1
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Duan L, Tang B, Luo S, Xiong D, Wang Q, Xu X, Zhang JZH. Entropy driven cooperativity effect in multi-site drug optimization targeting SARS-CoV-2 papain-like protease. Cell Mol Life Sci 2023; 80:313. [PMID: 37796323 PMCID: PMC11072831 DOI: 10.1007/s00018-023-04985-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 09/07/2023] [Accepted: 09/26/2023] [Indexed: 10/06/2023]
Abstract
Papain-like protease (PLpro), a non-structural protein encoded by SARS-CoV-2, is an important therapeutic target. Regions 1 and 5 of an existing drug, GRL0617, can be optimized to produce cooperativity with PLpro binding, resulting in stronger binding affinity. This work investigated the origin of the cooperativity using molecular dynamics simulations combined with the interaction entropy (IE) method. The regions' improvement exhibits cooperativity by calculating the binding free energies between the complex of PLpro-inhibitor. The thermodynamic integration method further verified the cooperativity generated in the drug improvement. To further determine the specific source of cooperativity, enthalpy and entropy in the complexes were calculated using molecular mechanics/generalized Born surface area and IE. The results show that the entropic change is an important contributor to the cooperativity. Our study also identified residues P248, Q269, and T301 that play a significant role in cooperativity. The optimization of the inhibitor stabilizes these residues and minimizes the entropic loss, and the cooperativity observed in the binding free energy can be attributed to the change in the entropic contribution of these residues. Based on our research, the application of cooperativity can facilitate drug optimization, and provide theoretical ideas for drug development that leverage cooperativity by reducing the contribution of entropy through multi-locus binding.
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Affiliation(s)
- Lili Duan
- School of Physics and Electronics, Shandong Normal University, Jinan, 250014, China.
| | - Bolin Tang
- School of Physics and Electronics, Shandong Normal University, Jinan, 250014, China
| | - Song Luo
- School of Physics and Electronics, Shandong Normal University, Jinan, 250014, China
| | - Danyang Xiong
- School of Physics and Electronics, Shandong Normal University, Jinan, 250014, China
| | - Qihang Wang
- School of Physics and Electronics, Shandong Normal University, Jinan, 250014, China
| | - Xiaole Xu
- School of Physics and Electronics, Shandong Normal University, Jinan, 250014, China
| | - John Z H Zhang
- Faculty of Synthetic Biology and Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200062, China.
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai, 200062, China.
- Department of Chemistry, New York University, New York, NY, 10003, USA.
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2
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Kostina NY, Rahimi K, Xiao Q, Haraszti T, Dedisch S, Spatz JP, Schwaneberg U, Klein ML, Percec V, Möller M, Rodriguez-Emmenegger C. Membrane-Mimetic Dendrimersomes Engulf Living Bacteria via Endocytosis. NANO LETTERS 2019; 19:5732-5738. [PMID: 31306030 DOI: 10.1021/acs.nanolett.9b02349] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
There is much interest in developing vesicular microcompartments from natural and synthetic amphiphiles, enabling programmable interactions with living matter. Of particular interest is the development of vesicles capable of endocytosis of living bacteria. Despite the complexity of this process, theoretical studies predict that the endocytosis of prolate micro-objects is possible without the need of active cell machinery if the energy released upon bacterial adhesion to the membrane surpasses the energy required to bend the membrane. Nonetheless, natural liposomes and synthetic polymersomes fail to sufficiently recapitulate membrane properties to perform this advanced function. Here we report the engulfment of living bacteria into endosomes by cell-like dendrimersomes assembled from Janus dendrimers. Full engulfment occurred in less than a minute after contact. The process is driven by the adhesion of the bacterium to the dendrimersome's membrane by ultraweak interactions, comparable to those utilized by nature. The key to success relies on the combination of high flexibility and stability of the dendrimersomes. The key properties of the dendrimersomes are programmed into the molecular structures of their building blocks. The ability to support endocytosis highlights opportunities for the design and programming of dendrimersomes in biomedical research.
