Protein Ensembles: How Does Nature Harness Thermodynamic Fluctuations for Life? The Diverse Functional Roles of Conformational Ensembles in the Cell
Cites (585)
Items 401–578 of 578
- Energy Landscape and Transition State of Protein-Protein AssociationRamzi A. Alsallaq, Huan‐Xiang Zhou · 2006 · Biophysical Journal
- Allosteric Conformational Barcodes Direct Signaling in the CellNussinov, Ruth, Ma, Buyong, Tsai, Chung-Jung, Csermely, Peter · 2013 · Structure
- Glasses with Strong Calorimetric .beta.-Glass Transitions and the Relation to the Protein Glass Transition ProblemJing Fan, Emanuel I. Cooper, C. Austen Angell · 1994 · The Journal of Physical Chemistry
- A Designed Conformational Shift To Control Protein Binding SpecificityMichielssens, Servaas, Peters, Jan Henning, Ban, David, Pratihar, Supriya, Seeliger, Daniel, Sharma, Monika, Giller, Karin, Sabo, Thomas Michael, Becker, Stefan, Lee, Donghan et al. · 2014 · Angewandte Chemie International Edition
- Modulation of folding energy landscape by charge–charge interactions: Linking experiments with computational modelingFranco O. Tzul, Katrina L. Schweiker, George I. Makhatadze · 2015 · Proceedings of the National Academy of Sciences
- Machines vs. Ensembles: Effective MAPK Signaling through Heterogeneous Sets of Protein ComplexesSuderman, Ryan, Deeds, Eric J. · 2013 · PLoS Computational Biology
- Entropic mechanism of large fluctuation in allosteric transitionKazuhito Itoh, Masaki Sasai · 2010 · Proceedings of the National Academy of Sciences
- Promiscuous and specific recognition among ephrins and Eph receptorsDai, Dandan, Huang, Qiang, Nussinov, Ruth, Ma, Buyong · 2014 · Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics
- Mechanical Operation and Intersubunit Coordination of Ring-Shaped Molecular Motors: Insights from Single-Molecule StudiesShixin Liu, Gheorghe Chistol, Carlos Bustamante · 2014 · Biophysical Journal
- Protein dynamics in living cells studied by in‐cell NMR spectroscopyConggang Li, Maili Liu · 2013 · FEBS Letters
- Allosteric Effects Govern Nuclear Receptor Action: DNA Appears as a PlayerHinrich Gronemeyer, William Bourguet · 2009 · Science Signaling
- Enzymatic Detoxication, Conformational Selection, and the Role of Molten Globule Active SitesMatthew T. Honaker, Mauro Acchione, Wei Zhang, Bengt Mannervik, William M. Atkins · 2013 · Journal of Biological Chemistry
- The spatial structure of cell signaling systemsRuth Nussinov · 2013 · Physical Biology
- Disordered Binding of Small Molecules to Aβ(12–28)Marino Convertino, Andreas Vitalis, Amedeo Caflisch · 2011 · Journal of Biological Chemistry
- Role of hydration on the functionality of a proteolytic enzyme α-chymotrypsin under crowded environmentPramod Kumar Verma, Surajit Rakshit, Rajib Kumar Mitra, Samir Kumar Pal · 2011 · Biochimie
- Generation and analysis of a protein–protein interface data set with similar chemical and spatial patterns of interactionsShira Mintz, Alexandra Shulman‐Peleg, Haim J. Wolfson, Ruth Nussinov · 2005 · Proteins Structure Function and Bioinformatics
- Fluctuations in ion pairs and their stabilities in proteinsSandeep Kumar, Ruth Nussinov · 2001 · Proteins Structure Function and Bioinformatics
- Predicting the Effect of a Point Mutation on a Protein Fold: The Villin and Advillin Headpieces and Their Pro62Ala MutantsPiana, Stefano, Laio, Alessandro, Marinelli, Fabrizio, Van Troys, Marleen, Bourry, David, Ampe, Christophe, Martins, José C. · 2008 · Journal of Molecular Biology
- Nucleic acid hydration: a volumetric perspectiveTigran V. Chalikian, Robert B. Macgregor · 2006 · Physics of Life Reviews
- Analysis of Nidogen-1/Laminin γ1 Interaction by Cross-Linking, Mass Spectrometry, and Computational Modeling Reveals Multiple Binding ModesPhilip Lössl, Knut Kölbel, Dirk Tänzler · 2014 · PLoS ONE
- The Role of Select Subtype Polymorphisms on HIV-1 Protease Conformational Sampling and DynamicsXi‐Ping Huang, Manuel D. Britto, Jamie L. Kear‐Scott et al. · 2014 · Journal of Biological Chemistry
- The Hydrolysis Activity of Adenosine Triphosphate in Myosin: A Theoretical Analysis of Anomeric Effects and the Nature of the Transition StateYang Yang, Qiang Cui · 2009 · The Journal of Physical Chemistry A
