1
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Dandekar BR, Majumdar BB, Mondal J. Nonmonotonic Modulation of the Protein-Ligand Recognition Event by Inert Crowders. J Phys Chem B 2023; 127:7449-7461. [PMID: 37590118 DOI: 10.1021/acs.jpcb.3c03946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/19/2023]
Abstract
The ubiquitous event of a protein recognizing small molecules or ligands at its native binding site is crucial for initiating major biological processes. However, how a crowded environment, as is typically represented by a cellular interior, would modulate the protein-ligand search process is largely debated. Excluded volume-based theory suggests that the presence of an inert crowder would reinforce a steady stabilization and enhancement of the protein-ligand recognition process. Here, we counter this long-held perspective via the molecular dynamics simulation and Markov state model of the protein-ligand recognition event in the presence of inert crowders. Specifically, we demonstrate that, depending on concentration, even purely inert crowders can exert a nonmonotonic effect via either stabilizing or destabilizing the protein-ligand binding event. Analysis of the kinetic network of binding pathways reveals that the crowders would either modulate precedent non-native on-pathway intermediates or would devise additional ones in a multistate recognition event across a wide range of concentrations. As an important insight, crowders gradually shift the relative transitional preference of these intermediates toward a native-bound state, with ligand residence time at the binding pocket dictating the trend of nonmonotonic concentration dependence by simple inert crowders.
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2
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Sun B, Kekenes-Huskey PM. Myofilament-associated proteins with intrinsic disorder (MAPIDs) and their resolution by computational modeling. Q Rev Biophys 2023; 56:e2. [PMID: 36628457 PMCID: PMC11070111 DOI: 10.1017/s003358352300001x] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The cardiac sarcomere is a cellular structure in the heart that enables muscle cells to contract. Dozens of proteins belong to the cardiac sarcomere, which work in tandem to generate force and adapt to demands on cardiac output. Intriguingly, the majority of these proteins have significant intrinsic disorder that contributes to their functions, yet the biophysics of these intrinsically disordered regions (IDRs) have been characterized in limited detail. In this review, we first enumerate these myofilament-associated proteins with intrinsic disorder (MAPIDs) and recent biophysical studies to characterize their IDRs. We secondly summarize the biophysics governing IDR properties and the state-of-the-art in computational tools toward MAPID identification and characterization of their conformation ensembles. We conclude with an overview of future computational approaches toward broadening the understanding of intrinsic disorder in the cardiac sarcomere.
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Affiliation(s)
- Bin Sun
- Research Center for Pharmacoinformatics (The State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Department of Medicinal Chemistry and Natural Medicine Chemistry, College of Pharmacy, Harbin Medical University, Harbin 150081, China
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3
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Lee S. Operator algebraic methods in the theory of
diffusion‐influenced
reaction kinetics. B KOREAN CHEM SOC 2021. [DOI: 10.1002/bkcs.12448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Sangyoub Lee
- Professor Sangyoub Lee, Department of Chemistry Seoul National University Seoul South Korea
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4
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Groover SE, Adegbuyiro A, Fan CK, Hodges BL, Beasley M, Taylor K, Stonebraker AR, Siriwardhana C, Legleiter J. Macromolecular crowding in solution alters huntingtin interaction and aggregation at interfaces. Colloids Surf B Biointerfaces 2021; 206:111969. [PMID: 34246856 DOI: 10.1016/j.colsurfb.2021.111969] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 06/16/2021] [Accepted: 07/05/2021] [Indexed: 10/20/2022]
Abstract
Huntington's disease (HD) is a fatal neurodegenerative disease caused by an extended polyglutamine (polyQ) domain within the first exon of the huntingtin protein (htt). PolyQ expansion directly invokes the formation of a heterogenous mixture of toxic htt aggregates, including fibrils and oligomers. While htt is a cytosolic protein, it also associates with numerous membranous surfaces within the cell, leading to altered organelle morphology and dysfunction. Here, the impact of macromolecular crowding on htt aggregation in bulk solution and at solid/liquid or membrane/liquid interfaces was investigated. Dextran, Ficoll, and polyethylene glycol (PEG) were used as crowding agents. In bulk solution, crowding enhanced the heterogeneity of non-fibrillar aggregate species formed in a crowder dependent manner. However, crowding agents interfered with the deposition of htt fibrils on mica, suggesting that a crowded aqueous phase influences the interaction of htt with interfaces. By use of in situ atomic force microcopy (AFM), the aggregation of htt directly at mica and bilayer interfaces was tracked. The predominate aggregates type observed to form at the mica interface was fibrillar, but oligomeric aggregates of various stabilities were also observed. Crowding in the aqueous phase suppressed deposition and formation of htt aggregates on mica. In contrast, the addition of crowders enhanced deposition of htt aggregates onto supported total brain lipid extract (TBLE) bilayers. Different crowding agents led to distinct htt aggregates on supported bilayers with unique morphological impact on bilayer integrity. Collectively, these observations point to the complexity of htt aggregation at interfaces and that crowding in the aqueous phase profoundly influences this process.
