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Publications

A cross-reactive human IgA monoclonal antibody blocks SARS-CoV-2 spike-ACE2 interaction.
Ejemel M, Li Q, Hou S, Schiller ZA, Tree JA, Wallace A, Amcheslavsky A, Kurt Yilmaz N, Buttigieg KR, Elmore MJ, Godwin K, Coombes N, Toomey JR, Schneider R, Ramchetty AS, Close BJ, Chen DY, Conway HL, Saeed M, Ganesa C, Carroll MW, Cavacini LA, Klempner MS, Schiffer CA, Wang Y.
Nat Commun. 2020 Aug 21;11(1):4198. doi: 10.1038/s41467-020-18058-8. 
 
Structural Analysis of Potent Hybrid HIV-1 Protease Inhibitors Containing Bis-tetrahydrofuran in a Pseudosymmetric Dipeptide Isostere.
Rusere LN, Lockbaum GJ, Henes M, Lee SK, Spielvogel E, Rao DN, Kosovrasti K, Nalivaika EA, Swanstrom R, Kurt Yilmaz N, Schiffer CA, Ali A.
J Med Chem. 2020 Aug 13;63(15):8296-8313. doi: 10.1021/acs.jmedchem.0c00529. Epub 2020 Aug 3.

Avoiding Drug Resistance by Substrate Envelope-Guided Design: Toward Potent and Robust HCV NS3/4A Protease Inhibitors.
Matthew AN, Zephyr J, Nageswara Rao D, Henes M, Kamran W, Kosovrasti K, Hedger AK, Lockbaum GJ, Timm J, Ali A, Kurt Yilmaz N, Schiffer CA.
mBio. 2020 Mar 31;11(2). pii: e00172-20. doi: 10.1128/mBio.00172-20.

Optimizing the refinement of merohedrally twinned P61 HIV-1 protease-inhibitor cocrystal structures.
Lockbaum GJ, Leidner F, Royer WE, Kurt Yilmaz N, Schiffer CA.
Acta Crystallogr D Struct Biol. 2020 Mar 1;76(Pt 3):302-310. doi: 10.1107/S2059798320001989. Epub 2020 Mar 2.

Molecular and structural mechanism of pan-genotypic HCV NS3/4A protease inhibition by glecaprevir.
Timm J, Kosovrasti K, Henes M, Leidner F, Hou S, Ali A, Kurt Yilmaz N, Schiffer CA.
ACS Chem Biol. 2019 Dec 23. doi: 10.1021/acschembio.9b00675. [Epub ahead of print]

Picomolar to Micromolar: Elucidating the Role of Distal Mutations in HIV-1 Protease in Conferring Drug Resistance.
Henes M, Lockbaum GJ, Kosovrasti K, Leidner F, Nachum GS, Nalivaika EA, Lee SK, Spielvogel E, Zhou S, Swanstrom R, Bolon DNA, Kurt Yilmaz N, Schiffer CA.
ACS Chem Biol. 2019 Nov 15;14(11):2441-2452. doi: 10.1021/acschembio.9b00370. Epub 2019 Aug 13.

Target-Specific Prediction of Ligand Affinity with Structure-Based Interaction Fingerprints.
Leidner F, Kurt Yilmaz N, Schiffer CA.
J Chem Inf Model. 2019 Sep 23. doi: 10.1021/acs.jcim.9b00457.

Molecular Determinants of Epistasis in HIV-1 Protease: Elucidating the Interdependence of L89V and L90M Mutations in Resistance.
Henes M, Kosovrasti K, Lockbaum GJ, Leidner F, Nachum GS, Nalivaika EA, Bolon DNA, Kurt YilmazN, Schiffer CA, Whitfield TW.
Biochemistry. 2019 Sep 3;58(35):3711-3726. doi: 10.1021/acs.biochem.9b00446. Epub 2019 Aug 19.

Mechanism for APOBEC3G catalytic exclusion of RNA and non-substrate DNA.
Solomon WC, Myint W, Hou S, Kanai T, Tripathi R, Kurt Yilmaz N, Schiffer CA, Matsuo H.
Nucleic Acids Res. 2019 Aug 22;47(14):7676-7689. doi: 10.1093/nar/gkz550.