- Exploiting Conformational Ensembles in Modeling Protein–Protein Interactions on the Proteome ScaleKuzu, Guray, Gursoy, Attila, Nussinov, Ruth, Keskin, Ozlem · 2013 · Journal of Proteome Research
- Conformational selection and adaptation to ligand binding in T4 lysozyme cavity mutantsCarlos J. López, Zhongyu Yang, Christian Altenbach · 2013 · Proceedings of the National Academy of Sciences
- A network of molecular switches controls the activation of the two-component response regulator NtrCDan K. Vanatta, Diwakar Shukla, Morgan Lawrenz, Vijay S. Pande · 2015 · Nature Communications
- U2AF65 adapts to diverse pre-mRNA splice sites through conformational selection of specific and promiscuous RNA recognition motifsJermaine L. Jenkins, Anant A. Agrawal, Ankit Gupta · 2013 · Nucleic Acids Research
- Cavity hydration as a gateway to unfolding: An NMR study of hen lysozyme at high pressure and low temperatureKamatari, Yuji O., Smith, Lorna J., Dobson, Christopher M., Akasaka, Kazuyuki · 2011 · Biophysical Chemistry
- Crowding effects on the temperature and pressure dependent structure, stability and folding kinetics of Staphylococcal NucleaseMirko Erlkamp, Sebastian Grobelny, Roland Winter · 2014 · Physical Chemistry Chemical Physics
- Conservation of Side-Chain Dynamics Within a Protein FamilyAnthony B. Law, Ernesto J. Fuentes, Andrew L. Lee · 2009 · Journal of the American Chemical Society
- Free energy landscapes for initiation and branching of protein aggregationWeihua Zheng, Nicholas P. Schafer, Peter Guy Wolynes · 2013 · Proceedings of the National Academy of Sciences
- Single-Molecule Dynamics Reveals Cooperative Binding-Folding in Protein RecognitionJin Wang, Qiang Lu, H. Peter Lu · 2006 · PLoS Computational Biology
- Energy Landscape of the Prion Protein Helix 1 Probed by Metadynamics and NMRCamilloni, Carlo, Schaal, Daniel, Schweimer, Kristian, Schwarzinger, Stephan, De Simone, Alfonso · 2012 · Biophysical Journal
- Druggable Orthosteric and Allosteric Hot Spots to Target Protein-protein InteractionsMa, Buyong, Nussinov, Ruth · 2014 · Current Pharmaceutical Design
- Amino Acid Repeats and the Structure and Evolution of ProteinsM. Mar Albà, Péter Tompa, Reiner A. Veitia · 2007 · KARGER eBooks
- Oligomerization and nanocluster organization render specificityRuth Nussinov, Hyunbum Jang, Chung‐Jung Tsai · 2014 · Biological reviews/Biological reviews of the Cambridge Philosophical Society
- Protein Conformational DynamicsKeli Han, Xin Zhang, Mingjun Yang · 2014 · Advances in experimental medicine and biology
- Identification of an Allosteric Signaling Network within Tec Family KinasesRaji E. Joseph, Qian Xie, Amy Hamilton Andreotti · 2010 · Journal of Molecular Biology
- Distinguishing the Interactions in the Fructose 1,6-Bisphosphate Binding Site of Human Liver Pyruvate Kinase That Contribute to AllosteryArjun Ishwar, Qingling Tang, Aron W. Fenton · 2015 · Biochemistry
- Conformational changes affect binding and catalysis by ester-hydrolysing antibodies 1 1Edited by J. KarnAriel B. Lindner, Zelig Eshhar, Dan S. Tawfik · 1999 · Journal of Molecular Biology
- Constraining Binding Hot Spots: NMR and Molecular Dynamics Simulations Provide a Structural Explanation for Enthalpy−Entropy Compensation in SH2−Ligand BindingJoshua M. Ward, Nina Gorenstein, Jianhua Tian, Stephen F. Martin, Carol Beth Post · 2010 · Journal of the American Chemical Society
- Transcription, translation, degradation, and circadian clockShu Yuan, Honghui Lin · 2004 · Biochemical and Biophysical Research Communications
- Thermally induced structural changes of intrinsically disordered small heat shock protein Hsp22Kazakov, Alexey S., Markov, Denis I., Gusev, Nikolai B., Levitsky, Dmitrii I. · 2009 · Biophysical Chemistry
- Energy Landscape of the Michaelis Complex of Lactate Dehydrogenase: Relationship to Catalytic MechanismHuo‐Lei Peng, Hua Deng, R. Brian Dyer · 2014 · Biochemistry
- Efficient Construction of Mesostate Networks from Molecular Dynamics TrajectoriesAndreas Vitalis, Amedeo Caflisch · 2012 · Journal of Chemical Theory and Computation
- Cavity as a Source of Conformational Fluctuation and High-Energy State: High-Pressure NMR Study of a Cavity-Enlarged Mutant of T4LysozymeAkihiro Maeno, Dan Sindhikara, Fumio Hirata · 2015 · Biophysical Journal