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Affiliation(s)
- Nina Yu Kostina
- DWI-Leibniz Institute for Interactive Materials , Forckenbeckstraße 50 , 52074 Aachen , Germany
- Institute of Technical and Macromolecular Chemistry , RWTH Aachen University , Forckenbeckstraße 50 , 52074 Aachen , Germany
| | - Khosrow Rahimi
- DWI-Leibniz Institute for Interactive Materials , Forckenbeckstraße 50 , 52074 Aachen , Germany
- Institute of Technical and Macromolecular Chemistry , RWTH Aachen University , Forckenbeckstraße 50 , 52074 Aachen , Germany
| | - Qi Xiao
- Roy & Diana Vagelos Laboratories, Department of Chemistry , University of Pennsylvania , Philadelphia , Pennsylvania 19104-6323 , United States
- Institute of Computational Molecular Science , Temple University , Philadelphia , Pennsylvania 19122 , United States
| | - Tamás Haraszti
- DWI-Leibniz Institute for Interactive Materials , Forckenbeckstraße 50 , 52074 Aachen , Germany
- Institute of Technical and Macromolecular Chemistry , RWTH Aachen University , Forckenbeckstraße 50 , 52074 Aachen , Germany
| | - Sarah Dedisch
- DWI-Leibniz Institute for Interactive Materials , Forckenbeckstraße 50 , 52074 Aachen , Germany
- Institute of Biotechnology , RWTH Aachen University , Worringerweg 3 , 52074 Aachen , Germany
| | - Joachim P Spatz
- Department of Cellular Biophysics , Max Planck Institute for Medical Research , Jahnstraße 29 , 69120 Heidelberg , Germany
- Department of Biophysical Chemistry , University of Heidelberg , Im Neuenheimer Feld 253 , 69120 Heidelberg , Germany
| | - Ulrich Schwaneberg
- DWI-Leibniz Institute for Interactive Materials , Forckenbeckstraße 50 , 52074 Aachen , Germany
- Institute of Biotechnology , RWTH Aachen University , Worringerweg 3 , 52074 Aachen , Germany
| | - Michael L Klein
- Institute of Computational Molecular Science , Temple University , Philadelphia , Pennsylvania 19122 , United States
| | - Virgil Percec
- Roy & Diana Vagelos Laboratories, Department of Chemistry , University of Pennsylvania , Philadelphia , Pennsylvania 19104-6323 , United States
| | - Martin Möller
- DWI-Leibniz Institute for Interactive Materials , Forckenbeckstraße 50 , 52074 Aachen , Germany
- Institute of Technical and Macromolecular Chemistry , RWTH Aachen University , Forckenbeckstraße 50 , 52074 Aachen , Germany
| | - Cesar Rodriguez-Emmenegger
- DWI-Leibniz Institute for Interactive Materials , Forckenbeckstraße 50 , 52074 Aachen , Germany
- Institute of Technical and Macromolecular Chemistry , RWTH Aachen University , Forckenbeckstraße 50 , 52074 Aachen , Germany
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3
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Wodak SJ, Paci E, Dokholyan NV, Berezovsky IN, Horovitz A, Li J, Hilser VJ, Bahar I, Karanicolas J, Stock G, Hamm P, Stote RH, Eberhardt J, Chebaro Y, Dejaegere A, Cecchini M, Changeux JP, Bolhuis PG, Vreede J, Faccioli P, Orioli S, Ravasio R, Yan L, Brito C, Wyart M, Gkeka P, Rivalta I, Palermo G, McCammon JA, Panecka-Hofman J, Wade RC, Di Pizio A, Niv MY, Nussinov R, Tsai CJ, Jang H, Padhorny D, Kozakov D, McLeish T. Allostery in Its Many Disguises: From Theory to Applications. Structure 2019; 27:566-578. [PMID: 30744993 PMCID: PMC6688844 DOI: 10.1016/j.str.2019.01.003] [Citation(s) in RCA: 234] [Impact Index Per Article: 46.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 11/29/2018] [Accepted: 01/02/2019] [Indexed: 12/19/2022]
Abstract
Allosteric regulation plays an important role in many biological processes, such as signal transduction, transcriptional regulation, and metabolism. Allostery is rooted in the fundamental physical properties of macromolecular systems, but its underlying mechanisms are still poorly understood. A collection of contributions to a recent interdisciplinary CECAM (Center Européen de Calcul Atomique et Moléculaire) workshop is used here to provide an overview of the progress and remaining limitations in the understanding of the mechanistic foundations of allostery gained from computational and experimental analyses of real protein systems and model systems. The main conceptual frameworks instrumental in driving the field are discussed. We illustrate the role of these frameworks in illuminating molecular mechanisms and explaining cellular processes, and describe some of their promising practical applications in engineering molecular sensors and informing drug design efforts.
