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Nese Kurt Yilmaz PhD

TitleAssociate Professor
InstitutionUMass Chan Medical School
DepartmentBiochemistry and Molecular Biotechnology
AddressUMass Chan Medical School
364 Plantation Street LRB
Worcester MA 01605
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    Other Positions
    InstitutionT.H. Chan School of Medicine
    DepartmentBiochemistry and Molecular Biotechnology

    InstitutionMorningside Graduate School of Biomedical Sciences
    DepartmentBiochemistry and Molecular Pharmacology


    Collapse Biography 
    Collapse education and training
    Bogazici University, Istanbul, , TurkeyBSChemical Engineering
    Bogazici University, Istanbul, , TurkeyMSChemical engineering
    Bogazici University, Istanbul, , TurkeyPHDChemical Engineering

    Collapse Overview 
    Collapse overview

    Academic Background

    Ph.D., Chemical Engineering, Bogazici University, Istanbul, Turkey, 2002

    Postdoc,  Department of Chemistry, University of Wisconsin-Madison, 2005

     

    Research Experience

    Associate Professor                                                                                    2017–present

    UMASS Medical School, Worcester, MA
    Department of Biochemistry and Molecular Pharmacology

     

    Research Assistant Professor                                                                    2011–2017

    UMASS Medical School, Worcester, MA
    Department of Biochemistry and Molecular Pharmacology

    ·     Drug resistance in viral proteases: Understanding the molecular basis of drug resistance in viral proteases, including HIV-1 and HCV protease.

    ·     Substrate recognition and product inhibition in HIV-1 protease.

    ·     Scientific writing and editing.

     

    Assistant Scientist                                                                                        2005–2011

    University of Wisconsin-Madison, Department of Chemistry

    ·     Protein folding and effect of chaperone interaction on misfolding polypeptides: Investigated protein folding, unfolding and misfolding under various experimental conditions, and the interaction of chaperones with truncated polypeptide chains by biochemical/biophysical methods incuding fluorescence and NMR techniques.

     

    Visiting TUBITAK fellow                                                                              2000 and 2001

    UMASS Medical School, Worcester, MA
    Department of Biochemistry and Molecular Pharmacology

    ·     Substrate specificity and simulation of conformational dynamics of HIV-1 protease.

     

    Graduate Researcher at the Polymer Research Center                                   1996–2002                 

    Bogazici University, Istanbul, Turkey

    ·     Coarse-grained simulations and analytical methods to study dynamics of globular proteins in native state.

     

     