- Dominant Kinetic Paths on Biomolecular Binding-Folding Energy LandscapeJin Wang, Kun Zhang, Hongyang Lu, Erkang Wang · 2006 · Physical Review Letters
- A Pre-equilibrium before Nucleotide Binding Limits Fingers Subdomain Closure by Klentaq1Paul J. Rothwell, Gabriel Waksman · 2007 · Journal of Biological Chemistry
- Molecular crowding and protein enzymatic dynamicsCarlos Echeverría, Raymond Kapral · 2012 · Physical Chemistry Chemical Physics
- Specificity of molecular interactions in transient protein–protein interaction interfacesKyu-Il Cho, KiYoung Lee, Kwang H. Lee, Dongsup Kim, Doheon Lee · 2006 · Proteins Structure Function and Bioinformatics
- Structural ensemble and microscopic elasticity of freely diffusing DNA by direct measurement of fluctuationsShi, Xuesong, Herschlag, Daniel, Harbury, Pehr A. B. · 2013 · Proceedings of the National Academy of Sciences
- Method to Predict Crowding Effects by Postprocessing Molecular Dynamics Trajectories: Application to the Flap Dynamics of HIV-1 ProteaseSanbo Qin, David D. L. Minh, James Andrew McCammon · 2009 · The Journal of Physical Chemistry Letters
- Protein charge and mass contribute to the spatio‐temporal dynamics of protein–protein interactions in a minimal proteomeYu Xu, Hong Wang, Ruth Nussinov, Buyong Ma · 2013 · PROTEOMICS
- Conformational Control of the Binding of the Transactivation Domain of the MLL Protein and c-Myb to the KIX Domain of CREBElif Nihal Korkmaz, Ruth Nussinov, Türkan Haliloǧlu · 2012 · PLoS Computational Biology
- Structure-relaxation mechanism for the response of T4 lysozyme cavity mutants to hydrostatic pressureMichael Lerch, Carlos J. López, Zhongyu Yang, Margaux J. Kreitman, Joseph Horwitz, Wayne L. Hubbell · 2015 · Proceedings of the National Academy of Sciences
- Conformational Dynamics at the Active Site of α-Chymotrypsin and Enzymatic ActivityDebapriya Banerjee, Samir Kumar Pal · 2008 · Langmuir
- Movement of Elongation Factor G between Compact and Extended ConformationsEnea Salsi, Elie N. Farah, Zoe Netter, Jillian Dann, Dmitri N. Ermolenko · 2014 · Journal of Molecular Biology
- Extensive conformational heterogeneity within protein coresBowman, Gregory R., Geissler, Phillip L. · 2014 · The Journal of Physical Chemistry B
- Specialized Dynamical Properties of Promiscuous Residues Revealed by Simulated Conformational EnsemblesArianna Fornili, Alessandro Pandini, Hui‐Chun Lu, Franca Fraternali · 2013 · Journal of Chemical Theory and Computation
- Analysis of Correlations between Energy and Residue Fluctuations in Native Proteins and Determination of Specific Sites for BindingHaliloglu, Turkan, Erman, Burak · 2009 · Physical Review Letters
- Dynamic multiprotein assemblies shape the spatial structure of cell signalingRuth Nussinov, Hyunbum Jang · 2014 · Progress in Biophysics and Molecular Biology
- From a structural average to the conformational ensemble of a DNA bulgeShi, Xuesong, Beauchamp, Kyle A., Harbury, Pehr B., Herschlag, Daniel · 2014 · Proceedings of the National Academy of Sciences
- Dynamics of Protein Kinases: Insights from Nuclear Magnetic ResonanceYao Xiao, Jennifer C. Liddle, Arthur Pardi, Natalie G. Ahn · 2015 · Accounts of Chemical Research
- Conformational Plasticity of an Enzyme during Catalysis: Intricate Coupling between Cyclophilin A Dynamics and Substrate TurnoverLauren C. McGowan, Donald Hamelberg · 2013 · Biophysical Journal
- Specificity and Affinity Quantification of Flexible Recognition from Underlying Energy Landscape TopographyXiakun Chu, Jin Wang · 2014 · PLoS Computational Biology
- How Conformational Flexibility Stabilizes the Hyperthermophilic Elongation Factor G-DomainMaria Kalimeri, Obaidur Rahaman, Simone Melchionna, Fabio Sterpone · 2013 · The Journal of Physical Chemistry B
- An allosteric model for control of pore opening by substrate binding in the E ut L microcompartment shell proteinMichael C. Thompson, Duilio Cascio, D.J. Leibly, Todd O. Yeates · 2015 · Protein Science
- Influence of protein structure databases on the predictive power of statistical pair potentialsEmiko Furuichi, Patrice Koehl · 1998 · Proteins Structure Function and Bioinformatics