NMR and MD studies combined to elucidate inhibitor and water interactions of HIV-1 protease and their modulations with resistance mutations.
Ishima R, Kurt Yilmaz N, Schiffer CA.
J Biomol NMR. 2019 Jun 26. doi: 10.1007/s10858-019-00260-6. [Epub ahead of print]

Structural analysis of the active site and DNA binding of human cytidine deaminase APOBEC3B.
Hou S, Silvas T, Leidner F, Nalivaika EA, Matsuo H, Kurt Yilmaz N, Schiffer CA.
J Chem Theory Comput. 2019 Jan 8;15(1):637-647. doi: 10.1021/acs.jctc.8b00545. Epub 2018 Dec 11.

Mutations in influenza A virus neuraminidase and hemagglutinin confer resistance against a broadly neutralizing hemagglutinin stem antibody.
Prachanronarong KL, Canale AS, Liu P, Somasundaran M, Hou S, Poh YP, Han T, Zhu Q, Renzette N, Zeldovich KB, Kowalik TF2, Kurt-Yilmaz N2, Jensen JD4, Bolon DNA2, Marasco WA3, Finberg RW2, Schiffer CA2, Wang JP1.
J Virol. 2019 Jan 4;93(2). pii: e01639-18. doi: 10.1128/JVI.01639-18. Print 2019 Jan 15.

Structural Adaptation of Darunavir Analogs Against Primary Mutations in HIV-1 Protease.
Lockbaum GJ, Leidner F, Rusere LN, Henes M, Kosovrasti K, Nachum GS, Nalivaika EA, Ali A, Kurt Yilmaz N, Schiffer CA.
ACS Infect Dis. 2018 Dec 13. doi: 10.1021/acsinfecdis.8b00336. [Epub ahead of print]

HIV-1 Protease Uses Bi-Specific S2/S2' Subsites to Optimize Cleavage of Two Classes of Target Sites.
Potempa M, Lee SK, Kurt Yilmaz N, Nalivaika EA, Rogers A, Spielvogel E, Carter CW Jr, Schiffer CA, Swanstrom R.
J Mol Biol. 2018 Dec 7;430(24):5182-5195. doi: 10.1016/j.jmb.2018.10.022. Epub 2018 Nov 7.

Molecular Mechanism of Resistance in a Clinically Significant Double-Mutant Variant of HCV NS3/4A Protease.
Matthew AN, Leidner F, Newton A, Petropoulos CJ, Huang W, Ali A, KurtYilmaz N, Schiffer CA.
Structure. 2018 Aug 07. PMID: 30146168. 

T cell epitope engineering: an avian H7N9 influenza vaccine strategy for pandemic preparedness and response.
Moise L, Girard B, Boyle C, Kurt Yilmaz N, Jang H, Schiffer C, Ross T, Martin WD, De Groot AS.
Hum Vaccin Immunother. 2018 Jul 17. PMID: 30015562.

Quinoxaline-Based Linear HCV NS3/4A Protease Inhibitors Exhibit Potent Activity against Drug Resistant Variants.
Rusere LN, Matthew AN, Lockbaum GJ, Jahangir M, Newton A, Petropoulos CJ, Huang W, Kurt Yilmaz N, Schiffer CA, Ali A.  
ACS Med Chem Lett. 2018 Jul 12; 9(7):691-696. PMID: 30034602.

Substrate sequence selectivity of APOBEC3A implicates intra-DNA interactions.
Silvas TV, Hou S, Myint W, Nalivaika E, Somasundaran M, Kelch BA, Matsuo H, Kurt Yilmaz N, Schiffer CA.  
Sci Rep. 2018 May 14; 8(1):7511. PMID: 29760455.

Hydration Structure and Dynamics of Inhibitor-Bound HIV-1 Protease.
Leidner F, Kurt Yilmaz N, Paulsen J, Muller YA, Schiffer CA.  
J Chem Theory Comput. 2018 May 08; 14(5):2784-2796. PMID: 29570286.

Probing Structural Changes among Analogous Inhibitor-Bound Forms of HIV-1 Protease and a Drug-Resistant Mutant in Solution by Nuclear Magnetic Resonance.
Khan SN, Persons JD, Paulsen JL, Guerrero M, Schiffer CA, Kurt-Yilmaz N, Ishima R.  
Biochemistry. 2018 03 13; 57(10):1652-1662. PMID: 29457713.

