also, the stand-alone natureof these domains seems conducive tomodular application of NRPSs tochemoenzymatic combinatorial synthe-sis of potentially bioactive compounds.

LnmQ is an adenylation domainwhich selectively adenylates D-alanineas opposed to the natural L isomer.The fact that LnmQ adenylates theunnatural D isomer of alanine isunique in NRPS systems. D-aminoacids are not rare in non-ribosomalpeptide natural products, but they areusually the result of epimerizationdomains associated with the NRPSmachinery. This is not the case withLnmQ, which is highly selective for D-alanine. LnmQ is also an isolatedadenylation domain, not followed byan NRPS condensation domain.Instead, the LnmQ/LnmP didomain isfollowed by two cyclization domains.3This unusual composition may repre-

sent a new paradigm of adenylationdomain function and chain elongationin NRPS systems. Following crystal-lization of LnmQ in its native form, theenzyme will be exposed to a specificsynthetic inhibitor in co-crystallizationexperiments to obtain a clear picture ofsubstrate recognition and catalysis.

Adenylation domains performchemistry homologous to the aminoa-cyl tRNA synthetases of ribosomalpeptide synthesis.4 Adenosine sul-famoyl amino acid derivatives havebeen used as inhibitors of theseenzymes and used in co-crystallizationexperiments to gain mechanisticinsights.5 Herein are reported the firstefforts towards the synthesis of a D-alanine sulfamoyl adenosine inhibitor(1) of LnmQ.Synthesis

The synthesis of the D-alanine sul-famoyl adenosine inhibitor begins withthe protection of adenosine as the2’,3’-dimethyl acetal (see Scheme 1).6A slurry of adenosine (2) in dry ace-tone is treated with excess amounts of2,2-dimethoxypropane, as well as p-toluenesulfonic acid (TsOH). Thisaffords 80% of the desired 1,2 ace-tonide-protected adenosine (3), withthe main byproduct being the 1,3 ace-tonide. Following purification by sil-ica gel flash chromatography, theacetonide-protected adenosine istreated with sodium hydride in 1,2-dimethoxyethane. The 5’ hydroxylgroup is deprotonated, resulting in theevolution of hydrogen gas, and theamine of the adenine base is transiently

Summer Research ScholarEfforts Towards the Structural Determination of LnmQ, a Novel Adenylation Domain William Hillmann and Steven D. Bruner Boston College, Department of Chemistry


the kind of scientifically literate citi-zens our technological society needs.His book could also be profitably readby someone with only a modest, or adimly-recalled, background in physics.

Personally, I thoroughly enjoyedreading The Physics of Superheroes,and I think I would have liked to be afly on the wall in Kakalios’ freshmanseminar. Unfortunately, being a merechemist of ordinary gifts, I have nei-ther the requisite size nor sufficientadhesiveness in my hands and feet toaccomplish this task. Maybe I shouldwander into the lab and wait for sometransformative mishap to occur …“ ◆◆

Book ReviewContinued from page 8


protected by the solvent. After stirringfor several hours, freshly prepared sul-famoyl chloride7 is coupled to the 5’hydroxyl in 65-80% yield to give 4.

Boc-D-alanine is then coupled tothe sulfamoyl moiety using a dicyclo-hexylcarbodiimide (DCC) couplingwith 1-hydroxybenzotriazole (HOBt)to activate the amino acid and preventracemization of the stereogenic center.This reaction proceeds with 60% yieldto give Boc-D-alanine 5’O-sulfamoyladenosine (5).

Following the formation of thepeptide bond, deprotection of the t-butyl carbamate and the acetonide pro-tecting groups should be accomplishedby treating the Boc-D-alanine 5’O-sul-

famoyl adenosine with acid. Severaldeprotection schemes were employed,using varying concentrations of trifluo-roacetic acid (TFA) and hydrochloricacid, which generally resulted indecomposition of the starting material.It was found that the glycosidic bondwas especially labile under the acidicconditions employed. Following manytrials, it was found that treating theBoc-D-alanine 5’O-sulfamoyl adeno-sine with 1 M HCl in 1:1 H2O/THFresulted in the formation of product (6),as seen by mass spectrographic analy-sis (ESI, m/z of 418.1 corresponds to[M+H]+). Purification of the crudeproduct has proved to be difficult,since the product is not amenable tosilica gel chromatography. Currently,preparatory HPLC is being investi-gated as a method of purification, and

should yield the pure D-alanine 5’ O-sulfamoyl adenosine inhibitor 6.

Another deprotection scheme, onewhich avoids the acidic deprotectionstep, would solve many of the prob-lems encountered with the synthesis.As such, another synthetic scheme wasattempted (see Scheme 2).

In this scheme, the 2’,3’-dimethylacetal protection is replaced by silicon-based bis-TBDMS protection of adeno-sine.8 This initial protection installsTBDMS groups on all three hydroxylsof adenosine to give 7. Followingselective deprotection of the 5’hydroxyl to give 8, the sulfamoyl cou-pling proceeds in the same manner aspreviously described to yield 9, as doesthe DCC coupling of D-alanine. How-ever, the amino acid protection hasbeen changed from a t-butyl carbamate

Scheme 1.

