Cited by 546Protein Structure and DynamicsAdvanced NMR Techniques and ApplicationsDiffusion and Search Dynamics

The DOI matches its Crossref record; 30 of the 30 references it cites were found in a registry or an index.

Protein activity regulation by conformational entropy

Tzeng, Shiou-Ru, Kalodimos, Charalampos G.·2012·Nature

Open this paper in CoChat — free account

Abstract

How the interplay between protein structure and internal dynamics regulates protein function is poorly understood. Often, ligand binding, post-translational modifications and mutations modify protein activity in a manner that is not possible to rationalize solely on the basis of structural data. It is likely that changes in the internal motions of proteins have a major role in regulating protein activity, but the nature of their contributions remains elusive, especially in quantitative terms. Here we show that changes in conformational entropy can determine whether protein-ligand interactions will occur, even among protein complexes with identical binding interfaces. We have used NMR spectroscopy to determine the changes in structure and internal dynamics that are elicited by the binding of DNA to several variants of the catabolite activator protein (CAP) that differentially populate the inactive and active DNA-binding domain states. We found that the CAP variants have markedly different affinities for DNA, despite the CAP−DNA-binding interfaces being essentially identical in the various complexes. Combined with thermodynamic data, the results show that conformational entropy changes can inhibit the binding of CAP variants that are structurally poised for optimal DNA binding or can stimulate the binding activity of CAP variants that only transiently populate the DNA-binding-domain active state. Collectively, the data show how changes in fast internal dynamics (conformational…

Integrity signals

Registry

Crossref · 10.1038/nature11271

Cites

30 of 30 references verified0 citation errors · 0 not checkable

Statistics

Recomputing p-values needs the paper’s full text.

Claims the paper makes

This paper’s full text isn’t openly available, so its claims and self-check weren’t run. The registry and citation checks still apply.

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

Dynamic personalities of proteins
Henzler-Wildman, K., & Kern, D. (2007) · Nature · doi:10.1038/nature06522 · Cited by 2,545
The role of dynamic conformational ensembles in biomolecular recognition
Boehr, D. D., Nussinov, R., & Wright, P. E. (2009) · Nature Chemical Biology · doi:10.1038/nchembio.232 · Cited by 2,008
Win some, lose some: enthalpy-entropy compensation in weak intermolecular interactions
Dunitz, J. D. (1995) · Chemistry & Biology · doi:10.1016/1074-5521(95)90097-7 · Cited by 665
Conformational entropy in molecular recognition by proteins
Frederick, K. K., Marlow, M. S., Valentine, K. G., & Wand, A. J. (2007) · Nature · doi:10.1038/nature05959 · Cited by 663
Dynamically driven protein allostery
Popovych, N., Sun, S., Ebright, R. H., & Kalodimos, C. G. (2006) · Nature Structural & Molecular Biology · doi:10.1038/nsmb1132 · Cited by 637
Binding of Small-Molecule Ligands to Proteins: “What You See” Is Not Always “What You Get”
Mobley, D. L., & Dill, K. A. (2009) · Structure · doi:10.1016/j.str.2009.02.010 · Cited by 598
Two-State Allosteric Behavior in a Single-Domain Signaling Protein
Volkman, B. F., Lipson, D., Wemmer, D. E., & Kern, D. (2001) · Science · doi:10.1126/science.291.5512.2429 · Cited by 594
Protein dynamics from NMR.
Ishima, R., & Torchia, D. A. (2000) · Nature Structural Biology · doi:10.1038/78963 · Cited by 530
Contributions to Conformational Entropy Arising from Bond Vector Fluctuations Measured from NMR-Derived Order Parameters: Application to Protein Folding
Yang, D., & Kay, L. E. (1996) · Journal of Molecular Biology · doi:10.1006/jmbi.1996.0581 · Cited by 459
NMR spectroscopy brings invisible protein states into focus
Baldwin, A. J., & Kay, L. E. (2009) · Nature Chemical Biology · doi:10.1038/nchembio.238 · Cited by 436

