This collection showcases the journal articles and other publications authored by researchers in the Schiffer Lab in the Department of Biochemistry and Molecular Pharmacology at the University of Massachusetts Medical School.

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Publications from 2009

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Human immunodeficiency virus type 1 protease-correlated cleavage site mutations enhance inhibitor resistance, Madhavi Kolli, Eric Stawiski, Colombe Chappey, and Celia A. Schiffer

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Toward the design of mutation-resistant enzyme inhibitors: further evaluation of the substrate envelope hypothesis, Visvaldas Kairys, Michael K. Gilson, Viney Lather, Celia A. Schiffer, and Miguel X. Fernandes

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New approaches to HIV protease inhibitor drug design II: testing the substrate envelope hypothesis to avoid drug resistance and discover robust inhibitors, Madhavi N. L. Nalam and Celia A. Schiffer

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Additivity in the analysis and design of HIV protease inhibitors, Robert N. Jorissen, G. S. Kiran Kumar Reddy, Akbar Ali, Michael D. Altman, Sripriya Chellappan, Saima G. Anjum, Bruce Tidor, Celia A. Schiffer, Tariq M. Rana, and Michael K. Gilson

Publications from 2008

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Insights into interferon regulatory factor activation from the crystal structure of dimeric IRF5, Weijun Chen, Suvana S. Lam, Hema Srinath, Zhaozhao Jiang, John J. Correia, Celia A. Schiffer, Katherine A. Fitzgerald, Kai Lin, and William E. Royer

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Resilience to resistance of HIV-1 protease inhibitors: profile of darunavir, Eric Lefebvre and Celia A. Schiffer

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Structural analysis of human immunodeficiency virus type 1 CRF01_AE protease in complex with the substrate p1-p6., Rajintha M. Bandaranayake, Moses Prabu-Jeyabalan, Junko Kakizawa, Wataru Sugiura, and Celia A. Schiffer

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Contribution of Ser386 and Ser396 to activation of interferon regulatory factor 3, Weijun Chen, Hema Srinath, Suvana S. Lam, Celia A. Schiffer, William E. Royer, and Kai Lin

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HIV-1 protease inhibitors from inverse design in the substrate envelope exhibit subnanomolar binding to drug-resistant variants, Michael D. Altman, Akbar Ali, G. S. Kiran Kumar Reddy, Madhavi N. L. Nalam, Saima G. Anjum, Hong Cao, Sripriya Chellappan, Visvaldas Kairys, Miguel X. Fernandes, Michael K. Gilson, Celia A. Schiffer, Tariq M. Rana, and Bruce Tidor

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Combating Drug Resistance – Identifying Resilient Molecular Targets and Robust Drugs, Celia A. Schiffer

Publications from 2007

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Mass spectrometry analysis of HIV-1 Vif reveals an increase in ordered structure upon oligomerization in regions necessary for viral infectivity, Jared R. Auclair, Karin M. Green, Shivender Shandilya, James E. Evans, Mohan Somasundaran, and Celia A. Schiffer

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Computational design and experimental study of tighter binding peptides to an inactivated mutant of HIV-1 protease, Michael D. Altman, Ellen A. Nalivaika, Moses Prabu-Jeyabalan, Celia A. Schiffer, and Bruce Tidor

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Design and synthesis of HIV-1 protease inhibitors incorporating oxazolidinones as P2/P2' ligands in pseudosymmetric dipeptide isosteres, G. S. Kiran Kumar Reddy, Akbar Ali, Madhavi N. L. Nalam, Saima G. Anjum, Hong Cao, Robin S. Nathans, Celia A. Schiffer, and Tariq M. Rana

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Crystal structure of lysine sulfonamide inhibitor reveals the displacement of the conserved flap water molecule in human immunodeficiency virus type 1 protease, Madhavi N. L. Nalam, Anik Peeters, Tim H. M. Jonckers, Inge Dierynck, and Celia A. Schiffer

