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Kurt Yilmaz, Nese
One or more keywords matched the following properties of Kurt Yilmaz, Nese
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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.

 

 
One or more keywords matched the following items that are connected to Kurt Yilmaz, Nese
Item TypeName
Academic Article 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.
Academic Article Extreme entropy-enthalpy compensation in a drug-resistant variant of HIV-1 protease.
Academic Article Structure-based prediction of potential binding and nonbinding peptides to HIV-1 protease.
Academic Article Structural and thermodynamic basis of amprenavir/darunavir and atazanavir resistance in HIV-1 protease with mutations at residue 50.
Concept Protein Binding
Concept DNA-Binding Proteins
Concept Protein Folding
Concept HSP70 Heat-Shock Proteins
Concept Carrier Proteins
Concept Protein Biosynthesis
Concept Recombinant Proteins
Concept Protein Interaction Domains and Motifs
Concept Mutant Proteins
Concept Serine Proteinase Inhibitors
Concept Protein Denaturation
Concept Protein Renaturation
Concept Viral Proteins
Concept Proteins
Concept Protein Structure, Secondary
Concept Protein Structure, Tertiary
Concept Cysteine Proteinase Inhibitors
Concept Crystallography, X-Ray
Concept Escherichia coli Proteins
Concept Bacterial Outer Membrane Proteins
Concept Viral Nonstructural Proteins
Concept Plant Proteins
Concept Protein Structure, Quaternary
Concept Structural Homology, Protein
Concept Protein Conformation
Concept Databases, Protein
Concept Sequence Analysis, Protein
Academic Article Substrate envelope-designed potent HIV-1 protease inhibitors to avoid drug resistance.
Academic Article HIV-1 protease-substrate coevolution in nelfinavir resistance.
Academic Article Drug resistance conferred by mutations outside the active site through alterations in the dynamic and structural ensemble of HIV-1 protease.
Academic Article Nonnative helical motif in a chaperone-bound protein fragment.
Academic Article Thermodynamic and kinetic characterization of apoHmpH, a fast-folding bacterial globin.
Academic Article Binding specificity of an alpha-helical protein sequence to a full-length Hsp70 chaperone and its minimal substrate-binding domain.
Academic Article Secondary structure mapping of DnaK-bound protein fragments: chain helicity and local helix unwinding at the binding site.
Academic Article Effect of hsp70 chaperone on the folding and misfolding of polypeptides modeling an elongating protein chain.
Academic Article Structural characterization of apomyoglobin self-associated species in aqueous buffer and urea solution.
Academic Article Residue-specific contact order and contact breadth in single-domain proteins: implications for folding as a function of chain elongation.
Academic Article Nonrandom distribution of intramolecular contacts in native single-domain proteins.
Academic Article High-resolution conformation and backbone dynamics of a soluble aggregate of apomyoglobin119.
Academic Article Sub-millisecond chain collapse of the Escherichia coli globin ApoHmpH.
Academic Article Conformational dynamics of chymotrypsin inhibitor 2 by coarse-grained simulations.
Academic Article Conformational dynamics of subtilisin-chymotrypsin inhibitor 2 complex by coarse-grained simulations.
Academic Article Burial of nonpolar surface area and thermodynamic stabilization of globins as a function of chain elongation.
Academic Article Electrostatic effect of the ribosomal surface on nascent polypeptide dynamics.
Academic Article The burial of solvent-accessible surface area is a predictor of polypeptide folding and misfolding as a function of chain elongation.
Academic Article Misbehaving Proteins: Protein (Mis)Folding, Aggregation and Stability, editors R.M. Murphy and A.M. Tsai
Academic Article Structural basis and distal effects of Gag substrate coevolution in drug resistance to HIV-1 protease.
Academic Article The ssDNA Mutator APOBEC3A Is Regulated by Cooperative Dimerization.
Academic Article Structural and Thermodynamic Effects of Macrocyclization in HCV NS3/4A Inhibitor MK-5172.
Academic Article Molecular and Dynamic Mechanism Underlying Drug Resistance in Genotype 3 Hepatitis C NS3/4A Protease.
Academic Article Dengue Protease Substrate Recognition: Binding of the Prime Side.
Academic Article Structural and molecular analysis of a protective epitope of Lyme disease antigen OspA and antibody interactions.
Academic Article Molecular Basis for Differential Patterns of Drug Resistance in Influenza N1 and N2 Neuraminidase.