- A structural, functional, and computational analysis suggests pore flexibility as the base for the poor selectivity of CNG channelsLuisa M. R. Napolitano, Ina Bisha, Matteo De March, Arin S. Marchesi, Manuel Arcangeletti, Nicola Demitri, Monica Mazzolini, Álex Rodríguez, Alessandra Magistrato, Silvia Onesti et al. · 2015 · Proceedings of the National Academy of Sciences
- Hydrogen‐Exchange Study of the Conformational Stability of Human Carbonic‐Anhydrase B and Its MetallocomplexesPéter Závodszky, J. Johansen, Aase Hvidt · 1975 · European Journal of Biochemistry
- Crystal structure of human platelet phosphofructokinase-1 locked in an activated conformationMarco Kloos, Antje Brüser, Jürgen Kirchberger, Torsten Schöneberg, Norbert Sträter · 2015 · Biochemical Journal
- Gene-specific transcription activation via long-range allosteric shape-shiftingChung‐Jung Tsai, Ruth Nussinov · 2011 · Biochemical Journal
- The role of allostery in the ubiquitin–proteasome systemJin Liu, Ruth Nussinov · 2012 · Critical Reviews in Biochemistry and Molecular Biology
- Probing the Free Energy Landscape of the Fast-Folding gpW Protein by Relaxation Dispersion NMRCelia Sanchez-Medina, Ashok Sekhar, Pramodh Vallurupalli · 2014 · Journal of the American Chemical Society
- Conservation of Flexible Residue Clusters among Structural and Functional Enzyme HomologuesDonald Gagné, Laurie-Anne Charest, Sébastien Morin, Evgenii L. Kovrigin, Nicolas Doucet · 2012 · Journal of Biological Chemistry
- The Cluster of Hydrophobic Residues Controls the Entrance to the Active Site of Choline OxidaseXin, Yao, Gadda, Giovanni, Hamelberg, Donald · 2009 · Biochemistry
- Conformational Events during Ternary Enzyme−Substrate Complex Formation Are Rate Limiting in the Catalytic Cycle of the Light-Driven Enzyme Protochlorophyllide OxidoreductaseDerren J. Heyes, Binuraj R. K. Menon, Michiyo Sakuma · 2008 · Biochemistry
- Comparing interfacial dynamics in protein-protein complexes: an elastic network approachAndrea Zen, Cristian Micheletti, Özlem Keskin, Ruth Nussinov · 2010 · BMC Structural Biology
- Identifying Key Residues for Protein Allostery through Rigid Residue ScanRobert J. B. Kalescky, Jin Liu, Peng Tao · 2014 · The Journal of Physical Chemistry A
- Volumetric Characterization of Tri-N-acetylglucosamine Binding to LysozymeIkbae Son, Yuen Lai Shek, David N. Dubins · 2012 · Biochemistry
- Structural fluctuation of protein in water around its native state: A new statistical mechanics formulationKim, Bongsoo, Hirata, Fumio · 2013 · The Journal of Chemical Physics
- Multi-scale Ensemble Modeling of Modular Proteins with Intrinsically Disordered Linker Regions: Application to p53Terakawa, Tsuyoshi, Higo, Junichi, Takada, Shoji · 2014 · Biophysical Journal
- Comprehensive genome-wide transcription factor analysis reveals that a combination of high affinity and low affinity DNA binding is needed for human gene regulationWang, Junbai, Malecka, Agnieszka, Trøen, Gunhild, Delabie, Jan · 2015 · BMC Genomics
- Structure and Non-Structure of Centrosomal ProteinsDos Santos, Helena G., Abia, David, Janowski, Robert, Mortuza, Gulnahar, Bertero, Michela G., Boutin, Maïlys, Guarín, Nayibe, Méndez-Giraldez, Raúl, Nuñez, Alfonso, Pedrero, Juan G. et al. · 2013 · PLoS ONE
- IntroductionJanin, Joel, Wodak, Shoshana J · 2002 · Advances in Protein Chemistry
- Conformational States of Human Purine Nucleoside Phosphorylase at Rest, at Work, and with Transition State AnaloguesAchelle A. Edwards, Jeremiah D. Tipton, Michael D. Brenowitz, Mark R. Emmett, Alan G. Marshall, Gary B. Evans, Peter C. Tyler, Vern L. Schramm · 2010 · Biochemistry
- Hormone Binding and Co-regulator Binding to the Glucocorticoid Receptor are Allosterically CoupledSamuel J. Pfaff, Robert J. Fletterick · 2010 · Journal of Biological Chemistry
- Determination of the Individual Roles of the Linker Residues in the Interdomain Motions of Calmodulin Using NMR Chemical ShiftsPredrag Kukić, Carlo Camilloni, Andrea Cavalli, Michele Vendruscolo · 2014 · Journal of Molecular Biology
- Protein disorder in the centrosome correlates with complexity in cell types numberGonzalo S. Nido, Raúl Méndez, Alberto Pascual‐García, David Abia, Ugo Bastolla · 2011 · Molecular BioSystems
- Selectivity by Small-Molecule Inhibitors of Protein Interactions Can Be Driven by Protein Surface FluctuationsDavid K. Johnson, John Karanicolas · 2015 · PLoS Computational Biology