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Affiliation(s)
- Sharon E Groover
- The C. Eugene Bennett Department of Chemistry, West Virginia University, 217 Clark Hall, Morgantown, WV 26506, United States
| | - Adewale Adegbuyiro
- The C. Eugene Bennett Department of Chemistry, West Virginia University, 217 Clark Hall, Morgantown, WV 26506, United States
| | - Caleb K Fan
- The C. Eugene Bennett Department of Chemistry, West Virginia University, 217 Clark Hall, Morgantown, WV 26506, United States
| | - Breanna L Hodges
- The C. Eugene Bennett Department of Chemistry, West Virginia University, 217 Clark Hall, Morgantown, WV 26506, United States
| | - Maryssa Beasley
- The C. Eugene Bennett Department of Chemistry, West Virginia University, 217 Clark Hall, Morgantown, WV 26506, United States
| | - Katelyn Taylor
- The C. Eugene Bennett Department of Chemistry, West Virginia University, 217 Clark Hall, Morgantown, WV 26506, United States
| | - Alyssa R Stonebraker
- The C. Eugene Bennett Department of Chemistry, West Virginia University, 217 Clark Hall, Morgantown, WV 26506, United States
| | - Chathuranga Siriwardhana
- The C. Eugene Bennett Department of Chemistry, West Virginia University, 217 Clark Hall, Morgantown, WV 26506, United States
| | - Justin Legleiter
- The C. Eugene Bennett Department of Chemistry, West Virginia University, 217 Clark Hall, Morgantown, WV 26506, United States; Rockefeller Neurosciences Institutes, West Virginia University, 1 Medical Center Dr., P.O. Box 9303, Morgantown, WV 26505, United States; Department of Neuroscience, West Virginia University, 1 Medical Center Dr., P.O. Box 9303, Morgantown, WV 26505, United States.
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5
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Deshwal A, Maiti S. Macromolecular Crowding Effect on the Activity of Liposome-Bound Alkaline Phosphatase: A Paradoxical Inhibitory Action. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:7273-7284. [PMID: 34086469 DOI: 10.1021/acs.langmuir.1c01177] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The cytoplasm of a cell is extremely crowded, with 20-30% being large biomolecules. This crowding enforces a significant amount of the physical and chemical barrier around biomolecules, so understanding any biomolecular event within the cellular system is challenging. Unsurprisingly, enzymes show a diverse kind of catalytic behavior inside a crowded environment and thus have remained an area of active interest in the last few decades. The situation can become even more complex and exciting in the case of understanding the behavior of a membrane-bound enzyme (almost 25-30% of enzymes are membrane-bound) in such a crowded environment that until now has remained unexplored. Herein, we have particularly investigated how a membrane-bound enzyme (using liposome-bound alkaline phosphatase) can behave in a crowded environment comprising polymer molecule-like poly(ethylene glycol) (PEG) of different weights (PEG400, PEG4000, and PEG9000) and Ficoll 400. We have compared the activity using a polymer microbead conjugated enzyme and have found that liposome-bound alkaline phosphatase had much higher activity in crowded environments, showing the importance and superiority of soft-deformable particles (i.e., vesicles) over hard spheres in macro-molecularly crowded media. Interstingly, we have found a paradoxical behavior of inhibitors in terms of both their extent and pathway of inhibitory action. For instance, phosphates, known as competitive inhibitors in buffer, behave as uncompetitive inhibitors in liposome-bound enzymes in crowded media with an ∼5-fold less inhibitory effect, whereas phenyl alanine (an uncompetitive inhibitor in buffer) did not show any inhibitory potential when the enzyme was membrane-bound and in crowded media containing PEG9000 (30 wt %). Overall, this demonstration elucidates aspects of membrane-bound enzymes in crowded media in terms of both catalytic behavior and inhibitory actions and can lead to further studies of the understanding of enzymatic behavior in such complex crowded environments having a dampening effect in regular diffusive transport.