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Design of mutation-resistant HIV protease inhibitors with the substrate envelope hypothesis, Sripriya Chellappan, G. S. Kiran Kumar Reddy, Akbar Ali, Madhavi N. L. Nalam, Saima G. Anjum, Hong Cao, Visvaldas Kairys, Miguel X. Fernandes, Michael D. Altman, Bruce Tidor, Tariq M. Rana, Celia A. Schiffer, and Michael K. Gilson

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Evaluation of the substrate envelope hypothesis for inhibitors of HIV-1 protease, Sripriya Chellappan, Visvaldas Kairys, Miguel X. Fernandes, Celia A. Schiffer, and Michael K. Gilson

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Hydrophobic sliding: a possible mechanism for drug resistance in human immunodeficiency virus type 1 protease, Jennifer E. Foulkes-Murzycki, Walter Robert Peter Scott, and Celia A. Schiffer

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Competition between Ski and CREB-binding protein for binding to Smad proteins in transforming growth factor-beta signaling, Weijun Chen, Suvana S. Lam, Hema Srinath, Celia A. Schiffer, William E. Royer, and Kai Lin

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N88D facilitates the co-occurrence of D30N and L90M and the development of multidrug resistance in HIV type 1 protease following nelfinavir treatment failure, Yumi Mitsuya, Mark A. Winters, W. Jeffrey Fessel, Soo-Yon Rhee, Leo Hurley, Michael Horberg, Celia A. Schiffer, Andrew R. Zolopa, and Robert W. Shafer

Publications from 2006

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Discovery of HIV-1 protease inhibitors with picomolar affinities incorporating N-aryl-oxazolidinone-5-carboxamides as novel P2 ligands, Akbar Ali, G. S. Kiran Kumar Reddy, Hong Cao, Saima G. Anjum, Madhavi N. L. Nalam, Celia A. Schiffer, and Tariq M. Rana

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RecA dimers serve as a functional unit for assembly of active nucleoprotein filaments, Anthony L. Forget, Michelle M. Kudron, Dharia A. McGrew, Melissa A. Calmann, Celia A. Schiffer, and Kendall L. Knight

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Role of invariant Thr80 in human immunodeficiency virus type 1 protease structure, function, and viral infectivity, Jennifer E. Foulkes-Murzycki, Moses Prabu-Jeyabalan, Deyna Cooper, Gavin J. Henderson, Janera Harris, Ronald I. Swanstrom, and Celia A. Schiffer

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Substrate specificity in HIV-1 protease by a biased sequence search method, Nevra Ozer, Turkan Haliloglu, and Celia A. Schiffer

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Co-evolution of nelfinavir-resistant HIV-1 protease and the p1-p6 substrate, Madhavi Kolli, Stephane Lastere, and Celia A. Schiffer

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Substrate envelope and drug resistance: crystal structure of RO1 in complex with wild-type human immunodeficiency virus type 1 protease, Moses Prabu-Jeyabalan, Nancy M. King, Ellen A. Nalivaika, Gabrielle Heilek-Snyder, Nick Cammack, and Celia A. Schiffer

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Mechanism of substrate recognition by drug-resistant human immunodeficiency virus type 1 protease variants revealed by a novel structural intermediate, Moses Prabu-Jeyabalan, Ellen A. Nalivaika, Keith Romano, and Celia A. Schiffer

Publications from 2005

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PTEN enters the nucleus by diffusion, Fenghua Liu, Stefan R. Wagner, Robert B. Campbell, Jeffrey A. Nickerson, Celia A. Schiffer, and Alonzo H. Ross

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Design of HIV-1 protease inhibitors active on multidrug-resistant virus, Dominique L. N. G. S Surleraux, Herman A. De Kock, Wim G. Verschueren, Geert M. E. Pille, Louis J. R. Maes, Anik Peeters, Sandrine Vendeville, Sandra De Meyer, Hilde Azijn, Rudi Pauwels, Marie-Pierre de Bethune, Nancy M. King, Moses Prabu-Jeyabalan, Celia A. Schiffer, and Piet B. T. P. Wigerinck