    Collapse Bibliographic 
    Collapse selected publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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    PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Shaqra AM, Zvornicanin SN, Huang QYJ, Lockbaum GJ, Knapp M, Tandeske L, Bakan DT, Flynn J, Bolon DNA, Moquin S, Dovala D, Kurt Yilmaz N, Schiffer CA. Defining the substrate envelope of SARS-CoV-2 main protease to predict and avoid drug resistance. Nat Commun. 2022 06 21; 13(1):3556. PMID: 35729165.
      Citations: 2     Fields:    Translation:HumansCellsPHPublic Health
    2. Zephyr J, Nageswara Rao D, Vo SV, Henes M, Kosovrasti K, Matthew AN, Hedger AK, Timm J, Chan ET, Ali A, Kurt Yilmaz N, Schiffer CA. Deciphering the Molecular Mechanism of HCV Protease Inhibitor Fluorination as a General Approach to Avoid Drug Resistance. J Mol Biol. 2022 05 15; 434(9):167503. PMID: 35183560.
      Citations:    Fields:    Translation:HumansCells
    3. Zephyr J, Kurt Yilmaz N, Schiffer CA. Viral proteases: Structure, mechanism and inhibition. Enzymes. 2021; 50:301-333. PMID: 34861941.
      Citations: 2     Fields:    Translation:HumansCells
    4. Lockbaum GJ, Henes M, Lee JM, Timm J, Nalivaika EA, Thompson PR, Kurt Yilmaz N, Schiffer CA. Pan-3C Protease Inhibitor Rupintrivir Binds SARS-CoV-2 Main Protease in a Unique Binding Mode. Biochemistry. 2021 10 05; 60(39):2925-2931. PMID: 34506130.
      Citations: 2     Fields:    Translation:Cells
    5. Nageswara Rao D, Zephyr J, Henes M, Chan ET, Matthew AN, Hedger AK, Conway HL, Saeed M, Newton A, Petropoulos CJ, Huang W, Kurt Yilmaz N, Schiffer CA, Ali A. Discovery of Quinoxaline-Based P1-P3 Macrocyclic NS3/4A Protease Inhibitors with Potent Activity against Drug-Resistant Hepatitis C Virus Variants. J Med Chem. 2021 08 26; 64(16):11972-11989. PMID: 34405680.
      Citations: 3     Fields:    Translation:AnimalsCells
    6. Hou S, Lee JM, Myint W, Matsuo H, Kurt Yilmaz N, Schiffer CA. Structural basis of substrate specificity in human cytidine deaminase family APOBEC3s. J Biol Chem. 2021 08; 297(2):100909. PMID: 34171358.
      Citations: 1     Fields:    Translation:HumansCells
    7. Leidner F, Kurt Yilmaz N, Schiffer CA. Deciphering Antifungal Drug Resistance in Pneumocystis jirovecii DHFR with Molecular Dynamics and Machine Learning. J Chem Inf Model. 2021 06 28; 61(6):2537-2541. PMID: 34138546.
      Citations:    Fields:    Translation:AnimalsCells
    8. Leidner F, Kurt Yilmaz N, Schiffer CA. Deciphering Complex Mechanisms of Resistance and Loss of Potency through Coupled Molecular Dynamics and Machine Learning. J Chem Theory Comput. 2021 Apr 13; 17(4):2054-2064. PMID: 33783217.
      Citations: 3     Fields:    Translation:Cells
    9. Kurt Yilmaz N, Schiffer CA. Introduction: Drug Resistance. Chem Rev. 2021 03 24; 121(6):3235-3237. PMID: 33757288.
      Citations: 4     Fields:    Translation:HumansCells
    10. Lockbaum GJ, Henes M, Talledge N, Rusere LN, Kosovrasti K, Nalivaika EA, Somasundaran M, Ali A, Mansky LM, Kurt Yilmaz N, Schiffer CA. Inhibiting HTLV-1 Protease: A Viable Antiviral Target. ACS Chem Biol. 2021 03 19; 16(3):529-538. PMID: 33619959.
      Citations: 4     Fields:    Translation:HumansCells
    11. Lockbaum GJ, Reyes AC, Lee JM, Tilvawala R, Nalivaika EA, Ali A, Kurt Yilmaz N, Thompson PR, Schiffer CA. Crystal Structure of SARS-CoV-2 Main Protease in Complex with the Non-Covalent Inhibitor ML188. Viruses. 2021 01 25; 13(2). PMID: 33503819.
      Citations: 22     Fields:    Translation:Cells