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Affiliation(s)
- Akshi Deshwal
- Indian Institute of Science Education and Research (IISER) Mohali, Department of Chemical Sciences, Knowledge City, Manauli 140306, India
| | - Subhabrata Maiti
- Indian Institute of Science Education and Research (IISER) Mohali, Department of Chemical Sciences, Knowledge City, Manauli 140306, India
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6
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Lee K, Lee S. Interplay of reactive interference and crowding effects in the diffusion-influenced reaction kinetics. J Chem Phys 2020; 153:044129. [PMID: 32752726 DOI: 10.1063/5.0016269] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
We investigate the interplay of reactive interference and crowding effects in the irreversible diffusion-influenced bimolecular reactions of the type A+B→P+B by using the Brownian dynamics simulation method. It is known that the presence of nonreactive crowding agents retards the reaction rate when the volume fraction of the crowding agents is large enough. On the other hand, a high concentration of B is known to increase the reaction rate more than expected from the mass action law, although the B's may also act as crowders. Therefore, it would be interesting to see which effect dominates when the number density of B as well as the number density of the crowders increases. We will present an approximate theory that provides a reasonable account for the Brownian dynamics simulation results.
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Affiliation(s)
- Kyusup Lee
- Department of Chemistry, Seoul National University, Seoul 151-747, South Korea
| | - Sangyoub Lee
- Department of Chemistry, Seoul National University, Seoul 151-747, South Korea
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7
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Löwe M, Kalacheva M, Boersma AJ, Kedrov A. The more the merrier: effects of macromolecular crowding on the structure and dynamics of biological membranes. FEBS J 2020; 287:5039-5067. [DOI: 10.1111/febs.15429] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 05/18/2020] [Accepted: 05/19/2020] [Indexed: 12/23/2022]
Affiliation(s)
- Maryna Löwe
- Synthetic Membrane Systems Institute of Biochemistry Heinrich Heine University Düsseldorf Germany
| | | | | | - Alexej Kedrov
- Synthetic Membrane Systems Institute of Biochemistry Heinrich Heine University Düsseldorf Germany
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8
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Dibak M, Fröhner C, Noé F, Höfling F. Diffusion-influenced reaction rates in the presence of pair interactions. J Chem Phys 2019; 151:164105. [PMID: 31675872 DOI: 10.1063/1.5124728] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The kinetics of bimolecular reactions in solution depends, among other factors, on intermolecular forces such as steric repulsion or electrostatic interaction. Microscopically, a pair of molecules first has to meet by diffusion before the reaction can take place. In this work, we establish an extension of Doi's volume reaction model to molecules interacting via pair potentials, which is a key ingredient for interacting-particle-based reaction-diffusion (iPRD) simulations. As a central result, we relate model parameters and macroscopic reaction rate constants in this situation. We solve the corresponding reaction-diffusion equation in the steady state and derive semi-analytical expressions for the reaction rate constant and the local concentration profiles. Our results apply to the full spectrum from well-mixed to diffusion-limited kinetics. For limiting cases, we give explicit formulas, and we provide a computationally inexpensive numerical scheme for the general case, including the intermediate, diffusion-influenced regime. The obtained rate constants decompose uniquely into encounter and formation rates, and we discuss the effect of the potential on both subprocesses, exemplified for a soft harmonic repulsion and a Lennard-Jones potential. The analysis is complemented by extensive stochastic iPRD simulations, and we find excellent agreement with the theoretical predictions.
