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Nese Kurt Yilmaz PhD

TitleAssociate Professor
InstitutionUniversity of Massachusetts Medical School
DepartmentBiochemistry and Molecular Pharmacology
AddressUniversity of Massachusetts Medical School
364 Plantation Street, LRB
Worcester MA 01605
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    Other Positions
    InstitutionUMMS - School of Medicine
    DepartmentBiochemistry and Molecular Pharmacology

    InstitutionUMMS - 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.
    List All   |   Timeline
    1. Hou S, Silvas T, 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. 2018 Nov 20. PMID: 30457868.
      View in: PubMed
    2. 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 Nov 07. PMID: 30414407.
      View in: PubMed
    3. 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 Aug 07. PMID: 30146168.
      View in: PubMed
    4. Moise L, Girard B, Boyle C, Kurt Yilmaz N, Jang H, Schiffer C, 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 Jul 17. PMID: 30015562.
      View in: PubMed
    5. 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.
      View in: PubMed
    6. 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 May 14; 8(1):7511. PMID: 29760455.
      View in: PubMed
    7. 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.
      View in: PubMed
    8. 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.
      View in: PubMed
    9. 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.
      View in: PubMed
    10. 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.
      View in: PubMed
    11. 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 Oct 09. PMID: 28915040.
      View in: PubMed
    12. 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 Jun 08. PMID: 28594175.
      View in: PubMed
    13. 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 Apr 28; 8:15024. PMID: 28452355.
      View in: PubMed
    14. Paulsen JL, Leidner F, Ragland DA, Kurt Yilmaz N, Schiffer CA. Interdependence of Inhibitor Recognition in HIV-1 Protease. J Chem Theory Comput. 2017 Mar 30. PMID: 28358514.
      View in: PubMed
    15. Lin KH, Ali A, Rusere L, Soumana DI, Yilmaz NK, Schiffer CA. Dengue Virus NS2B/NS3 Protease Inhibitors Exploiting the Prime Side. J Virol. 2017 Mar 15. PMID: 28298600.
      View in: PubMed
    16. 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.
      View in: PubMed
    17. 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. 2016 Nov 16. PMID: 27859766.
      View in: PubMed
    18. Lin KH, Nalivaika EA, Prachanronarong KL, Yilmaz NK, Schiffer CA. Dengue Protease Substrate Recognition: Binding of the Prime Side. ACS Infect Dis. 2016 Oct 14; 2(10):734-743. PMID: 27657335.
      View in: PubMed
    19. 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 Sep 14; 138(36):11850-9. PMID: 27512818.
      View in: PubMed
    20. Kurt Yilmaz N, Swanstrom R, Schiffer CA. Improving Viral Protease Inhibitors to Counter Drug Resistance. Trends Microbiol. 2016 Jul; 24(7):547-57. PMID: 27090931.
      View in: PubMed
    21. 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.
      View in: PubMed
    22. Bohn MF, Shandilya SM, 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 5; 23(5):903-11. PMID: 25914058.
      View in: PubMed
    23. 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.
      View in: PubMed
    24. 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.
      View in: PubMed
    25. 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.
      View in: PubMed
    26. 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.
      View in: PubMed
    27. 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.
      View in: PubMed
    28. 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.
      View in: PubMed
    29. 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 3; 117(26):7868-77. PMID: 23750553.
      View in: PubMed
    30. 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.
      View in: PubMed
    31. 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.
      View in: PubMed
    32. 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.
      View in: PubMed
    33. King NM, Prabu-Jeyabalan M, Bandaranayake RM, Nalam MN, Nalivaika EA, Özen A, Haliloglu 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.
      View in: PubMed
    34. 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 9; 8(10):3452-3462. PMID: 23144597.
      View in: PubMed
    35. Rajagopalan S, Kurt N, Cavagnero S. High-resolution conformation and backbone dynamics of a soluble aggregate of apomyoglobin119. Biophys J. 2011 Feb 2; 100(3):747-55. PMID: 21281590.
      View in: PubMed
    36. Mounce BC, Kurt N, Ellison PA, Cavagnero S. Nonrandom distribution of intramolecular contacts in native single-domain proteins. Proteins. 2009 May 1; 75(2):404-12. PMID: 18831044.
      View in: PubMed
    37. 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.
      View in: PubMed
    38. Kurt N, Cavagnero S. Nonnative helical motif in a chaperone-bound protein fragment. Biophys J. 2008 Apr 01; 94(7):L48-50. PMID: 18192369.
      View in: PubMed
    39. 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.
      View in: PubMed
    40. 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.
      View in: PubMed
    41. 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.
      View in: PubMed
    42. 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 .
    43. 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.
      View in: PubMed
    44. 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.
      View in: PubMed
    45. 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 1; 90(1):298-309. PMID: 16214860.
      View in: PubMed
    46. 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.
      View in: PubMed
    47. 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.
      View in: PubMed
    48. Kurt, N.; Haliloglu, T. Distribution of cooperative interactions in barnase at different time windows by coarse-grained simulations. Polymer. 2002; 43(2):403-408.
    49. Kurt N, Haliloglu 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.
      View in: PubMed
    50. Kurt N, Haliloglu T. Conformational dynamics of chymotrypsin inhibitor 2 by coarse-grained simulations. Proteins. 1999 Nov 15; 37(3):454-64. PMID: 10591104.
      View in: PubMed
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