    12. Matthew AN, Leidner F, Lockbaum GJ, Henes M, Zephyr J, Hou S, Rao DN, Timm J, Rusere LN, Ragland DA, Paulsen JL, Prachanronarong K, Soumana DI, Nalivaika EA, Kurt Yilmaz N, Ali A, Schiffer CA. Drug Design Strategies to Avoid Resistance in Direct-Acting Antivirals and Beyond. Chem Rev. 2021 03 24; 121(6):3238-3270. PMID: 33410674.
      Citations: 6     Fields:    Translation:HumansCells
    13. Maiti A, Myint W, Delviks-Frankenberry KA, Hou S, Kanai T, Balachandran V, Sierra Rodriguez C, Tripathi R, Kurt Yilmaz N, Pathak VK, Schiffer CA, Matsuo H. Crystal Structure of a Soluble APOBEC3G Variant Suggests ssDNA to Bind in a Channel that Extends between the Two Domains. J Mol Biol. 2020 11 20; 432(23):6042-6060. PMID: 33098858.
      Citations: 3     Fields:    Translation:HumansAnimalsCells
    14. 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. A cross-reactive human IgA monoclonal antibody blocks SARS-CoV-2 spike-ACE2 interaction. Nat Commun. 2020 08 21; 11(1):4198. PMID: 32826914.
      Citations: 55     Fields:    Translation:HumansAnimalsCells
    15. 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. Structural Analysis of Potent Hybrid HIV-1 Protease Inhibitors Containing Bis-tetrahydrofuran in a Pseudosymmetric Dipeptide Isostere. J Med Chem. 2020 08 13; 63(15):8296-8313. PMID: 32672965.
      Citations: 1     Fields:    Translation:HumansCells
    16. 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. Avoiding Drug Resistance by Substrate Envelope-Guided Design: Toward Potent and Robust HCV NS3/4A Protease Inhibitors. mBio. 2020 03 31; 11(2). PMID: 32234812.
      Citations: 7     Fields:    Translation:HumansCells
    17. Lockbaum GJ, Leidner F, Royer WE, Kurt Yilmaz N, Schiffer CA. Optimizing the refinement of merohedrally twinned P61 HIV-1 protease-inhibitor cocrystal structures. Acta Crystallogr D Struct Biol. 2020 Mar 01; 76(Pt 3):302-310. PMID: 32133994.
      Citations:    
    18. Timm J, Kosovrasti K, Henes M, Leidner F, Hou S, Ali A, Kurt Yilmaz N, Schiffer CA. Molecular and Structural Mechanism of Pan-Genotypic HCV NS3/4A Protease Inhibition by Glecaprevir. ACS Chem Biol. 2020 02 21; 15(2):342-352. PMID: 31868341.
      Citations: 4     Fields:    Translation:Cells
    19. Solomon WC, Myint W, Hou S, Kanai T, Tripathi R, Kurt Yilmaz N, Schiffer CA, Matsuo H. Mechanism for APOBEC3G catalytic exclusion of RNA and non-substrate DNA. Nucleic Acids Res. 2019 08 22; 47(14):7676-7689. PMID: 31424549.
      Citations: 1     Fields:    Translation:HumansCells
    20. Henes M, Kosovrasti K, Lockbaum GJ, Leidner F, Nachum GS, Nalivaika EA, Bolon DNA, Kurt Yilmaz N, Schiffer CA, Whitfield TW. Molecular Determinants of Epistasis in HIV-1 Protease: Elucidating the Interdependence of L89V and L90M Mutations in Resistance. Biochemistry. 2019 09 03; 58(35):3711-3726. PMID: 31386353.
      Citations: 7     Fields:    Translation:HumansCells
    21. Leidner F, Kurt Yilmaz N, Schiffer CA. Target-Specific Prediction of Ligand Affinity with Structure-Based Interaction Fingerprints. J Chem Inf Model. 2019 09 23; 59(9):3679-3691. PMID: 31381335.
      Citations: 7     Fields:    Translation:HumansCells
    22. 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. Picomolar to Micromolar: Elucidating the Role of Distal Mutations in HIV-1 Protease in Conferring Drug Resistance. ACS Chem Biol. 2019 11 15; 14(11):2441-2452. PMID: 31361460.
      Citations: 13     Fields:    Translation:HumansCells
    23. Ishima R, Kurt Yilmaz N, Schiffer CA. NMR and MD studies combined to elucidate inhibitor and water interactions of HIV-1 protease and their modulations with resistance mutations. J Biomol NMR. 2019 Jul; 73(6-7):365-374. PMID: 31243634.