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Affiliation(s)
| | | | - Nikolay V Dokholyan
- Department of Biochemistry & Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Departments of Pharmacology and Biochemistry & Molecular Biology, Penn State Medical Center, Hershey, PA, USA
| | - Igor N Berezovsky
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A(∗)STAR), and Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Amnon Horovitz
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Jing Li
- Departments of Biology and T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, USA
| | - Vincent J Hilser
- Departments of Biology and T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, USA
| | - Ivet Bahar
- School of Medicine, University of Pittsburgh, Pittsburgh, USA
| | | | - Gerhard Stock
- Biomolecular Dynamics, Institute of Physics, Albert Ludwigs University, Freiburg, Germany
| | - Peter Hamm
- Department of Chemistry, University of Zurich, Zurich, Switzerland
| | - Roland H Stote
- Department of Integrative Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France
| | - Jerome Eberhardt
- Department of Integrative Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France
| | - Yassmine Chebaro
- Department of Integrative Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France
| | - Annick Dejaegere
- Department of Integrative Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France
| | - Marco Cecchini
- Institut de Chimie de Strasbourg, UMR7177 CNRS & Université de Strasbourg, Strasbourg, France
| | | | - Peter G Bolhuis
- van 't Hoff Institute for Molecular Sciences (HIMS), University of Amsterdam, Amsterdam, Netherlands
| | - Jocelyne Vreede
- van 't Hoff Institute for Molecular Sciences (HIMS), University of Amsterdam, Amsterdam, Netherlands
| | - Pietro Faccioli
- Physics Department, Università di Trento and INFN-TIFPA, Trento, Italy
| | - Simone Orioli
- Physics Department, Università di Trento and INFN-TIFPA, Trento, Italy
| | - Riccardo Ravasio
- Institute of Physics, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Le Yan
- Kavli Institute for Theoretical Physics, University of California, Santa Barbara, CA 93106, USA
| | - Carolina Brito
- Instituto de Física, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS 91501-970, Brazil
| | - Matthieu Wyart
- Institute of Physics, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Paraskevi Gkeka
- Structure Design and Informatics, Sanofi R&D, Chilly-Mazarin, France
| | - Ivan Rivalta
- École Normale Supérieure de Lyon, Université de Lyon, CNRS, Université Claude Bernard Lyon 1, Lyon, France
| | - Giulia Palermo
- Department of Chemistry and Biochemistry, University of California, San Diego, USA; Department of Bioengineering, University of California Riverside, CA 92507, USA
| | - J Andrew McCammon
- Department of Chemistry and Biochemistry, University of California, San Diego, USA
| | - Joanna Panecka-Hofman
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Warsaw, Poland
| | - Rebecca C Wade
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS) and Center for Molecular Biology (ZMBH), DKFZ-ZMBH Alliance, Heidelberg University, Heidelberg, Germany; Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University, Heidelberg, Germany
| | - Antonella Di Pizio
- Leibniz-Institute for Food Systems Biology, Technical University of Munich, Munich, Germany
| | - Masha Y Niv
- Institute of Biochemistry, Food Science and Nutrition, Robert H Smith Faculty of Agriculture Food and Environment, The Hebrew University, Jerusalem, Israel
| | - Ruth Nussinov
- Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, USA; Sackler Institute of Molecular Medicine, Department of Human Genetics and Molecular Medicine Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Chung-Jung Tsai
- Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, USA
| | - Hyunbum Jang
- Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, USA
| | - Dzmitry Padhorny
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY 11794, USA
| | - Dima Kozakov
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY 11794, USA
| | - Tom McLeish
- Department of Physics, University of York, York, UK
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4