- Dynamically Driven Protein Allostery Exhibits Disparate Responses for Fast and Slow MotionsJingjing Guo, Huan‐Xiang Zhou · 2015 · Biophysical Journal
- The Role of Interchain Disulphide Bridges in the Conformational Stability of Human Immunoglobulin G1 SubclassS.Yu. Venyaminov, Éva Rajnavölgyi, György A. MFDGYESI · 1976 · European Journal of Biochemistry
- Direct Observation of T4 Lysozyme Hinge-Bending Motion by Fluorescence Correlation SpectroscopyYirdaw, Robel B., Mchaourab, Hassane S. · 2012 · Biophysical Journal
- Slow Conformational Changes in MutS and DNA Direct Ordered Transitions between Mismatch Search, Recognition and Signaling of DNA RepairAnushi Sharma, Christopher William Doucette, Francis Noah Biro · 2013 · Journal of Molecular Biology
- Enrichment of Druggable Conformations from Apo Protein Structures Using Cosolvent-Accelerated Molecular DynamicsAndrew Kalenkiewicz, Barry J. Grant, Chao‐Yie Yang · 2015 · Biology
- Interactions of Glycine Betaine with Proteins: Insights from Volume and Compressibility MeasurementsYuen Lai Shek, Tigran V. Chalikian · 2013 · Biochemistry
- Equilibrium Conformational Ensemble of the Intrinsically Disordered Peptide n16N: Linking Subdomain Structures and Function in NacreBrown, Aaron H., Rodger, P. Mark, Evans, John Spencer, Walsh, Tiffany R. · 2014 · Biomacromolecules
- A Systematic Study of the Vibrational Free Energies of Polypeptides in Folded and Random StatesBuyong Ma, Chung‐Jung Tsai, Ruth Nussinov · 2000 · Biophysical Journal
- Conformational Changes during Nucleotide Selection by Sulfolobus solfataricus DNA Polymerase Dpo4Robert Lawton Eoff, Raymundo Sánchez-Ponce, Frederick Peter Guengerich · 2009 · Journal of Biological Chemistry
- Why Does Binding of Proteins to DNA or Proteins to Proteins Not Necessarily Spell Function?Buyong Ma, Chung‐Jung Tsai, Yongping Pan, Ruth Nussinov · 2010 · ACS Chemical Biology
- Cooperative DNA Recognition Modulated by an Interplay between Protein-Protein Interactions and DNA-Mediated AllosteryFelipe Merino, Benjamin Bouvier, Vlad Cojocaru · 2015 · PLoS Computational Biology
- Structural dynamics of nucleosomes at single-molecule resolutionChoy, John S., Lee, Tae-Hee · 2012 · Trends in Biochemical Sciences
- Evidence of Conformational Selection Driving the Formation of Ligand Binding Sites in Protein-Protein InterfacesBohnuud, Tanggis, Kozakov, Dima, Vajda, Sandor · 2014 · PLoS Computational Biology
- Finding Order within Disorder: Elucidating the Structure of Proteins Associated with Neurodegenerative DiseaseAustin Huang, Collin M. Stultz · 2009 · Future Medicinal Chemistry
- Intrinsic Domain and Loop Dynamics Commensurate with Catalytic Turnover in an Induced-Fit EnzymeOmar Davulcu, Peter F. Flynn, Michael Stewart Chapman, Jack J. Skalicky · 2009 · Structure
- Disorder in a Target for the Smad2 Mad Homology 2 Domain and Its Implications for Binding and SpecificityP. Andrew Chong, Barish Ozdamar, Jeffrey L. Wrana, Julie Deborah Forman-Kay · 2004 · Journal of Biological Chemistry
- Role of Ordered Proteins in the Folding-Upon-Binding of Intrinsically Disordered ProteinsLawrence, Chad W., Kumar, Sushant, Noid, William G., Showalter, Scott A. · 2014 · The Journal of Physical Chemistry Letters
- Multiple barriers in forced rupture of protein complexesChangbong Hyeon, Dave Thirumalai · 2012 · The Journal of Chemical Physics
- Coupling of protein and environment fluctuationsR.D. Young, Paul W. Fenimore · 2011 · Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics
- Coupled folding and binding with 2D Window‐Exchange Umbrella SamplingAlex Dickson, Logan S. Ahlstrom, Charles L. Brooks · 2015 · Journal of Computational Chemistry
- Structural fluctuation of proteins induced by thermodynamic perturbationFumio Hirata, Kazuyuki Akasaka · 2015 · The Journal of Chemical Physics
- A natural and readily available crowding agent: NMR studies of proteins in hen egg whiteGabriel Martorell, Miquel Adrover, Geoff P. Kelly, Piero Andrea Temussi, Annalisa Pastore · 2010 · Proteins Structure Function and Bioinformatics
- Statistical mechanics of protein allostery: Roles of backbone and side-chain structural fluctuationsKazuhito Itoh, Masaki Sasai · 2011 · The Journal of Chemical Physics