Show all 30 references

Sorted by citations

Items 401–500 of 546

DNA Electric Charge Oscillations Govern Protein–DNA Recognition
Štěpánek, J., Kopecký, V., Turpin, P., Li, Z., Alpert, B., & Zentz, C. (2015) · PLoS ONE · doi:10.1371/journal.pone.0124444 · Cited by 5
The multi-facet aspects of cell sentience and their relevance for the integrative brain actions: role of membrane protein energy landscape
Agnati, L. F., Marcoli, M., Maura, G., Fuxé, K., & Guidolin, D. (2016) · Reviews in the Neurosciences · doi:10.1515/revneuro-2015-0049 · Cited by 5
Conformational Dynamics Govern the Free-Energy Landscape of a Membrane-Interacting Protein
Frotscher, E., Krainer, G., Hartmann, A. J., Schlierf, M., & Keller, S. (2018) · ACS Omega · doi:10.1021/acsomega.8b01609 · Cited by 4
Biochemistry & Physiology: Open Access
(2019) · Biochemistry & Physiology Open Access · doi:10.4172/2168-9652 · Cited by 5
LSP-MD: A Fast Computational Method to Study Allostery Driven by Thermal Vibrations
Kornev, A. P. (2025) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.5c01094 · Cited by 4
Spectroscopic methods to study the thermodynamics of biomolecular interactions
Bharti, & Nair, M. S. (2022) · Elsevier eBooks · doi:10.1016/b978-0-323-99127-8.00001-5 · Cited by 4
Computational modeling studies reveal the origin of the binding preference of 3‐(3,4‐di hydroisoquinolin‐2( 1H )‐ylsulfonyl)benzoic acids for AKR1C3 over its isoforms
Kong, X., Xing, E., Wu, S., Zhuang, T., Li, P., Li, C., & Cheng, X. (2022) · Protein Science · doi:10.1002/pro.4499 · Cited by 4
Thermal Responses and the Energy Spectral of Diatomic Molecules Using Nikiforov–Uvarov Methodology
Roshanzamir, M. (2023) · Mathematics · doi:10.3390/math11153338 · Cited by 4
Computational Studies of Allosteric Regulation in the Hsp90 Molecular Chaperone: From Functional Dynamics and Protein Structure Networks to Allosteric Communications and Targeted Anti‐Cancer Modulators
Verkhivker, G. M. (2014) · Israel Journal of Chemistry · doi:10.1002/ijch.201300143 · Cited by 4
Elucidating the energetic contributions to the binding free energy
Ahmad, M., Helms, V., Kalinina, O. V., & Lengauer, T. (2017) · The Journal of Chemical Physics · doi:10.1063/1.4973349 · Cited by 4
Deciphering Conformational Changes Associated with the Maturation of Thrombin Anion Binding Exosite I
Billur, R., Ban, D., Sabo, T. M., & Maurer, M. C. (2017) · Biochemistry · doi:10.1021/acs.biochem.7b00970 · Cited by 4
Thermodynamics of Protein-Ligand Binding
Khatri, K. S., Modi, P., Sharma, S., & Deep, S. (2020) · Springer eBooks · doi:10.1007/978-981-15-5530-5_7 · Cited by 4
Reversible regulation of esterase activity via host–guest molecular recognition at the nanoparticle surface
Pahwa, M., Sharma, M., Meethal, S. K., & Agasti, S. S. (2020) · Bulletin of Materials Science · doi:10.1007/s12034-020-02165-9 · Cited by 4
Eigenvalues and thermal properties of the A1Σu+ state of sodium dimers
Horchani, R., Sulaiman, N., & Shafii, S. A. (2022) · Molecular Physics · doi:10.1080/00268976.2022.2046194 · Cited by 4
The Archaeal Exosome: Identification and Quantification of Site‐Specific Motions That Correlate with Cap and RNA Binding
Audin, M., Dorn, G., Fromm, S. A., Reiß, K., Schütz, S., Vorländer, M. K., & Sprangers, R. (2013) · Angewandte Chemie · doi:10.1002/ange.201302811 · Cited by 4
Computer‐Aided Discovery of Potent Broad‐Spectrum Vaccine Adjuvants
Ma, J., Wang, S., Zhao, C., Yan, X., Ren, Q., Dong, Z., Qiu, J., Liu, Y., Shan, Q., Xu, M., et al. (2023) · Angewandte Chemie · doi:10.1002/ange.202301059 · Cited by 4
Theoretical investigation of functional responses of bio-molecular assembly networks
Gautam, P., & Sinha, S. K. (2023) · Soft Matter · doi:10.1039/d2sm01530g · Cited by 4
NMR Shows Why a Small Chemical Change Almost Abolishes the Antimicrobial Activity of Glycocin F