      Citations: 4     Fields:    Translation:HumansCells
    24. Lockbaum GJ, Leidner F, Rusere LN, Henes M, Kosovrasti K, Nachum GS, Nalivaika EA, Bolon DNA, Ali A, Kurt Yilmaz N, Schiffer CA. Correction to Structural Adaptation of Darunavir Analogues against Primary Mutations in HIV-1 Protease. ACS Infect Dis. 2019 Jun 14; 5(6):1044. PMID: 30990653.
      Citations:    Fields:    
    25. Hou S, Silvas TV, Leidner F, Nalivaika EA, Matsuo H, Kurt Yilmaz N, Schiffer CA. Structural Analysis of the Active Site and DNA Binding of Human Cytidine Deaminase APOBEC3B. J Chem Theory Comput. 2019 Jan 08; 15(1):637-647. PMID: 30457868.
      Citations: 9     Fields:    Translation:HumansCells
    26. Potempa M, Lee SK, Kurt Yilmaz N, Nalivaika EA, Rogers A, Spielvogel E, Carter CW, Schiffer CA, Swanstrom R. HIV-1 Protease Uses Bi-Specific S2/S2' Subsites to Optimize Cleavage of Two Classes of Target Sites. J Mol Biol. 2018 12 07; 430(24):5182-5195. PMID: 30414407.
      Citations: 5     Fields:    Translation:Cells
    27. Moise L, M Biron B, Boyle CM, Kurt Yilmaz N, Jang H, Schiffer C, M Ross T, Martin WD, De Groot AS. T cell epitope engineering: an avian H7N9 influenza vaccine strategy for pandemic preparedness and response. Hum Vaccin Immunother. 2018; 14(9):2203-2207. PMID: 30015562.
      Citations: 7     Fields:    Translation:HumansAnimalsCells
    28. Matthew AN, Leidner F, Newton A, Petropoulos CJ, Huang W, Ali A, KurtYilmaz N, Schiffer CA. Molecular Mechanism of Resistance in a Clinically Significant Double-Mutant Variant of HCV NS3/4A Protease. Structure. 2018 10 02; 26(10):1360-1372.e5. PMID: 30146168.
      Citations: 10     Fields:    Translation:HumansCells
    29. Rusere LN, Matthew AN, Lockbaum GJ, Jahangir M, Newton A, Petropoulos CJ, Huang W, Kurt Yilmaz N, Schiffer CA, Ali A. Quinoxaline-Based Linear HCV NS3/4A Protease Inhibitors Exhibit Potent Activity against Drug Resistant Variants. ACS Med Chem Lett. 2018 Jul 12; 9(7):691-696. PMID: 30034602.
      Citations:    
    30. Silvas TV, Hou S, Myint W, Nalivaika E, Somasundaran M, Kelch BA, Matsuo H, Kurt Yilmaz N, Schiffer CA. Substrate sequence selectivity of APOBEC3A implicates intra-DNA interactions. Sci Rep. 2018 05 14; 8(1):7511. PMID: 29760455.
      Citations: 22     Fields:    Translation:HumansCells
    31. Leidner F, Kurt Yilmaz N, Paulsen J, Muller YA, Schiffer CA. Hydration Structure and Dynamics of Inhibitor-Bound HIV-1 Protease. J Chem Theory Comput. 2018 May 08; 14(5):2784-2796. PMID: 29570286.
      Citations: 13     Fields:    Translation:Cells
    32. Khan SN, Persons JD, Paulsen JL, Guerrero M, Schiffer CA, Kurt-Yilmaz N, Ishima R. Probing Structural Changes among Analogous Inhibitor-Bound Forms of HIV-1 Protease and a Drug-Resistant Mutant in Solution by Nuclear Magnetic Resonance. Biochemistry. 2018 03 13; 57(10):1652-1662. PMID: 29457713.
      Citations: 7     Fields:    Translation:Cells
    33. 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. Structural Determination of the Broadly Reactive Anti-IGHV1-69 Anti-idiotypic Antibody G6 and Its Idiotope. Cell Rep. 2017 Dec 12; 21(11):3243-3255. PMID: 29241550.
      Citations: 8     Fields:    Translation:HumansCells
    34. Matthew AN, Kurt Yilmaz N, Schiffer CA. Mavyret: A Pan-Genotypic Combination Therapy for the Treatment of Hepatitis C InfectionPublished as part of the Biochemistry series "Biochemistry to Bedside". Biochemistry. 2018 02 06; 57(5):481-482. PMID: 29192768.
      Citations: 2     Fields:    Translation:HumansCells
    35. Ragland DA, Whitfield TW, Lee SK, Swanstrom R, Zeldovich KB, Kurt-Yilmaz N, Schiffer CA. Elucidating the Interdependence of Drug Resistance from Combinations of Mutations. J Chem Theory Comput. 2017 Nov 14; 13(11):5671-5682. PMID: 28915040.