- Protein dynamics at Eph receptor-ligand interfaces as revealed by crystallography, NMR and MD simulationsQin, Haina, Lim, Liangzhong, Song, Jianxing · 2012 · BMC Biophysics
- Dynamical Phase Transitions Reveal Amyloid-like States on Protein Folding LandscapesJeffrey K. Weber, Robert L. Jack, Christian R. Schwantes, Vijay S. Pande · 2014 · Biophysical Journal
- The Cell as a Thermostat: How Much does it Know?Dennis Bray · 2011 · Advances in experimental medicine and biology
- Estimation of Interdomain Flexibility of N-Terminus of Factor H Using Residual Dipolar CouplingsMateusz Maciejewski, Nico Tjandra, Paul Nigel Barlow · 2011 · Biochemistry
- Allosteric Dynamic Control of BindingFidan Sumbul, Saliha Ece Acuner, Türkan Haliloǧlu · 2015 · Biophysical Journal
- Conformational Heterogeneity Within the LID Domain Mediates Substrate Binding to Escherichia coli Adenylate Kinase: Function Follows FluctuationsTravis Parke Schrank, James O. Wrabl, Vincent J. Hilser · 2013 · Topics in current chemistry
- A Conformational Ensemble Derived Using NMR Methyl Chemical Shifts Reveals a Mechanical Clamping Transition That Gates the Binding of the HU Protein to DNAArvind Kannan, Carlo Camilloni, Aleksandr B. Sahakyan · 2013 · Journal of the American Chemical Society
- Dynamics and the Free-Energy Landscape of Proteins, Explored with the Mössbauer Effect and Quasi-Elastic Neutron ScatteringHans Frauenfelder, Robert Young, Paul W. Fenimore · 2013 · The Journal of Physical Chemistry B
- Comparison of native and non-native ubiquitin oligomers reveals analogous structures and reactivitiesPham, Grace H., Rana, Ambar S. J. B., Korkmaz, E. Nihal, Trang, Vivian H., Cui, Qiang, Strieter, Eric R. · 2016 · Protein Science
- Inclusion of the orientational entropic effect and low‐resolution experimental information for protein–protein docking in Critical Assessment of PRedicted Interactions (CAPRI)Sheng‐You Huang, Chengfei Yan, Sam Z. Grinter, Shan Chang, Lin Jiang, Xiaoqin Zou · 2013 · Proteins Structure Function and Bioinformatics
- Reconciling the lock‐and‐key and dynamic views of canonical serine protease inhibitor actionGáspári, Zoltán, Várnai, Péter, Szappanos, Balázs, Perczel, András · 2010 · FEBS Letters
- ATP turnover by individual myosin molecules hints at two conformers of the myosin active siteAmrute-Nayak, Mamta, Lambeck, Katharina-Antonia, Radocaj, Ante, Huhnt, Helen Elisabeth, Scholz, Tim, Hahn, Nils, Tsiavaliaris, Georgios, Walter, Wilhelm J., Brenner, Bernhard · 2014 · Proceedings of the National Academy of Sciences
- Correlated Inter-Domain Motions in Adenylate KinaseSanti Esteban-Martín, Robert Bryn Fenwick, Jörgen Ådén · 2014 · PLoS Computational Biology
- Activation of the West Nile virus NS3 protease: Molecular dynamics evidence for a conformational selection mechanismDariusz Ekonomiuk, Amedeo Caflisch · 2009 · Protein Science
- Resolving anisotropic distributions of correlated vibrational motion in protein hydration waterMatthias Heyden · 2014 · The Journal of Chemical Physics
- Characterization of Protein Flexibility Using Small-Angle X-Ray Scattering and Amplified Collective Motion SimulationsWen, Bin, Peng, Junhui, Zuo, Xiaobing, Gong, Qingguo, Zhang, Zhiyong · 2014 · Biophysical Journal
- Network of long‐range concerted chemical shift displacements upon ligand binding to human angiogeninDonald Gagné, Chitra Narayanan, Nicolas Doucet · 2014 · Protein Science
- Binding Free Energy Landscape of Domain-Peptide InteractionsIskra Staneva, Stefan Wallin · 2011 · PLoS Computational Biology
- According to current textbooks, a well-defined three-dimensional structure is a prerequisite for the function of a protein. Is this correct?H. Jane Dyson, Peter E. Wright · 2006 · IUBMB Life
- Molecular Basis for the pH Dependent Structural Transition of Nitrophorin 4Marcelo Adrian Marti, Dario Ariel Estrin, Adrián E. Roitberg · 2009 · The Journal of Physical Chemistry B
- Interactions of Urea with Native and Unfolded Proteins: A Volumetric StudyIkbae Son, Yuen Lai Shek, Anna Tikhomirova · 2014 · The Journal of Physical Chemistry B
- Cyclophilin A Inhibition: Targeting Transition-State-Bound Enzyme Conformations for Structure-Based Drug DesignNagaraju, Mulpuri, McGowan, Lauren C., Hamelberg, Donald · 2013 · Journal of Chemical Information and Modeling