Academic Article Dengue Virus NS2B/NS3 Protease Inhibitors Exploiting the Prime Side.
Academic Article Interdependence of Inhibitor Recognition in HIV-1 Protease.
Academic Article Hepatitis C Virus NS3/4A Protease Inhibitors Incorporating Flexible P2 Quinoxalines Target Drug Resistant Viral Variants.
Academic Article Structural Determination of the Broadly Reactive Anti-IGHV1-69 Anti-idiotypic Antibody G6 and Its Idiotope.
Academic Article Substrate sequence selectivity of APOBEC3A implicates intra-DNA interactions.
Academic Article Crystal structure of APOBEC3A bound to single-stranded DNA reveals structural basis for cytidine deamination and specificity.
Academic Article Molecular Mechanism of Resistance in a Clinically Significant Double-Mutant Variant of HCV NS3/4A Protease.
Academic Article Probing Structural Changes among Analogous Inhibitor-Bound Forms of HIV-1 Protease and a Drug-Resistant Mutant in Solution by Nuclear Magnetic Resonance.
Academic Article Structural Analysis of the Active Site and DNA Binding of Human Cytidine Deaminase APOBEC3B.
Academic Article HIV-1 Protease Uses Bi-Specific S2/S2' Subsites to Optimize Cleavage of Two Classes of Target Sites.
Academic Article NMR and MD studies combined to elucidate inhibitor and water interactions of HIV-1 protease and their modulations with resistance mutations.
Academic Article Picomolar to Micromolar: Elucidating the Role of Distal Mutations in HIV-1 Protease in Conferring Drug Resistance.
Academic Article Target-Specific Prediction of Ligand Affinity with Structure-Based Interaction Fingerprints.
Academic Article Molecular Determinants of Epistasis in HIV-1 Protease: Elucidating the Interdependence of L89V and L90M Mutations in Resistance.
Academic Article Mechanism for APOBEC3G catalytic exclusion of RNA and non-substrate DNA.
Academic Article Molecular and Structural Mechanism of Pan-Genotypic HCV NS3/4A Protease Inhibition by Glecaprevir.
Academic Article Optimizing the refinement of merohedrally twinned P61 HIV-1 protease-inhibitor cocrystal structures.
Academic Article Avoiding Drug Resistance by Substrate Envelope-Guided Design: Toward Potent and Robust HCV NS3/4A Protease Inhibitors.
Academic Article Structural Analysis of Potent Hybrid HIV-1 Protease Inhibitors Containing Bis-tetrahydrofuran in a Pseudosymmetric Dipeptide Isostere.
Academic Article A cross-reactive human IgA monoclonal antibody blocks SARS-CoV-2 spike-ACE2 interaction.
Academic Article Crystal Structure of a Soluble APOBEC3G Variant Suggests ssDNA to Bind in a Channel that Extends between the Two Domains.
Academic Article Drug Design Strategies to Avoid Resistance in Direct-Acting Antivirals and Beyond.
Academic Article Crystal Structure of SARS-CoV-2 Main Protease in Complex with the Non-Covalent Inhibitor ML188.
Academic Article Inhibiting HTLV-1 Protease: A Viable Antiviral Target.
Academic Article Introduction: Drug Resistance.
Academic Article Structural basis of substrate specificity in human cytidine deaminase family APOBEC3s.
Academic Article Discovery of Quinoxaline-Based P1-P3 Macrocyclic NS3/4A Protease Inhibitors with Potent Activity against Drug-Resistant Hepatitis C Virus Variants.
Academic Article Pan-3C Protease Inhibitor Rupintrivir Binds SARS-CoV-2 Main Protease in a Unique Binding Mode.
Concept Protein Domains
Academic Article Defining the substrate envelope of SARS-CoV-2 main protease to predict and avoid drug resistance.
Academic Article Allosteric quinoxaline-based inhibitors of the flavivirus NS2B/NS3 protease.
Academic Article Elucidating the Substrate Envelope of Enterovirus 68-3C Protease: Structural Basis of Specificity and Potential Resistance.
Academic Article Direct delivery of Cas-embedded cytosine base editors as ribonucleoprotein complexes for efficient and accurate editing of clinically relevant targets.
Academic Article Structural Analysis of Inhibitor Binding to Enterovirus-D68 3C Protease.
Search Criteria
  • Protein
  • Crystallography