      Citations: 11     Fields:    Translation:HumansCells
    36. Matthew AN, Zephyr J, Hill CJ, Jahangir M, Newton A, Petropoulos CJ, Huang W, Kurt-Yilmaz N, Schiffer CA, Ali A. Hepatitis C Virus NS3/4A Protease Inhibitors Incorporating Flexible P2 Quinoxalines Target Drug Resistant Viral Variants. J Med Chem. 2017 07 13; 60(13):5699-5716. PMID: 28594175.
      Citations: 10     Fields:    Translation:HumansCells
    37. Lin KH, Ali A, Rusere L, Soumana DI, Kurt Yilmaz N, Schiffer CA. Dengue Virus NS2B/NS3 Protease Inhibitors Exploiting the Prime Side. J Virol. 2017 05 15; 91(10). PMID: 28298600.
      Citations: 13     Fields:    Translation:HumansCells
    38. Kouno T, Silvas TV, Hilbert BJ, Shandilya SMD, Bohn MF, Kelch BA, Royer WE, Somasundaran M, Kurt Yilmaz N, Matsuo H, Schiffer CA. Crystal structure of APOBEC3A bound to single-stranded DNA reveals structural basis for cytidine deamination and specificity. Nat Commun. 2017 04 28; 8:15024. PMID: 28452355.
      Citations: 68     Fields:    Translation:HumansCells
    39. Paulsen JL, Leidner F, Ragland DA, Kurt Yilmaz N, Schiffer CA. Interdependence of Inhibitor Recognition in HIV-1 Protease. J Chem Theory Comput. 2017 May 09; 13(5):2300-2309. PMID: 28358514.
      Citations: 12     Fields:    Translation:HumansCells
    40. 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. Molecular Basis for Differential Patterns of Drug Resistance in Influenza N1 and N2 Neuraminidase. J Chem Theory Comput. 2016 Dec 13; 12(12):6098-6108. PMID: 27951676.
      Citations: 7     Fields:    Translation:HumansCells
    41. Shandilya S, Kurt Yilmaz N, Sadowski A, Monir E, Schiller ZA, Thomas WD, Klempner MS, Schiffer CA, Wang Y. Structural and molecular analysis of a protective epitope of Lyme disease antigen OspA and antibody interactions. J Mol Recognit. 2017 05; 30(5). PMID: 27859766.
      Citations: 4     Fields:    Translation:HumansAnimalsCells
    42. Lin KH, Nalivaika EA, Prachanronarong KL, Yilmaz NK, Schiffer CA. Dengue Protease Substrate Recognition: Binding of the Prime Side. ACS Infect Dis. 2016 10 14; 2(10):734-743. PMID: 27657335.
      Citations: 7     Fields:    Translation:HumansCells
    43. Soumana DI, Kurt Yilmaz N, Ali A, Prachanronarong KL, Schiffer CA. Molecular and Dynamic Mechanism Underlying Drug Resistance in Genotype 3 Hepatitis C NS3/4A Protease. J Am Chem Soc. 2016 09 14; 138(36):11850-9. PMID: 27512818.
      Citations: 25     Fields:    Translation:Cells
    44. Kurt Yilmaz N, Swanstrom R, Schiffer CA. Improving Viral Protease Inhibitors to Counter Drug Resistance. Trends Microbiol. 2016 07; 24(7):547-557. PMID: 27090931.
      Citations: 42     Fields:    Translation:Humans
    45. Soumana DI, Kurt Yilmaz N, Prachanronarong KL, Aydin C, Ali A, Schiffer CA. Structural and Thermodynamic Effects of Macrocyclization in HCV NS3/4A Inhibitor MK-5172. ACS Chem Biol. 2016 Apr 15; 11(4):900-9. PMID: 26682473.
      Citations: 15     Fields:    
    46. Bohn MF, Shandilya SMD, Silvas TV, Nalivaika EA, Kouno T, Kelch BA, Ryder SP, Kurt-Yilmaz N, Somasundaran M, Schiffer CA. The ssDNA Mutator APOBEC3A Is Regulated by Cooperative Dimerization. Structure. 2015 May 05; 23(5):903-911. PMID: 25914058.
      Citations: 56     Fields:    Translation:HumansCells
    47. Özen A, Lin KH, Kurt Yilmaz N, Schiffer CA. Structural basis and distal effects of Gag substrate coevolution in drug resistance to HIV-1 protease. Proc Natl Acad Sci U S A. 2014 Nov 11; 111(45):15993-8. PMID: 25355911.