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Discovery and selection of TMC114, a next generation HIV-1 protease inhibitor, Dominique L. N. G. S Surleraux, Abdellah Tahri, Wim G. Verschueren, Geert M. E. Pille, Herman A. De Kock, Tim H. M. Jonckers, Anik Peeters, Sandra De Meyer, Hilde Azijn, Rudi Pauwels, Marie-Pierre de Bethune, Nancy M. King, Moses Prabu-Jeyabalan, Celia A. Schiffer, and Piet B. T. P. Wigerinck

Publications from 2004

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Association of a novel human immunodeficiency virus type 1 protease substrate cleft mutation, L23I, with protease inhibitor therapy and in vitro drug resistance, Elizabeth Johnston, Mark A. Winters, Soo-Yon Rhee, Thomas C. Merigan, Celia A. Schiffer, and Robert W. Shafer

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Structural basis for coevolution of a human immunodeficiency virus type 1 nucleocapsid-p1 cleavage site with a V82A drug-resistant mutation in viral protease, Moses Prabu-Jeyabalan, Ellen A. Nalivaika, Nancy M. King, and Celia A. Schiffer

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Combating susceptibility to drug resistance: lessons from HIV-1 protease, Nancy M. King, Moses Prabu-Jeyabalan, Ellen A. Nalivaika, and Celia A. Schiffer

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Structural and thermodynamic basis for the binding of TMC114, a next-generation human immunodeficiency virus type 1 protease inhibitor, Nancy M. King, Moses Prabu-Jeyabalan, Ellen A. Nalivaika, Piet B. T. P. Wigerinck, Marie-Pierre de Bethune, and Celia A. Schiffer

Publications from 2003

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Promise of advances in simulation methods for protein crystallography: implicit solvent models, time-averaging refinement, and quantum mechanical modeling, Celia A. Schiffer and Jan Hermans

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Covariation of amino acid positions in HIV-1 protease, Noah G. Hoffman, Celia A. Schiffer, and Ronald I. Swanstrom

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Structure-based prediction of potential binding and nonbinding peptides to HIV-1 protease, Nese Kurt, Turkan Haliloglu, and Celia A. Schiffer

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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, Nese Kurt, Walter Robert Peter Scott, Celia A. Schiffer, and Turkan Haliloglu

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Mutation patterns and structural correlates in human immunodeficiency virus type 1 protease following different protease inhibitor treatments, Thomas D. Wu, Celia A. Schiffer, Matthew J. Gonzales, Jonathan Taylor, Rami Kantor, Sunwen Chou, Dennis Israelski, Andrew R. Zolopa, W. Jeffrey Fessel, and Robert W. Shafer

Publications from 2002

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Viability of a drug-resistant human immunodeficiency virus type 1 protease variant: structural insights for better antiviral therapy, Moses Prabu-Jeyabalan, Ellen A. Nalivaika, Nancy M. King, and Celia A. Schiffer

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Nitric oxide-mediated inhibition of Hdm2-p53 binding, Christopher M. Schonhoff, Marie-Claire Daou, Stephen N. Jones, Celia A. Schiffer, and Alonzo H. Ross

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Point mutants of EHEC intimin that diminish Tir recognition and actin pedestal formation highlight a putative Tir binding pocket, Hui Liu, Padhma Radhakrishnan, Loranne Magoun, Moses Prabu-Jeyabalan, Kenneth Geno Campellone, Pamela Joyce Savage, Feng He, Celia A. Schiffer, and John M. Leong

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Replacement of the P1 amino acid of human immunodeficiency virus type 1 Gag processing sites can inhibit or enhance the rate of cleavage by the viral protease, Steve C. Pettit, Gavin J. Henderson, Celia A. Schiffer, and Ronald I. Swanstrom

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Substrate shape determines specificity of recognition for HIV-1 protease: analysis of crystal structures of six substrate complexes, Moses Prabu-Jeyabalan, Ellen A. Nalivaika, and Celia A. Schiffer

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Structure of a phage display-derived variant of human growth hormone complexed to two copies of the extracellular domain of its receptor: evidence for strong structural coupling between receptor binding sites, Celia A. Schiffer, Mark Ultsch, Scott Walsh, William Somers, Abraham M. de Vos, and Anthony A. Kossiakoff