Harjes, E., Edwards, P. J. B., Bisset, S. W., Patchett, M. L., Jameson, G. B., Yang, S., Navo, C. D., Harris, P. W. R., Brimble, M. A., & Norris, G. E. (2023) · Biochemistry · doi:10.1021/acs.biochem.3c00197 · Cited by 4
Directional Selection Precedes Conformational Selection in Ubiquitin–UIM Binding
Long, D., & Brüschweiler, R. (2013) · Angewandte Chemie International Edition · doi:10.1002/anie.201208683 · Cited by 4
Crystallographic Ensembles Reveal the Structural Basis of Binding Entropy in SARS-CoV2 MacrodomainPreprint
Seo, L., Farran, I., Aslam, A., Li, X., Jaishankar, P., Ashworth, A., Fraser, J. S., Renslo, A. R., & Wankowicz, S. A. M. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.11.25.690589 · Cited by 4
Lowering Entropic Barriers in Triplex DNA Switches Facilitating Biomedical Applications at Physiological pH
Lei, Y., Li, C., Ji, X., Sun, H., Liu, X., Mao, Z., Chen, W., Qing, Z., & Liu, J. (2024) · Angewandte Chemie · doi:10.1002/ange.202402123 · Cited by 3
Dynamic protein interactions probed by NMR spectroscopy
Lee, J., & Lee, J. H. (2025) · Bulletin of the Korean Chemical Society · doi:10.1002/bkcs.70036 · Cited by 3
Molecular mechanism by which SARS-CoV-2 Orf9b suppresses the Tom70-Hsp90 interaction to evade innate immunity
Sherer, N., Bastiray, A., Chen, X., Molugu, T. R., Yadav, G. P., Igumenova, T. I., & Cho, J. (2026) · Science Advances · doi:10.1126/sciadv.aee5276 · Cited by 9
Development and validation of signature peptide-based isotope dilution liquid chromatography-mass spectrometry for bovine lactoferrin purity assessment
Yan, J., Yang, M., Wang, M., Han, Y., Zhou, J. F., Ma, Y., Wang, T., & Li, L. (2024) · Microchemical Journal · doi:10.1016/j.microc.2024.112458 · Cited by 3
Protein Dynamics at the Heart of Chaperone Function: Insights from Solution NMR
Ge, P., Dai, L., Kalodimos, C. G., & Huang, C. (2025) · Journal of Molecular Biology · doi:10.1016/j.jmb.2025.169377 · Cited by 4
A Semiautomated Assignment Protocol for Methyl Group Side Chains in Large Proteins
Kim, J., Wang, Y., Li, G., & Veglia, G. (2015) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/bs.mie.2015.08.033 · Cited by 3
Ligand-Induced Protein Mobility in Complexes of Carbonic Anhydrase II and Benzenesulfonamides with Oligoglycine Chains
Krishnamurthy, V. M., Raman, V. S., Mowery, R. A., Hentz, M., Baleja, J., Shaw, B. F., & Kumar, K. (2013) · PLoS ONE · doi:10.1371/journal.pone.0057629 · Cited by 3
Thermodynamic perspective of protein disorder and phase separation: model systems
Workman, R. J., Drake, J. A., & Pettitt, B. M. (2022) · Elsevier eBooks · doi:10.1016/b978-0-323-99533-7.00015-7 · Cited by 3
A parameterized two-domain thermodynamic model explains diverse mutational effects on protein allostery
Liu, Z., Gillis, T., Raman, S., & Cui, Q. (2023) · eLife · doi:10.7554/elife.92262 · Cited by 12
Kinematic Vibrational Entropy Assessment and Analysis of SARS CoV-2 Main Protease
Chen, X., Leyendecker, S., & Bedem, H. V. D. (2022) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.2c00126 · Cited by 3
Structural versus energetic approaches for protein conformational entropy
Chong, S., & Ham, S. (2015) · Chemical Physics Letters · doi:10.1016/j.cplett.2015.03.047 · Cited by 3
Conformational diversity of bacterial FabH: Implications for molecular recognition specificity
Mittal, A., & Johnson, M. E. (2014) · Journal of Molecular Graphics and Modelling · doi:10.1016/j.jmgm.2014.11.004 · Cited by 3
Prediction of thermodynamic instabilities of protein solutions from simple protein–protein interactions
D’Agostino, T., Solana, J. R., & Emanuele, A. (2013) · Chemical Physics · doi:10.1016/j.chemphys.2013.01.041 · Cited by 3
Understanding the Role of Conformational Dynamics in Protein-Ligand Interactions Using NMR Relaxation Methods