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Yu M, Ma X, Cao H, Chong B, Lai L, Liu Z. Singular value decomposition for the correlation of atomic fluctuations with arbitrary angle. Proteins 2018; 86:1075-1087. [PMID: 30019778 DOI: 10.1002/prot.25586] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 06/22/2018] [Accepted: 07/04/2018] [Indexed: 01/21/2023]
Abstract
Many proteins exhibit a critical property called allostery, which enables intra-molecular transmission of information between distal sites. Microscopically, allosteric response is closely related to correlated atomic fluctuations. Conventional correlation analysis correlates the atomic fluctuations at two sites by taking the dot product (DP) between the fluctuations, which accounts only for the parallel and antiparallel components. Here, we present a singular value decomposition (SVD) method that analyzes the correlation coefficient of fluctuation dynamics with an arbitrary angle between the correlated directions. In a model allosteric system, the second PDZ domain (PDZ2) in the human PTP1E protein, approximately one third of the strong correlations have near-perpendicular directions, which are underestimated in the conventional method. The discrimination becomes more prominent for residue pairs with larger separation. The results of the proposed SVD method are more consistent with the experimentally determined PDZ2 dynamics than those of conventional method. In addition, the SVD method improved the prediction accuracy of the allosteric sites in a dataset of 23 known allosteric monomer proteins. The proposed method may inspire extended investigation not only into allostery, but also into protein dynamics and drug design.
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Affiliation(s)
- Miao Yu
- College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Xiaomin Ma
- Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong Province, China
| | - Huaiqing Cao
- College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Bin Chong
- College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Luhua Lai
- College of Chemistry and Molecular Engineering, Peking University, Beijing, China.,Center for Quantitative Biology, and BNLMS, Peking University, Beijing, China.,State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Peking University, Beijing, China
| | - Zhirong Liu
- College of Chemistry and Molecular Engineering, Peking University, Beijing, China.,Center for Quantitative Biology, and BNLMS, Peking University, Beijing, China.,State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Peking University, Beijing, China
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5
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Vural D, Hu X, Lindner B, Jain N, Miao Y, Cheng X, Liu Z, Hong L, Smith JC. Quasielastic neutron scattering in biology: Theory and applications. Biochim Biophys Acta Gen Subj 2016; 1861:3638-3650. [PMID: 27316321 DOI: 10.1016/j.bbagen.2016.06.015] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Revised: 06/08/2016] [Accepted: 06/09/2016] [Indexed: 02/03/2023]
Abstract
Neutrons scatter quasielastically from stochastic, diffusive processes, such as overdamped vibrations, localized diffusion and transitions between energy minima. In biological systems, such as proteins and membranes, these relaxation processes are of considerable physical interest. We review here recent methodological advances and applications of quasielastic neutron scattering (QENS) in biology, concentrating on the role of molecular dynamics simulation in generating data with which neutron profiles can be unambiguously interpreted. We examine the use of massively-parallel computers in calculating scattering functions, and the application of Markov state modeling. The decomposition of MD-derived neutron dynamic susceptibilities is described, and the use of this in combination with NMR spectroscopy. We discuss dynamics at very long times, including approximations to the infinite time mean-square displacement and nonequilibrium aspects of single-protein dynamics. Finally, we examine how neutron scattering and MD can be combined to provide information on lipid nanodomains. This article is part of a Special Issue entitled "Science for Life" Guest Editor: Dr. Austen Angell, Dr. Salvatore Magazù and Dr. Federica Migliardo.