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Lack of synergy for inhibitors targeting a multi-drug-resistant HIV-1 protease, Nancy M. King, Laurence Melnick, Moses Prabu-Jeyabalan, Ellen A. Nalivaika, Shiow-Shong Yang, Yun Gao, Xiaoyi Nie, Charles Zepp, Donald L. Heefner, and Celia A. Schiffer

Publications from 2001

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Curling of flap tips in HIV-1 protease as a mechanism for substrate entry and tolerance of drug resistance, Walter Robert Peter Scott and Celia A. Schiffer

Publications from 2000

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How does a symmetric dimer recognize an asymmetric substrate? A substrate complex of HIV-1 protease, Moses Prabu-Jeyabalan, Ellen A. Nalivaika, and Celia A. Schiffer

Publications from 1999

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Accessibility and order of water sites in and around proteins: A crystallographic time-averaging study, Celia A. Schiffer and Wilfred F. van Gunsteren

Publications from 1996

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Investigations of peptide hydration using NMR and molecular dynamics simulations: A study of effects of water on the conformation and dynamics of antamanide, Jeffrey W. Peng, Celia A. Schiffer, Ping Xu, Wilfred F. van Gunsteren, and Richard R. Ernst

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Structural stability of disulfide mutants of basic pancreatic trypsin inhibitor: a molecular dynamics study, Celia A. Schiffer and Wilfred F. van Gunsteren

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The role of protein-solvent interactions in protein unfolding, Celia A. Schiffer and Volker Dötsch

Publications from 1995

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Crystal structure of human thymidylate synthase: a structural mechanism for guiding substrates into the active site, Celia A. Schiffer, Ian J. Clifton, V. Jo Davisson, Daniel V. Santi, and Robert M. Stroud

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Exploring the role of the solvent in the denaturation of a protein: a molecular dynamics study of the DNA binding domain of the 434 repressor, Celia A. Schiffer, Volker Dötsch, Kurt Wuthrich, and Wilfred F. van Gunsteren

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Stabilization of Type-I .beta.-Turn Conformations in Peptides Containing the NPNA-Repeat Motif of the Plasmodium falciparum Circumsporozoite Protein by Substituting Proline for (S)-.alpha.-Methylproline, Christian Bisang, Christoph Weber, Janice Inglis, Celia A. Schiffer, Wilfred F. van Gunsteren, Ilian Jelesarov, Hans R. Bosshard, and John A. Robinson

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Investigation of protein unfolding and stability by computer simulation, Wilfred F. van Gunsteren, P. H. Hunenberger, H. Kovacs, A. E. Mark, and Celia A. Schiffer

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Time-averaging crystallographic refinement: possibilities and limitations using alpha-cyclodextrin as a test system, Celia A. Schiffer, P. Gros, and Wilfred F. van Gunsteren

Publications from 1994

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Simultaneous refinement of the structure of BPTI against NMR data measured in solution and X-ray diffraction data measured in single crystals, Celia A. Schiffer, Robert Huber, Kurt Wuthrich, and Wilfred F. van Gunsteren

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Expression, purification, and characterization of thymidylate synthase from Lactococcus lactis, Patricia J. Greene, Pak-Lam Yu, Jia Zhao, Celia A. Schiffer, and Daniel V. Santi

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Accounting for molecular mobility in structure determination based on nuclear magnetic resonance spectroscopic and X-ray diffraction data, Wilfred F. van Gunsteren, Roger M. Brunne, P. Gros, René C. Van Schaik, Celia A. Schiffer, and Andrew E. Torda

Publications from 1992

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Inclusion of solvation free energy with molecular mechanics energy: alanyl dipeptide as a test case, Celia A. Schiffer, James W. Caldwell, Robert M. Stroud, and Peter A. Kollman

Publications from 1991

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Crystallization of human thymidylate synthase, Celia A. Schiffer, V. Jo Davisson, Daniel V. Santi, and Robert M. Stroud

Publications from 1990

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Prediction of homologous protein structures based on conformational searches and energetics, Celia A. Schiffer, James W. Caldwell, Peter A. Kollman, and Robert M. Stroud