Ertekin, A., & Massi, F. (2014) · Wiley eBooks · doi:10.1002/9780470034590.emrstm1363 · Cited by 3
Coping with Complexity in Molecular Design
Hann, M. M., & Leach, A. R. (2013) · doi:10.1002/9783527677016.ch2 · Cited by 3
Probing the toxic interactions between the reactive dye Drimaren Red and Human Serum AlbuminPreprint
Menezes, T. M., Assis, C. R. D., Neto, A. M. D. S., Gubert, P., Ghislandi, M. G., & Neves, J. L. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.07.17.452798 · Cited by 3
Sparse networks of conformational fluctuations communicate signals within proteinsPreprint
Trenfield, K., & Lin, M. M. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.05.28.656549 · Cited by 3
Tuning the affinity of probes with transmembrane proteins by constructing peptide-conjugated cis / trans isomers based on molecular scaffolds
Hu, J., Yang, J., Liu, Y., Lu, G., Zhao, Z., Xia, F., & Lou, X. (2024) · Journal of Materials Chemistry B · doi:10.1039/d4tb01801j · Cited by 2
Theoretical study on the conformation-dependent charge transfer of the excited state of dopamine
An, H., Asiya, Yaermaimaiti, G., Abulimiti, B., Xiang, M., & Wang, X. (2025) · Heliyon · doi:10.1016/j.heliyon.2025.e42058 · Cited by 2
Enthalpy driven temperature-sensitive conformational changes in a metamorphic protein involved in the cyanobacterial circadian clock
Ma, B., Ma, Z., & Zhang, N. (2025) · International Journal of Biological Macromolecules · doi:10.1016/j.ijbiomac.2025.140360 · Cited by 2
Dynamic networks connect the USP14 active site region with the proteasome interaction surface
Salomonsson, J., Sjöstrand, L., Eskilson, A., Derbyshire, D. J., D’Arcy, P., Sunnerhagen, M., & Ahlner, A. (2025) · Protein Science · doi:10.1002/pro.70077 · Cited by 2
Dynamics of single enzymes confined inside a nanopore
Galenkamp, N. S., van den Noort, M., & Maglia, G. (2025) · RSC Chemical Biology · doi:10.1039/d5cb00149h · Cited by 5
Selective control of ligand binding through a distal mutation that alters the protein native ensemble
Dani, R., Kurbah, I., Chaurasiya, D. K., Nath, R., Krishnan, A., Fushman, D., & Naganathan, A. N. (2026) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2519658123 · Cited by 1
Exploring the Role of Conformational Heterogeneity in cis -Autoproteolytic Activation of ThnT
Buller, A. R., Freeman, M. F., Schildbach, J. F., & Townsend, C. A. (2014) · Biochemistry · doi:10.1021/bi500385d · Cited by 2
Identification of nitrile-containing isoquinoline-related natural product derivatives as coronavirus entry inhibitors in silico and in vitro
Shahhamzehei, N., Abdelfatah, S., Sperber, H. S., Sutter, K., Yücer, R., Bringmann, G., Schwarzer, R., & Efferth, T. (2024) · Biomedicine & Pharmacotherapy · doi:10.1016/j.biopha.2024.117517 · Cited by 2
Mechanical prions as self-assembling microstructures
Ouellet, M., Bassett, D. S., Bassett, L. C., Murphy, K., & Patankar, S. P. (2025) · Newton · doi:10.1016/j.newton.2025.100098 · Cited by 2
A Novel Detection Scheme for High-Resolution Two-Dimensional Spin-Echo Correlated Spectra in Inhomogeneous Fields
Huang, Y., Zhang, Z., Cai, S., & Chen, Z. (2014) · PLoS ONE · doi:10.1371/journal.pone.0084032 · Cited by 2
Fusion with Anticodon Binding Domain of GluRS is Not Sufficient to Alter the Substrate Specificity of a Chimeric Glu-Q-RS
Ray, S., Blaise, M., Roy, B., Ghosh, S., Kern, D., & Banerjee, R. (2013) · The Protein Journal · doi:10.1007/s10930-013-9537-7 · Cited by 2
Unraveling Entropic Rate Acceleration Induced by Solvent Dynamics in Membrane Enzymes
Kürten, C., & Syrén, P. (2016) · Journal of Visualized Experiments · doi:10.3791/53168 · Cited by 2
Resolving Internal Motional Correlations to Complete the Conformational Entropy Meter
Urbančič, I., Ljubetič, A., & Štrancar, J. (2014) · The Journal of Physical Chemistry Letters · doi:10.1021/jz5020828 · Cited by 2