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Affiliation(s)
- Derya Vural
- Center for Molecular Biophysics, Oak Ridge National Laboratory, TN 37831, USA; Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - Xiaohu Hu
- Center for Molecular Biophysics, Oak Ridge National Laboratory, TN 37831, USA; Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - Benjamin Lindner
- Institute of Natural Sciences & Department of Physics and Astronomy, Shanghai Jiao Tong University, 200240, China
| | - Nitin Jain
- Center for Molecular Biophysics, Oak Ridge National Laboratory, TN 37831, USA; Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - Yinglong Miao
- Center for Molecular Biophysics, Oak Ridge National Laboratory, TN 37831, USA; Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - Xiaolin Cheng
- Center for Molecular Biophysics, Oak Ridge National Laboratory, TN 37831, USA; Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - Zhuo Liu
- Institute of Natural Sciences & Department of Physics and Astronomy, Shanghai Jiao Tong University, 200240, China
| | - Liang Hong
- Institute of Natural Sciences & Department of Physics and Astronomy, Shanghai Jiao Tong University, 200240, China
| | - Jeremy C Smith
- Center for Molecular Biophysics, Oak Ridge National Laboratory, TN 37831, USA; Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA.
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6
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Magazù S, Mamontov E. A neutron spectrometer concept implementing RENS for studies in life sciences. Biochim Biophys Acta Gen Subj 2016; 1861:3632-3637. [PMID: 27118237 DOI: 10.1016/j.bbagen.2016.04.017] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2016] [Accepted: 04/18/2016] [Indexed: 11/28/2022]
Abstract
BACKGROUND Resolution Elastic Neutron Scattering (RENS) method involves performing elastic scattering intensity scans as a function of the instrumental energy resolution and as a function of temperature. METHODS In the framework of RENS, numerical simulation and experimental data show that in the measured elastic scattering law against the logarithm of the instrumental energy resolution an inflection point occurs when the resolution time intersects the system relaxation time; conversely, in the measured elastic scattering law against temperature an inflection point turns up when the system relaxation time intersects the resolution time. RESULTS For practical implementation of the RENS technique, a dedicated neutron spectrometer would be needed. Here we propose a concept of such a spectrometer that utilizes mechanical velocity selection of both incident and scattered neutrons over a wide angular range. The instrument is able to collect intensity scans vs energy resolution where the instrumental resolution time changes crisscrossing the system relaxation time, and intensity scans vs temperature where the system relaxation time changes intersecting the instrumental resolution time. CONCLUSIONS We propose a RENS spectrometer concept based on velocity selection of incident neutrons and wide-angle velocity selection of scattered neutrons achieved by the same rotating collimator-type mechanical device with the optimized shape of blades. GENERAL SIGNIFICANCE RENS spectrometer is strongly appealing and innovative because of the simultaneous data collection as a function of energy resolution, wide wavevector range and temperature. Such a spectrometer would be the first practical implementation of RENS concept with a broad range of applications in Life Sciences. This article is part of a Special Issue entitled "Science for Life" Guest Editor: Dr. Austen Angell, Dr. Salvatore Magazù and Dr. Federica Migliardo.
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Affiliation(s)
- S Magazù
- Department of Mathematics and Informatics Sciences, Physics Sciences and Earth Sciences, University of Messina, Viale F. S. D'Alcontres 31, 98166 Messina, Italy.