Structural Determination of the Broadly Reactive Anti-IGHV1-69 Anti-idiotypic Antibody G6 and Its Idiotope.
Avnir Y, Prachanronarong KL, Zhang Z, Hou S, Peterson EC, Sui J, Zayed H, Kurella VB, McGuire AT, Stamatatos L, Hilbert BJ, Bohn MF, Kowalik TF, Jensen JD, Finberg RW, Wang JP, Goodall M, Jefferis R, Zhu Q, Kurt Yilmaz N, Schiffer CA, Marasco WA.  
Cell Rep. 2017 Dec 12; 21(11):3243-3255. PMID: 29241550.

Elucidating the Interdependence of Drug Resistance from Combinations of Mutations.
Ragland DA, Whitfield TW, Lee SK, Swanstrom R, Zeldovich KB, Kurt-Yilmaz N, Schiffer CA.  
J Chem Theory Comput. 2017 Oct 09. PMID: 28915040.

Hepatitis C Virus NS3/4A Protease Inhibitors Incorporating Flexible P2 Quinoxalines Target Drug Resistant Viral Variants.
Matthew AN, Zephyr J, Hill CJ, Jahangir M, Newton A, Petropoulos CJ, Huang W, Kurt Yilmaz N, Schiffer CA, Ali A.  
J Med Chem. 2017 Jun 08. PMID: 28594175.

Crystal structure of APOBEC3A bound to single-stranded DNA reveals structural basis for cytidine deamination and specificity.
Kouno T, Silvas TV, Hilbert BJ, Shandilya SMD, Bohn MF, Kelch BA, Royer WE, Somasundaran M, Kurt Yilmaz N, Matsuo H, Schiffer CA.  
Nat Commun. 2017 Apr 28; 8:15024. PMID: 28452355.

Interdependence of Inhibitor Recognition in HIV-1 Protease.
Paulsen JL, Leidner F, Ragland DA, Kurt Yilmaz N, Schiffer CA.  
J Chem Theory Comput. 2017 Mar 30. PMID: 28358514.

Dengue Virus NS2B/NS3 Protease Inhibitors Exploiting the Prime Side.
Lin KH, Ali A, Rusere L, Soumana DI, Yilmaz NK, Schiffer CA.  
J Virol. 2017 Mar 15. PMID: 28298600.

"Drug Resistance to HIV-1 Protease Inhibitors: Molecular Mechanisms and Substrate Coevolution" in Antimicrobial Drug Resistance - Mechanisms of Drug Resistance, Volume 1
Kurt Yilmaz, N.; Schiffer, C.A., (Douglas Mayers, Ed)
Springer Nature, pp. 535-544 (2017).

Molecular Basis for Differential Patterns of Drug Resistance in Influenza N1 and N2 Neuraminidase.
Prachanronarong KL, Özen A, Thayer KM, Yilmaz LS, Zeldovich KB, Bolon DN, Kowalik TF, Jensen JD, Finberg RW, Wang JP, Kurt-Yilmaz N, Schiffer CA.  
J Chem Theory Comput. 2016 Dec 13; 12(12):6098-6108. PMID: 27951676.

Structural and molecular analysis of a protective epitope of Lyme disease antigen OspA and antibody interactions.
Shandilya S, Kurt Yilmaz N, Sadowski A, Monir E, Schiller ZA, Thomas WD, Klempner MS, Schiffer CA, Wang Y.  
J Mol Recognit. 2016 Nov 16. PMID: 27859766.

Dengue Protease Substrate Recognition: Binding of the Prime Side.
Lin KH, Nalivaika EA, Prachanronarong KL, Yilmaz NK, Schiffer CA.  
ACS Infect Dis. 2016 Oct 14; 2(10):734-743. PMID: 27657335.

Molecular and Dynamic Mechanism Underlying Drug Resistance in Genotype 3 Hepatitis C NS3/4A Protease.
Soumana DI, Kurt Yilmaz N, Ali A, Prachanronarong KL, Schiffer CA.  
J Am Chem Soc. 2016 Sep 14; 138(36):11850-9. PMID: 27512818.

Improving Viral Protease Inhibitors to Counter Drug Resistance.
Kurt Yilmaz N, Swanstrom R, Schiffer CA.  
Trends Microbiol. 2016 Jul; 24(7):547-57. PMID: 27090931.