Minimization-Aware Recursive $$K^{*}$$ K ∗ ( $${ MARK}^{*}$$ MARK ∗ ): A Novel, Provable Algorithm that Accelerates Ensemble-Based Protein Design and Provably Approximates the Energy Landscape
Jou, J., Holt, G. T., Lowegard, A. U., & Donald, B. R. (2019) · Lecture notes in computer science · doi:10.1007/978-3-030-17083-7_7 · Cited by 2
Engineering the Active Site Lid Dynamics to Improve the Catalytic Efficiency of Yeast Cytosine Deaminase
Deng, H., Qin, M., Liu, Z., Yang, Y., Wang, Y., & Yao, L. (2023) · International Journal of Molecular Sciences · doi:10.3390/ijms24076592 · Cited by 2
New insight on the S100A1–STIP1 complex highlights the important relationship between allostery and entropy in protein function
Nucci, N. V. (2017) · Biochemical Journal · doi:10.1042/bcj20170275 · Cited by 2
Ligand Strain and Its Conformational Complexity Is a Major Factor in the Binding of Cyclic Dinucleotides to STING Protein
Smola, M., Gutten, O., Dejmek, M., Kožíšek, M., Evangelidis, T., Tehrani, Z. A., Novotná, B., Nencka, R., Birkuš, G., Rulı́šek, L., et al. (2021) · Angewandte Chemie · doi:10.1002/ange.202016805 · Cited by 3
How much entropy is contained in NMR relaxation parameters?Preprint
Hoffmann, F., Mulder, F. A. A., & Schäfer, L. V. (2021) · doi:10.33774/chemrxiv-2021-l686w-v2 · Cited by 2
How much entropy is contained in NMR relaxation parameters?Preprint
Hoffmann, F., Mulder, F. A. A., & Schäfer, L. V. (2021) · doi:10.33774/chemrxiv-2021-l686w · Cited by 2
Making sense of chaos: uncovering the mechanisms of conformational entropyPreprint
Wankowicz, S. A. M., & Fraser, J. S. (2023) · ChemRxiv · doi:10.26434/chemrxiv-2023-9b5k7 · Cited by 3
Double and triple thermodynamic mutant cycles reveal the basis for specific MsbA-lipid interactionsPreprint
Lyu, J., Zhang, T., Marty, M. T., Clemmer, D. E., Russell, D. H., & Laganowsky, A. D. (2024) · eLife · doi:10.7554/elife.91094.2 · Cited by 2
Making sense of chaos: uncovering the mechanisms of conformational entropyPreprint
Wankowicz, S. A. M., & Fraser, J. S. (2024) · ChemRxiv · doi:10.26434/chemrxiv-2023-9b5k7-v2 · Cited by 1
The Speed of Allosteric Signaling Within a Single-Domain Protein
Božović, O., Ruf, J., Zanobini, C., Janković, B. G., Buhrke, D., Johnson, P. J. M., & Hamm, P. M. (2021) · The Journal of Physical Chemistry Letters · doi:10.1021/acs.jpclett.1c00915 · Cited by 28
Conformational and vibrational contributions to configurational entropy change of a flexible peptide ligand upon binding: The role of higher-order correlations between backbone and side-chains
Kalathingal, M., & Rhee, Y. M. (2024) · Chemical Physics Letters · doi:10.1016/j.cplett.2024.141827 · Cited by 1
How protein disorder turns internal dynamics into a long-range regulatory switch
(2025) · Nature Structural & Molecular Biology · doi:10.1038/s41594-025-01588-4 · Cited by 1
From biophysical interaction to structural modeling: bi-terminal G and TGS domains drive rice OsYchF1-OsGAP1 complex formation
Huang, S., Wu, Z., Wang, K., Liao, Y., Zeng, J., & Miao, R. (2025) · Botanical studies · doi:10.1186/s40529-025-00480-0 · Cited by 2
An Integrative Biophysical and Computational Workflow Uncovers New Allosteric Sites and Modulators of the Human A 2A Adenosine Receptor
Prudent, R., Ray, A. P., Thakur, N., Moréno, A., Tandarić, T., Kanonenberg, K., Lemoine, H., Forcellini, E., Cecon, E., Roche, D., et al. (2026) · ACS Chemical Biology · doi:10.1021/acschembio.6c00003 · Cited by 1
Site-directed mutagenesis of rat α-parvalbumin: replacement of canonical CD-site residues with their non-consensus counterparts from rat β-parvalbumin
Henzl, M. T., Sirianni, A. G., Markus, L. A., & Davis, C. M. (2014) · Biophysical Chemistry · doi:10.1016/j.bpc.2014.12.002 · Cited by 1