Scheme 2

Summer ScholarContinued from page 9


group to an 9-fluorenylmethyl carba-mate group (Fmoc), resulting in 10.Following this coupling, deprotectionof the TBDMS and the Fmoc protect-ing groups can be accomplished usingtetrabutylammonium fluoride (TBAF)to give the final D-alanine 5’ O-sul-famoyl adenosine inhibitor 6.9,10 IfTBAF does not remove the Fmocgroup, it can be removed with base andthen both TBDMS groups can beremoved with TBAF. This synthesishas been completed through the pep-tide coupling in the yields shown inScheme 2. Following deprotection,preparative reverse phase HPLC willbe used to purify the final product.Crystallography of LnmQ

Efforts were also made towardsthe crystallography of LnmQ. An E.coli expression vector (pET37b) con-taining the gene for LnmQ wasobtained from Professor Ben Shen (U.Wisconsin, Madison). This expressionvector contains an engineered hexa-histidine tag on the N-terminus of theprotein used to aid in purification ofthe protein. LnmQ was expressed inthe BL21(DE3) strain of E. coli,obtained by cell lysis, and purified bysuccessive chromatographic methods.

The first utilizes the hexa-histidinetag to bind to a nickel +2 resin. Thehistidines interact strongly with thenickel, allowing non tagged proteins tobe removed by washing. The enzymeof interest may then be eluted by wash-ing the resin with a buffer containing ahigh concentration of imidazole, whichreleases the hexa-histidine tag throughcompetitive binding. Following nickelresin purification, the protein is puri-fied, first using a strong anionexchange MonoQ column and finallyusing a gel filtration column. Thepurity of the enzyme is assessed bySDS-PAGE (see Figure 2A), and, fol-lowing concentration to 10 mg/mL, thepure enzyme can be used in crystallog-raphy screens.

Initial crystal hits for LnmQ canbe seen in Figure 2B. These crystalshave a needle-like morphology and areof a relatively low quality. Many dif-ferent conditions have been screenedto try to optimize the morphology,

including commercially available addi-tive screens; however, only needle-like,burst crystals are obtained. Further tri-als will be attempted, and it is hopedthat, upon obtaining the D-alanine 5’O-sulfamoyl inhibitor, it can be used asan additive to aid in obtaining crystalswith a good morphology. One of themajor challenges of macromolecularcrystallography is the disorder inherentin large molecules like enzymes. Byadding the inhibitor which will bind inthe active site, the structure of theenzyme will become more ordered andmore amenable to crystal formation.

Conclusions and Future DirectionsAdvances have been made

towards the synthesis of a D-alanine 5’O-sulfamoyl adenosine inhibitor of theNRPS adenylation domain LnmQusing two different synthetic schemes.Also, progress has been made towardsobtaining high quality crystals ofLnmQ, with hundreds of different con-ditions tested.

Future research entails the com-pletion of both syntheses of the LnmQinhibitor and the development of asuitable HPLC purification method.Following this, the inhibitor can be

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used as an additive in obtaining highquality crystals of LnmQ, as well as inco-crystallization screens once a nativeLnmQ structure is obtained. After thestructure of LnmQ is known, it can beused in co-crystallization experimentswith other enzymes in the LnmQbiosynthetic pathway such as LnmP.These studies may provide insightsinto how NRPS systems are organizedand how the different modular compo-nents interact to perform chemistry. References1. Gates, K.S. Chem. Res. Toxicol. 2000,

13, 953-56.2. Cheng, Y.Q., Tang, G.L., Shen, B. Proc.

Natl. Acad. Sci. 2003, 100, 3144-54.3. Tang, G. L., Cheng, Y. Q., and Shen, B.

Chem Biol. 2004, 11, 33-45.4. Stachelhaus, T., Mootz, H. D., and

Marahiel, M. A. Chem Biol. 1999, 6,493-505.

5. Ueda, H., Shoku, Y., Hayashi, N., Mit-sunaga, J., In, Y., Doi, M., Inoue, M.,and Ishida, T. Biochim Biophys Acta.1991, 1080, 126-34.

6. Moriguchi, T., Asai, N., Okada, K.,Seio, K., Sasaki, T., and Sekine, M. J.Org. Chem. 2002, 67, 3290-300.

7. Appel, R. and Berger, G. ChemischeBerichte Jahrg. 1958, 91, 1339-1341.

8. Ferreras, J.A., Ryu, J., Di Lello, F.,Tans, D.S., Quadri, L.E. Nature: Chemi-cal Biology. 2005, 1, 29-32.

9. Ueki, M., Amemiya, M. TetrahedronLett. 1987, 28, 6617-6620.

10.Corey, E.J., Venkateswarlu, A. J. Am.Chem. Soc. 1972, 94, 6190-6191. ◆◆

Summer ScholarContinued from page 11


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Check the NESACS Homepagefor late additions:http://www.NESACS.orgNote also the Chemistry Department webpages for travel directions and updates.These include:http://chemserv.bc.edu/seminar.htmlhttp://www.bu.edu/chemistry/events/http://www.chem.brandeis.edu/colloquium.shtmlhttp://www-chem.harvard.edu/events/http://web.mit.edu/chemistry/www.chem.neu.edu/web/calendar/index.htmlhttp://chem.tufts.edu/seminars.html [CHEM.]http://ase.tufts.edu/chemical/seminar.htm