- Ligand-Receptor Affinities Computed by an Adapted Linear Interaction Model for Continuum Electrostatics and by Protein Conformational AveragingAriane Nunes-Alves, G. M. Arantes · 2014 · Journal of Chemical Information and Modeling
- Allosteric modulators can restore function in an amino acid neurotransmitter receptor by slightly altering intra‐molecular communication pathwaysRuth Nussinov · 2011 · British Journal of Pharmacology
- Volume and Compressibility of ProteinsKunihiko Gekko · 2015 · Sub-cellular biochemistry/Subcellular biochemistry
- Unique Structure and Dynamics of the EphA5 Ligand Binding Domain Mediate Its Binding Specificity as Revealed by X-ray Crystallography, NMR and MD SimulationsHuan, Xuelu, Shi, Jiahai, Lim, Liangzhong, Mitra, Sayantan, Zhu, Wanlong, Qin, Haina, Pasquale, Elena B., Song, Jianxing · 2013 · PLoS ONE
- Promiscuity in protein‐RNA interactions: Conformational ensembles facilitate molecular recognition in the spliceosomeDavid D. Boehr · 2011 · BioEssays
- Multiple‐Targeting and Conformational Selection in the Estrogen Receptor: Computation and ExperimentPeng Yuan, Kaiwei Liang, Buyong Ma, Nan Zheng, Ruth Nussinov, Jian Huang · 2011 · Chemical Biology & Drug Design
- Flipping a SwitchMatthias Buck, Michael K. Rosen · 2001 · Science
- Allostery and Conformational Dynamics in cAMP-binding AcyltransferasesMarjetka Podobnik, Nida Siddiqui, Katja Rebolj · 2014 · Journal of Biological Chemistry
- A Broad Range of Conformations Contribute to the Solution Ensemble of the Essential Splicing Factor U2AF65Jermaine L. Jenkins, Kholiswa M. Laird, Clara L. Kielkopf · 2012 · Biochemistry
- Intersubunit coordination and cooperativity in ring-shaped NTPasesRyota Iino, Hiroyuki Noji · 2013 · Current Opinion in Structural Biology
- Lengthening the Intersubunit Linker of Procaspase 3 Leads to Constitutive ActivationMacKenzie, Sarah H., Schipper, Joshua L., England, Erika J., Thomas, Melvin E., Blackburn, Kevin, Swartz, Paul, Clark, A. Clay · 2013 · Biochemistry
- Ultrasonic and Densimetric Characterization of the Association of Cyclic AMP with the cAMP-Binding Domain of the Exchange Protein EPAC1Ikbae Son, Rajeevan Selvaratnam, David N. Dubins, Giuseppe Melacini, Tigran V. Chalikian · 2013 · The Journal of Physical Chemistry B
- The histone H3 N-terminal tail: a computational analysis of the free energy landscape and kineticsYuqing Zheng, Qiang Cui · 2015 · Physical Chemistry Chemical Physics
- Comparative Laboratory Evolution of Ordered and Disordered EnzymesCindy Schulenburg, Yvonne Stark, Matthias Künzle · 2015 · Journal of Biological Chemistry
- Volumetric Characterization of Tri-N-Acetylglucosamine Binding to LysozymeIkbae Son, Yuen Lai Shek, David N. Dubins · 2013 · Biophysical Journal
- Analysis of conformational motions and related key residue interactions responsible for a specific function of proteins with elastic network modelJi Guo Su, Xiao Ming Han, Xiao Zhang, Yan Xue Hou, Jian Zhuo Zhu, Yi Dong Wu · 2015 · Journal of Biomolecular Structure and Dynamics
- Thermodynamic Stability and Flexibility Characteristics of Antibody Fragment ComplexesLi, Tong, Verma, Deeptak, Tracka, Malgorzata, Casas-Finet, Jose, Livesay, Dennis, Jacobs, Donald · 2013 · Protein & Peptide Letters
- Ensemble‐Averaged QM/MM Kinetic Isotope Effects for the SN2 Reaction of Cyanide Anions with Chloroethane in DMSO SolutionJ. Javier Ruiz‐Pernía, Ian H. Williams · 2012 · Chemistry - A European Journal
- Simulation of the activation of α‐chymotrypsin: Analysis of the pathway and role of the propeptideJanka Mátrai, Gert Verheyden, Peter Krüger · 2004 · Protein Science
- PeptiSite: A structural database of peptide binding sites in 4DChayan Acharya, Irina Kufareva, Andrey V. Ilatovskiy, Ruben A Abagyan · 2014 · Biochemical and Biophysical Research Communications
- Structural Basis for the Regulation of the Mitogen-activated Protein (MAP) Kinase p38α by the Dual Specificity Phosphatase 16 MAP Kinase Binding Domain in SolutionKumar, Ganesan Senthil, Zettl, Heiko, Page, Rebecca, Peti, Wolfgang · 2013 · Journal of Biological Chemistry
- A Direct Coupling between Global and Internal Motions in a Single Domain Protein? MD Investigation of Extreme ScenariosMehdi Bagheri Hamaneh, Liqun Zhang, Matthias Buck · 2011 · Biophysical Journal