Imaginative Order from Reasonable Chaos: Conformation-Driven Activity and Reactivity in Exploring Protein–Ligand Interactions
Moore, A. F., Newman, D. J., Ranganathan, S., & Liu, F. (2018) · Australian Journal of Chemistry · doi:10.1071/ch18416 · Cited by 1
Perspective on the potential of tandem-ion mobility/mass spectrometry methods for structural proteomics applications
Cropley, T. C., Chai, M., Liu, F. C., & Bleiholder, C. (2023) · Frontiers in Analytical Science · doi:10.3389/frans.2023.1106752 · Cited by 1
Glycosylation and charge distribution orchestrates the conformational ensembles of a biotechnologically promissory phytase in different pHs – a computational study
de Souza, T. P. P., Cantão, L. X. S., Rodrigues, M. Q. R. B., Gonçalves, D. B., Nagem, R. A. P., Rocha, R. E. O., Godoi, R. R., Lima, W. J. N., Galdino, A. S., de Melo-Minardi, R. C., et al. (2023) · Journal of Biomolecular Structure and Dynamics · doi:10.1080/07391102.2023.2223685 · Cited by 1
Hydrogen‐Atom Tunneling in a Homochiral Environment
Xie, F., Sun, W., Hartwig, B., Obenchain, D. A., & Schnell, M. (2023) · Angewandte Chemie · doi:10.1002/ange.202308273 · Cited by 1
Influence of metal binding on the conformational landscape of neurofilament peptides
Silva-Brea, D., Sancho, D. D., & López, X. (2023) · Physical Chemistry Chemical Physics · doi:10.1039/d3cp03179a · Cited by 1
Solution structures and thermodynamics of cis-trans X-Pro conformers of a novel single disulfide conopeptide
Kancherla, A. K., & Sarma, S. P. (2023) · Indian Journal of Biochemistry and Biophysics · doi:10.56042/ijbb.v60i9.4061 · Cited by 1
Comprehensive structural and functional analyses of RAD50 nsSNPs: from prediction to impact assessment
Malik, S., Hasnain, M. J. U., Zaib, G., Saadia, H., Malik, A., & Zahid, A. (2025) · Frontiers in Bioinformatics · doi:10.3389/fbinf.2025.1535482 · Cited by 1
Local and distal changes in dynamics are caused by an L205R Cushing’s syndrome mutant in PRKACA
Kalle, A., Wu, J., Tawfeeq, C., Kornev, A. P., Veglia, G., Maillard, R. A., Taylor, S. S., & Jonniya, N. A. (2025) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2502898122 · Cited by 1
Towards understanding the mechanisms of allostery: the investigation of the relationship between dynamics, structure and function in the model allosteric protein CheY
McDonald, L. R. (2019) · Carolina Digital Repository (University of North Carolina at Chapel Hill) · doi:10.17615/pm3c-ht64 · Cited by 1
Fuzzy and fast nuclear transport
Mulder, F. A. A. (2018) · Journal of Biological Chemistry · doi:10.1074/jbc.h118.002129 · Cited by 1
Water in Enzyme Catalysis as a Promoter and Chemical Reagent
Likhtenshtein, G. I. (2021) · Soft and biological matter · doi:10.1007/978-3-030-82503-4_8 · Cited by 1
A single-molecule stochastic theory of protein-ligand binding in the presence of multiple unfolding/folding and ligand binding pathways
Singh, D. K., & Chaudhury, S. (2022) · Biophysical Chemistry · doi:10.1016/j.bpc.2022.106803 · Cited by 1
Order Parameters and Conformational Entropies Derived from Combined NMR and Molecular Dynamics Approach
Akke, M. (2014) · doi:10.1002/9780470034590.emrstm1357 · Cited by 1
A Practical Guide to Structural Aspects of Macrocycles (NMR, X‐Ray, and Modeling)
Craik, D. J., Kaas, Q., & Wang, C. K. L. (2017) · Wiley eBooks · doi:10.1002/9781119092599.ch2 · Cited by 1
Structural origins of protein conformational entropyPreprint
José, A., Valentine, K. G., & Wand, A. J. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.02.12.430981 · Cited by 1
Double and triple thermodynamic mutant cycles reveal the basis for specific MsbA-lipid interactionsPreprint
Lyu, J., Zhang, T., Marty, M. T., Clemmer, D. E., Russell, D. H., & Laganowsky, A. D. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.07.03.547565 · Cited by 1