| | - E Mamontov
- Chemical and Engineering Materials Division, Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
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7
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Firman T, Ghosh K. Competition enhances stochasticity in biochemical reactions. J Chem Phys 2014; 139:121915. [PMID: 24089727 DOI: 10.1063/1.4816527] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We study stochastic dynamics of two competing complexation reactions (i) A + B↔AB and (ii) A + C↔AC. Such reactions are common in biology where different reactants compete for common resources--examples range from binding enzyme kinetics to gene expression. On the other hand, stochasticity is inherent in biological systems due to small copy numbers. We investigate the complex interplay between competition and stochasticity, using coupled complexation reactions as the model system. Within the master equation formalism, we compute the exact distribution of the number of complexes to analyze equilibrium fluctuations of several observables. Our study reveals that the presence of competition offered by one reaction (say A + C↔AC) can significantly enhance the fluctuation in the other (A + B↔AB). We provide detailed quantitative estimates of this enhanced fluctuation for different combinations of rate constants and numbers of reactant molecules that are typical in biology. We notice that fluctuations can be significant even when two of the reactant molecules (say B and C) are infinite in number, maintaining a fixed stoichiometry, while the other reactant (A) is finite. This is purely due to the coupling mediated via resource sharing and is in stark contrast to the single reaction scenario, where large numbers of one of the components ensure zero fluctuation. Our detailed analysis further highlights regions where numerical estimates of mass action solutions can differ from the actual averages. These observations indicate that averages can be a poor representation of the system, hence analysis that is purely based on averages such as mass action laws can be potentially misleading in such noisy biological systems. We believe that the exhaustive study presented here will provide qualitative and quantitative insights into the role of noise and its enhancement in the presence of competition that will be relevant in many biological settings.
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Affiliation(s)
- Taylor Firman
- Department of Physics and Astronomy, University of Denver, Denver, Colorado 80208, USA
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Vural D, Glyde HR. Intrinsic mean-square displacements in proteins. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2012; 86:011926. [PMID: 23005471 DOI: 10.1103/physreve.86.011926] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2012] [Indexed: 06/01/2023]
Abstract
The thermal mean-square displacement (MSD) of hydrogen in proteins and its associated hydration water is measured by neutron scattering experiments and used an indicator of protein function. The observed MSD as currently determined depends on the energy resolution width of the neutron scattering instrument employed. We propose a method for obtaining the intrinsic MSD of H in the proteins, one that is independent of the instrument resolution width. The intrinsic MSD is defined as the infinite time value of (r(2)) that appears in the Debye-Waller factor. The method consists of fitting a model to the resolution broadened elastic incoherent structure factor or to the resolution dependent MSD. The model contains the intrinsic MSD, the instrument resolution width, and a rate constant characterizing the motions of H in the protein. The method is illustrated by obtaining the intrinsic MSD (r(2)) of heparan sulphate (HS-0.4), ribonuclease A, and staphysloccal nuclase (SNase) from data in the literature.
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Affiliation(s)
- Derya Vural
- Department of Physics and Astronomy, University of Delaware, Newark, Delaware 19716-2570, USA
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9
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Qian H. Cooperativity in Cellular Biochemical Processes: Noise-Enhanced Sensitivity, Fluctuating Enzyme, Bistability with Nonlinear Feedback, and Other Mechanisms for Sigmoidal Responses. Annu Rev Biophys 2012; 41:179-204. [DOI: 10.1146/annurev-biophys-050511-102240] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Hong Qian
- Department of Applied Mathematics, University of Washington, Seattle, Washington 98195;
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10
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Hong L, Smolin N, Lindner B, Sokolov AP, Smith JC. Three classes of motion in the dynamic neutron-scattering susceptibility of a globular protein. PHYSICAL REVIEW LETTERS 2011; 107:148102. [PMID: 22107237 DOI: 10.1103/physrevlett.107.148102] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2011] [Indexed: 05/31/2023]
Abstract
A simplified description of the 295 K dynamics of a globular protein over a wide frequency range (1-1000 GHz) is obtained by combining neutron scattering of lysozyme with molecular dynamics simulation. The molecular dynamics simulation agrees quantitatively with experiment for both the protein and the hydration water and shows that, whereas the hydration water molecules subdiffuse, the protein atoms undergo confined motion decomposable into three distinct classes: localized diffusion, methyl group rotations, and jumps. Each of the three classes gives rise to a characteristic neutron susceptibility signal.
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Affiliation(s)
- Liang Hong
- University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics, P.O.Box 2008, Oak Ridge Tennessee 37831-6164, USA
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