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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, , TurkeyPHD

    Collapse Overview 
    Collapse overview


    Academic Background



    PhD, Chemical Engineering, Bogazici University, Istanbul, Turkey, 2002



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



     



    Research Experience



    Research Assistant Professor                                                                   Nov 2011–present



    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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    1. 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
    2. 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
    3. 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
    4. 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
    5. 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
    6. 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
    7. 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
    8. 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
    9. 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
    10. 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
    11. 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
    12. 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
    13. 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
    14. 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
    15. 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
    16. 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
    17. 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
    18. 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
    19. 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
    20. 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
    21. 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
    22. 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
    23. 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
    24. 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
    25. 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 .
    26. 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
    27. 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
    28. 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
    29. 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
    30. 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
    31. Kurt, N.; Haliloglu, T. Distribution of cooperative interactions in barnase at different time windows by coarse-grained simulations. Polymer. 2002; 43(2):403-408.
    32. 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
    33. 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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