Structural and Thermodynamic Effects of Macrocyclization in HCV NS3/4A Inhibitor MK-5172.
Soumana DI, Kurt Yilmaz N, Prachanronarong KL, Aydin C, Ali A, Schiffer CA.  
ACS Chem Biol. 2016 Apr 15; 11(4):900-9. PMID: 26682473.

The ssDNA Mutator APOBEC3A Is Regulated by Cooperative Dimerization.
Bohn MF, Shandilya SM, Silvas TV, Nalivaika EA, Kouno T, Kelch BA, Ryder SP, Kurt-Yilmaz N, Somasundaran M, Schiffer CA.  
Structure. 2015 May 5; 23(5):903-11. PMID: 25914058.

Structural basis and distal effects of Gag substrate coevolution in drug resistance to HIV-1 protease.
Özen A, Lin KH, Kurt Yilmaz N, Schiffer CA.  
Proc Natl Acad Sci U S A. 2014 Nov 11; 111(45):15993-8. PMID: 25355911.

Drug resistance conferred by mutations outside the active site through alterations in the dynamic and structural ensemble of HIV-1 protease.
Ragland DA, Nalivaika EA, Nalam MN, Prachanronarong KL, Cao H, Bandaranayake RM, Cai Y, Kurt-Yilmaz N, Schiffer CA.  
J Am Chem Soc. 2014 Aug 27; 136(34):11956-63. PMID: 25091085.

Drug Resistance Mutations Alter Dynamics of Inhibitor-Bound HIV-1 Protease.
Cai Y, Myint W, Paulsen JL, Schiffer CA, Ishima R, Kurt Yilmaz N.  
J Chem Theory Comput. 2014 Aug 12; 10(8):3438-3448. PMID: 25136270.

Burial of nonpolar surface area and thermodynamic stabilization of globins as a function of chain elongation.
Jennaro TS, Beaty MR, Kurt-Yilmaz N, Luskin BL, Cavagnero S.  
Proteins. 2014 Oct; 82(10):2318-31. PMID: 24752983.

HIV-1 protease-substrate coevolution in nelfinavir resistance.
Kolli M, Ozen A, Kurt-Yilmaz N, Schiffer CA.  
J Virol. 2014 Jul; 88(13):7145-54. PMID: 24719428.

Substrate envelope-designed potent HIV-1 protease inhibitors to avoid drug resistance.
Nalam MN, Ali A, Reddy GS, Cao H, Anjum SG, Altman MD, Yilmaz NK, Tidor B, Rana TM, Schiffer CA.  
Chem Biol. 2013 Sep 19; 20(9):1116-24. PMID: 24012370.

Sub-millisecond chain collapse of the Escherichia coli globin ApoHmpH.
Zhu L, Kurt N, Choi J, Lapidus LJ, Cavagnero S.  
J Phys Chem B. 2013 Jul 3; 117(26):7868-77. PMID: 23750553.

Electrostatic effect of the ribosomal surface on nascent polypeptide dynamics.
Knight AM, Culviner PH, Kurt-Yilmaz N, Zou T, Ozkan SB, Cavagnero S.  
ACS Chem Biol. 2013; 8(6):1195-204. PMID: 23517476.

Structural and thermodynamic basis of amprenavir/darunavir and atazanavir resistance in HIV-1 protease with mutations at residue 50.
Mittal S, Bandaranayake RM, King NM, Prabu-Jeyabalan M, Nalam MN, Nalivaika EA, Yilmaz NK, Schiffer CA.  
J Virol. 2013 Apr; 87(8):4176-84. PMID: 23365446.

Cooperative effects of drug-resistance mutations in the flap region of HIV-1 protease.
Foulkes-Murzycki JE, Rosi C, Kurt Yilmaz N, Shafer RW, Schiffer CA.  
ACS Chem Biol. 2013 Mar 15; 8(3):513-8. PMID: 23252515.

Extreme entropy-enthalpy compensation in a drug-resistant variant of HIV-1 protease.
King NM, Prabu-Jeyabalan M, Bandaranayake RM, Nalam MN, Nalivaika EA, Özen A, Haliloglu T, Yilmaz NK, Schiffer CA.  
ACS Chem Biol. 2012 Sep 21; 7(9):1536-46. PMID: 22712830.