      Citations: 23     Fields:    Translation:HumansCells
    48. Ragland DA, Nalivaika EA, Nalam MN, Prachanronarong KL, Cao H, Bandaranayake RM, Cai Y, Kurt-Yilmaz N, Schiffer CA. Drug resistance conferred by mutations outside the active site through alterations in the dynamic and structural ensemble of HIV-1 protease. J Am Chem Soc. 2014 Aug 27; 136(34):11956-63. PMID: 25091085.
      Citations: 43     Fields:    Translation:Cells
    49. Cai Y, Myint W, Paulsen JL, Schiffer CA, Ishima R, Kurt Yilmaz N. Drug Resistance Mutations Alter Dynamics of Inhibitor-Bound HIV-1 Protease. J Chem Theory Comput. 2014 Aug 12; 10(8):3438-3448. PMID: 25136270.
      Citations: 23     Fields:    
    50. Jennaro TS, Beaty MR, Kurt-Yilmaz N, Luskin BL, Cavagnero S. Burial of nonpolar surface area and thermodynamic stabilization of globins as a function of chain elongation. Proteins. 2014 Oct; 82(10):2318-31. PMID: 24752983.
      Citations:    Fields:    Translation:Cells
    51. Kolli M, Ozen A, Kurt-Yilmaz N, Schiffer CA. HIV-1 protease-substrate coevolution in nelfinavir resistance. J Virol. 2014 Jul; 88(13):7145-54. PMID: 24719428.
      Citations: 9     Fields:    Translation:HumansCells
    52. Nalam MN, Ali A, Reddy GS, Cao H, Anjum SG, Altman MD, Yilmaz NK, Tidor B, Rana TM, Schiffer CA. Substrate envelope-designed potent HIV-1 protease inhibitors to avoid drug resistance. Chem Biol. 2013 Sep 19; 20(9):1116-24. PMID: 24012370.
      Citations: 25     Fields:    Translation:HumansCells
    53. Zhu L, Kurt N, Choi J, Lapidus LJ, Cavagnero S. Sub-millisecond chain collapse of the Escherichia coli globin ApoHmpH. J Phys Chem B. 2013 Jul 03; 117(26):7868-77. PMID: 23750553.
      Citations: 4     Fields:    Translation:Cells
    54. Knight AM, Culviner PH, Kurt-Yilmaz N, Zou T, Ozkan SB, Cavagnero S. Electrostatic effect of the ribosomal surface on nascent polypeptide dynamics. ACS Chem Biol. 2013; 8(6):1195-204. PMID: 23517476.
      Citations: 37     Fields:    Translation:Cells
    55. Mittal S, Bandaranayake RM, King NM, Prabu-Jeyabalan M, Nalam MN, Nalivaika EA, Yilmaz NK, Schiffer CA. Structural and thermodynamic basis of amprenavir/darunavir and atazanavir resistance in HIV-1 protease with mutations at residue 50. J Virol. 2013 Apr; 87(8):4176-84. PMID: 23365446.
      Citations: 11     Fields:    Translation:HumansCells
    56. Foulkes-Murzycki JE, Rosi C, Kurt Yilmaz N, Shafer RW, Schiffer CA. Cooperative effects of drug-resistance mutations in the flap region of HIV-1 protease. ACS Chem Biol. 2013 Mar 15; 8(3):513-8. PMID: 23252515.
      Citations: 10     Fields:    
    57. King NM, Prabu-Jeyabalan M, Bandaranayake RM, Nalam MN, Nalivaika EA, Özen A, Halilo?lu T, Yilmaz NK, Schiffer CA. Extreme entropy-enthalpy compensation in a drug-resistant variant of HIV-1 protease. ACS Chem Biol. 2012 Sep 21; 7(9):1536-46. PMID: 22712830.
      Citations: 27     Fields:    Translation:Cells
    58. Cai Y, Yilmaz NK, Myint W, Ishima R, Schiffer CA. Differential Flap Dynamics in Wild-type and a Drug Resistant Variant of HIV-1 Protease Revealed by Molecular Dynamics and NMR Relaxation. J Chem Theory Comput. 2012 Oct 09; 8(10):3452-3462. PMID: 23144597.
      Citations: 29     Fields:    
    59. Rajagopalan S, Kurt N, Cavagnero S. High-resolution conformation and backbone dynamics of a soluble aggregate of apomyoglobin119. Biophys J. 2011 Feb 02; 100(3):747-755. PMID: 21281590.
      Citations: 3     Fields:    Translation:AnimalsCells
    60. Mounce BC, Kurt N, Ellison PA, Cavagnero S. Nonrandom distribution of intramolecular contacts in native single-domain proteins. Proteins. 2009 May 01; 75(2):404-12. PMID: 18831044.