A parametrized two-domain thermodynamic model explains diverse mutational effects on protein allosteryPreprint
Liu, Z., Gillis, T., Raman, S., & Cui, Q. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.08.06.552196 · Cited by 1
A parametrized two-domain thermodynamic model explains diverse mutational effects on protein allosteryPreprint
Liu, Z., Gillis, T., Raman, S., & Cui, Q. (2023) · eLife · doi:10.7554/elife.92262.1 · Cited by 1
A parametrized two-domain thermodynamic model explains diverse mutational effects on protein allosteryPreprint
Liu, Z., Gillis, T., Raman, S., & Cui, Q. (2024) · eLife · doi:10.7554/elife.92262.2 · Cited by 1
Binding Entropy Can Be Predicted by Crystallographic EnsemblesPreprint
Miller, C. A., & Wankowicz, S. A. M. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.01.19.699807 · Cited by 1
Incidental conformational switching in an allosteric enzymePreprint
Sapienza, P. J., Vera-Rodriguez, D. J., Mileur, T. R., & Lee, A. L. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.08.04.741757 · Cited by 1
Ideal gas behavior of rotamerically defined conformers in native globular proteinsPreprint
Wang, K., Long, S., Zhang, Z., Liu, L., Wang, Q., & Tian, P. (2014) · arXiv (Cornell University) · doi:10.48550/arxiv.1408.5803
Multi-scale Approaches to Dynamical Transmission of Protein Allostery
Townsend, P. D., Rodgers, T. L., Pohl, E., Wilson, M. R., Cann, M. J., & McLeish, T. C. B. (2015) · Springer eBooks · doi:10.1007/978-3-319-21687-4_8
Structure and Dynamics of a Small Multidrug Resistance Transporter, EmrE
Wu, C. (2016) · Open Scholarship Institutional Repository (Washington University in St. Louis) · doi:10.7936/k73r0r53
Study of signal transduction in reconstituted membranes: Ras activation by SOS and RasGRP1
Tu, H. (2013) · eScholarship (California Digital Library)
Movimentos coletivos harmônicos, suas frequências e combinações lineares, na regulação de três proteínas: na transição alostérica da DEA, na ativação por redução da MosR e na ligação da ElrR ao DNA
Câmara, A. S. (2017) · Digital Library of Theses and Dissertations (Universidade de São Paulo) · doi:10.11606/t.76.2017.tde-17102017-151821
Biophysical exploration of conformational environments in zymogen prothrombin and blood coagulant thrombin.
Billur, R. (2018) · doi:10.18297/etd/2904
Symmetry, Rigidity, and Allosteric Signaling: From Monomeric Proteins to Molecular MachinesPreprint
Thirumalai, D., Hyeon, C., Zhuravlev, P. I., & Lorimer, G. H. (2018) · arXiv (Cornell University) · doi:10.48550/arxiv.1812.04969
NMR Studies of Protein Hydration and Protein-Ligand Interactions
Chong, Y. (2019) · Carolina Digital Repository (University of North Carolina at Chapel Hill) · doi:10.17615/q0rc-0v89
Probing subunit communication via a singly ligated state of dimeric thymidylate synthase
Falk, B. T. (2019) · Carolina Digital Repository (University of North Carolina at Chapel Hill) · doi:10.17615/0yxy-wz79
Dynamic Order in Allosteric InteractionsPreprint
Türeli, S., & Haliloǧlu, T. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.01.27.920850
The Non-continuum Nature of Eukaryotic Transcriptional Regulation
Poon, G. M. K. (2021) · Advances in experimental medicine and biology · doi:10.1007/5584_2021_618
Assembly status transition offers an avenue for allosteric activity modulation of a supramolecular enzymePreprint
Chen, Y., Xu, W., Yu, S., Ni, K., She, G., Ye, X., Xing, Q., Zhao, J. H., & Huang, C. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.08.20.457084
Hydration of Simple Biological Molecules and Ions
Likhtenshtein, G. I. (2021) · Soft and biological matter · doi:10.1007/978-3-030-82503-4_6
Unraveling Entropic Rate Acceleration Induced by Solvent Dynamics in Membrane Enzymes
Kürten, C., & Syrén, P. (2016) · Journal of Visualized Experiments · doi:10.3791/53168-v