- The β-Strand-Loop-β-Strand Conformation Is Marginally Populated in β2-Microglobulin (20–41) Peptide in Solution as Revealed by Replica Exchange Molecular Dynamics SimulationsChungwen Liang, Philippe Derreumaux, Normand Mousseau, Guanghong Wei · 2008 · Biophysical Journal
- ReFlexIn: A Flexible Receptor Protein-Ligand Docking Scheme Evaluated on HIV-1 ProteaseSimon Leis, Martin Zacharias · 2012 · PLoS ONE
- Energy landscape and dynamics of proteins: An exact analysis of a simplified lattice modelMarek Cieplak, Jayanth R. Banavar · 2013 · Physical Review E
- Investigation of the interactions between the EphB2 receptor and SNEW peptide variantsMa, Buyong, Kolb, Stephanie, Diprima, Michael, Karna, Molleshree, Tosato, Giovanna, Yang, Qiqi, Huang, Qiang, Nussinov, Ruth · 2014 · Growth Factors
- Thermodynamic, Dynamic and Solvational Properties of PDEδ Binding to Farnesylated Cystein: A Model Study for Uncovering the Molecular Mechanism of PDEδ Interaction with Prenylated ProteinsSaba Suladze, Shehab Ismail, Roland Winter · 2014 · The Journal of Physical Chemistry B
- Conformational flexibility of loops of myosin enhances the global bias in the actin–myosin interaction landscapeQingmiao Nie, Masaki Sasai, Tomoki P. Terada · 2014 · Physical Chemistry Chemical Physics
- Emergence of structure through protein–protein interactions and pH changes in dually predicted coiled-coil and disordered regions of centrosomal proteinsMiguel Á. Treviño, María Flor García‐Mayoral, María Angeles Jiménez, Ugo Bastolla, Marta Bruix · 2014 · Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics
- Determination of the Individual Roles of the Linker Residues in the Inter-Domain Motions of Calmodulin using NMR Chemical ShiftsPredrag Kukić, Carlo Camilloni, Andrea Cavalli, Michele Vendruscolo · 2014 · Biophysical Journal
- A conformation‐equilibrium model captures ligand–ligand interactions and ligand‐biased signalling by G ‐protein coupled receptorsSusanne Roth, Frank J. Bruggeman · 2014 · FEBS Journal
- Bioinformatics Study of Cancer-Related Mutations within p53 Phosphorylation Site MotifsXiaona Ji, Qiang Huang, Long Yu, Ruth Nussinov, Buyong Ma · 2014 · International Journal of Molecular Sciences
- Stochastic Ensembles, Conformationally Adaptive Teamwork, and Enzymatic DetoxificationWilliam M. Atkins, Hong Qian · 2011 · Biochemistry
- Effective Temperature of MutationsImre Derényi, Gergely J. Szöllősi · 2015 · Physical Review Letters
- The Predicted Ensemble of Low‐Energy Conformations of Human Somatostatin Receptor Subtype 5 and the Binding of AntagonistsSijia S. Dong, Ravinder Abrol, William A. Goddard · 2015 · ChemMedChem
- Multiscale computational methods for mapping conformational ensembles of G-protein-coupled receptorsNagarajan Vaidehi, S. Bhattacharya · 2011 · Advances in protein chemistry and structural biology
- Single-Molecule FRET Reveals Hidden Complexity in a Protein Energy LandscapeMaksym Tsytlonok, Shehu Ibrahim, Pamela J. E. Rowling · 2015 · Structure
- Sparse networks of directly coupled, polymorphic, and functional side chains in allosteric proteinsLaleh Soltan Ghoraie, Forbes J. Burkowski, Mu Zhu · 2014 · Proteins Structure Function and Bioinformatics
- Entropy of a network ensemble: definitions and applications to genomic data.Giulia Menichetti, Daniel Remondini · 2014 · PubMed
- Method for identification of rigid domains and hinge residues in proteins based on exhaustive enumerationJaehyun Sim, Jun Gyu Sim, Eunsung Park · 2015 · Proteins Structure Function and Bioinformatics
- Exploration of the activation pathway of Δα-Chymotrypsin with molecular dynamics simulations and correlation with kinetic experimentsJanka Mátrai, Abel Jonckheer, Eddy Joris · 2008 · European Biophysics Journal
- Basic Equations in Statics and Kinetics of Protein Polymerization and the Mechanism of the Formation and Dissociation of Amyloid Fibrils Revealed by Pressure PerturbationHideki Tachibana · 2015 · Sub-cellular biochemistry/Subcellular biochemistry
- Computational prediction of hinge axes in proteinsRittika Shamsuddin, Milka Doktorova, Sheila S. Jaswal · 2014 · BMC Bioinformatics
- Dynamic regulation on energy landscape evolution of single-molecule protein by conformational fluctuationChien Yu Lin, Jung Yaw Huang, Leu‐Wei Lo · 2012 · Physical Review E