Differential Flap Dynamics in Wild-type and a Drug Resistant Variant of HIV-1 Protease Revealed by Molecular Dynamics and NMR Relaxation.
Cai Y, Yilmaz NK, Myint W, Ishima R, Schiffer CA.  
J Chem Theory Comput. 2012 Oct 9; 8(10):3452-3462. PMID: 23144597.

High-resolution conformation and backbone dynamics of a soluble aggregate of apomyoglobin119.
Rajagopalan S, Kurt N, Cavagnero S.  
Biophys J. 2011 Feb 2; 100(3):747-55. PMID: 21281590.

Nonrandom distribution of intramolecular contacts in native single-domain proteins.
Mounce BC, Kurt N, Ellison PA, Cavagnero S.  
Proteins. 2009 May 1; 75(2):404-12. PMID: 18831044.

Residue-specific contact order and contact breadth in single-domain proteins: implications for folding as a function of chain elongation.
Kurt N, Mounce BC, Ellison PA, Cavagnero S.  
Biotechnol Prog. 2008 May-Jun; 24(3):570-5. PMID: 18471028.

Nonnative helical motif in a chaperone-bound protein fragment.
Kurt N, Cavagnero S.  
Biophys J. 2008 Apr 01; 94(7):L48-50. PMID: 18192369.

Thermodynamic and kinetic characterization of apoHmpH, a fast-folding bacterial globin.
Eun YJ, Kurt N, Sekhar A, Cavagnero S.  
J Mol Biol. 2008 Feb 22; 376(3):879-97. PMID: 18187151.

Binding specificity of an alpha-helical protein sequence to a full-length Hsp70 chaperone and its minimal substrate-binding domain.
Vega CA, Kurt N, Chen Z, Rüdiger S, Cavagnero S.  
Biochemistry. 2006 Nov 21; 45(46):13835-46. PMID: 17105202.

Secondary structure mapping of DnaK-bound protein fragments: chain helicity and local helix unwinding at the binding site.
Chen Z, Kurt N, Rajagopalan S, Cavagnero S.  
Biochemistry. 2006 Oct 10; 45(40):12325-33. PMID: 17014085.

"Folding and Misfolding as a Function of Polypeptide Chain Elongation: Conformational Trends and Implications for Intracellular Events" in Misbehaving Proteins: Protein (Mis)Folding, Aggregation and Stability.
Cavagnero, S.; Kurt, N. (Regina M. Murphy and Amos M. Tsai, Eds)
Springer, pp. 217-246 (2006).

The burial of solvent-accessible surface area is a predictor of polypeptide folding and misfolding as a function of chain elongation.
Kurt N, Cavagnero S.  
J Am Chem Soc. 2005 Nov 16; 127(45):15690-1. PMID: 16277496.

Effect of hsp70 chaperone on the folding and misfolding of polypeptides modeling an elongating protein chain.
Kurt N, Rajagopalan S, Cavagnero S.  
J Mol Biol. 2006 Jan 27; 355(4):809-20. PMID: 16309705.

Structural characterization of apomyoglobin self-associated species in aqueous buffer and urea solution.
Chow C, Kurt N, Murphy RM, Cavagnero S.
Biophys J. 2006 Jan 1; 90(1):298-309. PMID: 16214860.

Structure-based prediction of potential binding and nonbinding peptides to HIV-1 protease.
Kurt N, Haliloglu T, Schiffer CA.  
Biophys J. 2003 Aug; 85(2):853-63. PMID: 12885633.

Cooperative fluctuations of unliganded and substrate-bound HIV-1 protease: a structure-based analysis on a variety of conformations from crystallography and molecular dynamics simulations.
Kurt N, Scott WR, Schiffer CA, Haliloglu T.  
Proteins. 2003 May 15; 51(3):409-22. PMID: 12696052.

Distribution of cooperative interactions in barnase at different time windows by coarse-grained simulations.
Kurt, N.; Haliloglu, T.  
Polymer. 2002; 43(2):403-408.

Conformational dynamics of subtilisin-chymotrypsin inhibitor 2 complex by coarse-grained simulations.
Kurt N, Haliloglu T.  
J Biomol Struct Dyn. 2001 Apr; 18(5):713-31. PMID: 11334109.

Conformational dynamics of chymotrypsin inhibitor 2 by coarse-grained simulations.
Kurt N, Haliloglu T.  
Proteins. 1999 Nov 15; 37(3):454-64. PMID: 10591104.