[CHEM. ENGG.]http://www.chem.umb.edu/www.umassd.edu/cas/chemistry/seminars.cfmwww.uml.edu/Dept/Chemistry/speakers.htmlhttp://www.unh.edu/chemistry/seminars.html

April 3 F. Dean Toste, (Univ.of California Berkeley) ;John Hartwig (Yale Univ.) ; James Audia, (EliLilly & Co.)Eli Lilly Symposium.Harvard Univ. Mallinckrodt: Pfizer Lecture Hall,2:30 PM.Maurice Brookhart (Univ. of North Carolina)“Catalytic Transformations Based on C-H BondActivation Reactions”Brandeis Univ. Gerstenzang 122, 3:45PM.

April 3-4Michael A. Marletta (Univ. of California,Berkeley) TBAMIT, Rm TBA, 9:00AM

April 5Mahdi Abu-Omar (Purdue Univ.)TBAMIT Rm 6-120 4:00PMCatherine Fenselau (Univ. Maryland, CollegePark) “Rapid Detection of Airborne Microorganismsby Mass Spectrometry”Northeastern Univ. 129 Hurtig Hall. 12 Noon

April 6Klaus Schulten, (Univ. of Illinois Urbana-Champaign)“Towards Understanding Membrane Channels.” (Woodward Lecture Series)Harvard University, Mallinckrodt:Pfizer LectureHall, 5:00PM

April 10Melanie S. Sanford (Univ. of Michigan)“Synthetic Applications and MechanisticInvestigations Transition-Metal Catalyzed CHBond Functionalization.”(Woodward Lecture Series.)Harvard Univ.Mallinckrodt: Pfizer Lecture Hall,4:15PM.Anne Gershenson (Brandeis Univ.): “Investigating Molecular Mousetraps: SingleMolecule Studies of Protease-SerpinComplexes”MIT: 56-114, 4:30PM

April 11Krishna Kumar (Tufts Univ) “A New Paradigm for Protein Design andMolecular Engineering”MIT. Room .TBD. All DayMukund Sibi, Ph.D.(North Dakota State Univ.)TBA; Novartis Lecture Series, Part 4 Boston College. Merkert 130 4:00 PM

April 12Professor Jeffrey Zaleski (Indiana Univ.)TBAMIT: 6-120, 4:00 PMEric Anslyn (Univ. Texas, Austin)“Organic Chemistry Approaches to Single andMulti-Analyte Sensing”Northeastern Univ. 129 Hurtig Hall. 12 Noon

April 14Karl Weiss Symposium on Membrane andMembrane Systems.Northeastern Univ. Curry Student Ctr, McLeodSuites#318-322.9:40AM-1:50PM.

April 18James M. Cook (Univ. of Wisconsin,Milwaukee)“General Approach to the Synthesis of Ring-AAlkoxy Substituted Indole Alkaloids via theAsymmetric Pictet-Spengler Reaction”Brandeis Univ. Gerstenzang 122 3:45PM.Pamela Bjorkman (Cal Tech)“ The Molecular Basis of Iron Overload inHereditary Hemochromatosis” Univ. of New Hampshire, Iddles Auditorium,Room L101, 11AM Pamela Bjorkman (Cal Tech)“What We can Learn from 3D Structures ofProteins” Univ. of New Hampshire Iddles Auditorium,Room L101,4 PM

April 19-20Jackie Barton (California Institute ofTechnology)TBA; Arthur D. Little Lecture in InorganicChemistry. MIT, Rm: TBA, 4:00PM

April 24Philip Baran, (The Scripps Research Institute);Erik Sorensen (Princeton Univ.)Pfizer Symposium.Harvard. Mallinckrodt Pfizer Lecture Hall 2:30PM.Dr. Gerhard Hummer (NIH)“Water, Proton, and Ion Transport: FromNanotubes to Biomolecular Machines”Brandeis Univ. Gerstenzang 122 Time: 3:45 PM.

April 25Alanna Schepartz (Yale Univ.)“Miniature and Non-Natural Proteins?”MIT: 56-114, 4:00PM

April 26John P Fackler (Texas A&M Univ.)TBAMIT. Location: TBA, 4:00PM

April 27David Chandler, (Univ. of California, Berkeley)TBA; G. B. Kistiakowsky Lecture, Harvard Mallinckrodt: Pfizer Lecture Hall, ,8:00PM.

April 27-28Fred Wudl (Univ. of California Los Angeles)TBAMIT, Rm 6-120, 4:00PM

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