Authors: Tzeng, S.-R., & Kalodimos, C. G.
Affiliations: Rutgers, The State University of New Jersey (US)
Corresponding author: Kalodimos, Charalampos G.
ORCID: Tzeng, Shiou-Ru
Kalodimos, Charalampos G.
Venue: Nature
Publisher: Springer Science and Business Media LLC
Published: 2012-07-11
Volume: 488
Issue: 7410
Pages: 236-240
ISSN: 0028-0836 (ISSN-L)
1476-4687
DOI: 10.1038/nature11271
OpenAlex: W2009239521
Cited by: 545
References: 30
Citations by year: 2026: 25 · 2025: 27 · 2024: 33 · 2023: 43 · 2022: 26 · 2021: 30 · 2020: 29 · 2019: 42 · 2018: 53 · 2017: 40 · 2016: 42 · 2015: 48 · 2014: 47 · 2013: 51 · 2012: 9
FWCI: 19.86
Type: journal article
Language: en
Open access: closed
Licence: www.springer.com/tdm (tdm)
Locations: Nature (publishedVersion)
PubMed (publishedVersion)
RePEc: Research Papers in Economics (submittedVersion)
Funders: National Science Foundation
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
Physical Sciences › Chemistry › Spectroscopy › Advanced NMR Techniques and Applications
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Diffusion and Search Dynamics
Keywords: CAP, protein-DNA interactions, conformational entropy, protein internal dynamics, protein conformational states, DNA-binding domain, protein structure-function relationship, protein variants, binding affinity, binding thermodynamics
MeSH terms: Binding Sites, Cyclic AMP Receptor Protein, DNA, Models, Molecular, Motion, Protein Binding, Time Factors, Protein Structure, Tertiary, Entropy, Nuclear Magnetic Resonance, Biomolecular

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review

Protein activity regulation by conformational entropy

Abstract

Overview

Integrity signals

Verification

Claims the paper makes

Claims other papers make about this one

Citations

Cites

Cited by

Related

Metadata

Record

About these checks