      Citations: 2     Fields:    Translation:Cells
    61. Kurt N, Mounce BC, Ellison PA, Cavagnero S. Residue-specific contact order and contact breadth in single-domain proteins: implications for folding as a function of chain elongation. Biotechnol Prog. 2008 May-Jun; 24(3):570-5. PMID: 18471028.
      Citations: 4     Fields:    Translation:Cells
    62. Kurt N, Cavagnero S. Nonnative helical motif in a chaperone-bound protein fragment. Biophys J. 2008 Apr 01; 94(7):L48-50. PMID: 18192369.
      Citations: 8     Fields:    Translation:Cells
    63. Eun YJ, Kurt N, Sekhar A, Cavagnero S. Thermodynamic and kinetic characterization of apoHmpH, a fast-folding bacterial globin. J Mol Biol. 2008 Feb 22; 376(3):879-97. PMID: 18187151.
      Citations: 5     Fields:    Translation:AnimalsCells
    64. Vega CA, Kurt N, Chen Z, Rüdiger S, Cavagnero S. Binding specificity of an alpha-helical protein sequence to a full-length Hsp70 chaperone and its minimal substrate-binding domain. Biochemistry. 2006 Nov 21; 45(46):13835-46. PMID: 17105202.
      Citations: 8     Fields:    Translation:Cells
    65. Chen Z, Kurt N, Rajagopalan S, Cavagnero S. Secondary structure mapping of DnaK-bound protein fragments: chain helicity and local helix unwinding at the binding site. Biochemistry. 2006 Oct 10; 45(40):12325-33. PMID: 17014085.
      Citations: 14     Fields:    Translation:Cells
    66. Cavagnero, S.; Kurt, N. Misbehaving Proteins: Protein (Mis)Folding, Aggregation and Stability, editors R.M. Murphy and A.M. Tsai. Folding and Misfolding as a Function of Polypeptide Chain Elongation: Conformational Trends and Implications for Intracellular Events. 2006; 217-246 .
    67. Kurt N, Cavagnero S. The burial of solvent-accessible surface area is a predictor of polypeptide folding and misfolding as a function of chain elongation. J Am Chem Soc. 2005 Nov 16; 127(45):15690-1. PMID: 16277496.
      Citations: 7     Fields:    Translation:Cells
    68. Kurt N, Rajagopalan S, Cavagnero S. Effect of hsp70 chaperone on the folding and misfolding of polypeptides modeling an elongating protein chain. J Mol Biol. 2006 Jan 27; 355(4):809-20. PMID: 16309705.
      Citations: 16     Fields:    Translation:Cells
    69. Chow C, Kurt N, Murphy RM, Cavagnero S. Structural characterization of apomyoglobin self-associated species in aqueous buffer and urea solution. Biophys J. 2006 Jan 01; 90(1):298-309. PMID: 16214860.
      Citations: 5     Fields:    Translation:AnimalsCells
    70. Kurt N, Haliloglu T, Schiffer CA. Structure-based prediction of potential binding and nonbinding peptides to HIV-1 protease. Biophys J. 2003 Aug; 85(2):853-63. PMID: 12885633.
      Citations: 4     Fields:    Translation:Cells
    71. Kurt N, Scott WR, Schiffer CA, Haliloglu T. 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. Proteins. 2003 May 15; 51(3):409-22. PMID: 12696052.
      Citations: 21     Fields:    Translation:Cells
    72. Kurt, N.; Haliloglu, T. Distribution of cooperative interactions in barnase at different time windows by coarse-grained simulations. Polymer. 2002; 43(2):403-408. View Publication.
    73. Kurt N, Halilo?lu T. Conformational dynamics of subtilisin-chymotrypsin inhibitor 2 complex by coarse-grained simulations. J Biomol Struct Dyn. 2001 Apr; 18(5):713-31. PMID: 11334109.
      Citations: 2     Fields:    
    74. Kurt N, Halilo?lu T. Conformational dynamics of chymotrypsin inhibitor 2 by coarse-grained simulations. Proteins. 1999 Nov 15; 37(3):454-64. PMID: 10591104.
      Citations: 5     Fields:    Translation:Cells
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