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Affiliation(s)
- Manuel Dibak
- Freie Universität Berlin, Fachbereich Mathematik und Informatik, Arnimallee 6, 14195 Berlin, Germany
| | - Christoph Fröhner
- Freie Universität Berlin, Fachbereich Mathematik und Informatik, Arnimallee 6, 14195 Berlin, Germany
| | - Frank Noé
- Freie Universität Berlin, Fachbereich Mathematik und Informatik, Arnimallee 6, 14195 Berlin, Germany
| | - Felix Höfling
- Freie Universität Berlin, Fachbereich Mathematik und Informatik, Arnimallee 6, 14195 Berlin, Germany
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9
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Graham J, Raghunath M, Vogel V. Fibrillar fibronectin plays a key role as nucleator of collagen I polymerization during macromolecular crowding-enhanced matrix assembly. Biomater Sci 2019; 7:4519-4535. [PMID: 31436263 PMCID: PMC6810780 DOI: 10.1039/c9bm00868c] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Macromolecular crowding is used by tissue engineers to accelerate extracellular matrix assembly in vitro, however, most mechanistic studies focus on the impact of crowding on collagen fiber assembly and largely ignore the highly abundant provisional matrix protein fibronectin. We show that the accelerated collagen I assembly as induced by the neutral crowding molecule Ficoll is regulated by cell access to fibronectin. Ficoll treatment leads to significant increases in the amount of surface adherent fibronectin, which can readily be harvested by cells to speed up fibrillogenesis. FRET studies reveal that Ficoll crowding also upregulates the total amount of fibronectin fibers in a low-tension state through upregulating fibronectin assembly. Since un-stretched fibronectin fibers have more collagen binding sites to nucleate the onset of collagen fibrillogenesis, our data suggest that the Ficoll-induced upregulation of low-tension fibronectin fibers contributes to enhanced collagen assembly in crowded conditions. In contrast, chemical cross-linking of fibronectin to the glass substrate prior to cell seeding prevents early force mediated fibronectin harvesting from the substrate and suppresses upregulation of collagen I assembly in the presence of Ficoll, even though the crowded environment is known to drive enzymatic cleavage of procollagen and collagen fiber formation. To show that our findings can be exploited for tissue engineering applications, we demonstrate that the addition of supplemental fibronectin in the form of an adsorbed coating markedly improves the speed of tissue formation under crowding conditions.
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Affiliation(s)
- Jenna Graham
- Department of Health Sciences and Technology, ETH Zürich, CH-8093 Zürich, Switzerland.
| | - Michael Raghunath
- ZHAW School of Life Sciences and Facility Management, Institute for Chemistry and Biotechnology, Center for Cell Biology and Tissue Engineering, CH-8820 Wädenswil, Switzerland
| | - Viola Vogel
- Department of Health Sciences and Technology, ETH Zürich, CH-8093 Zürich, Switzerland.
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10
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Petersen CF, Franosch T. Anomalous transport in the soft-sphere Lorentz model. SOFT MATTER 2019; 15:3906-3913. [PMID: 30998231 DOI: 10.1039/c9sm00442d] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The sensitivity of anomalous transport in crowded media to the form of the inter-particle interactions is investigated through computer simulations. We extend the highly simplified Lorentz model towards realistic natural systems by modeling the interactions between the tracer and the obstacles with a smooth potential. We find that the anomalous transport at the critical point happens to be governed by the same universal exponent as for hard exclusion interactions, although the mechanism of how narrow channels are probed is rather different. The scaling behavior of simulations close to the critical point confirm this exponent. Our result indicates that the simple Lorentz model may be applicable to describing the fundamental properties of long-range transport in real crowded environments.
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Affiliation(s)
- Charlotte F Petersen
- Institut für Theoretische Physik, Leopold-Franzens-Universität Innsbruck, Technikerstraße 21A, A-6020 Innsbruck, Austria.
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11
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Macromolecular crowding and membrane binding proteins: The case of phospholipase A1. Chem Phys Lipids 2019; 218:91-102. [DOI: 10.1016/j.chemphyslip.2018.12.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 10/10/2018] [Accepted: 12/13/2018] [Indexed: 11/24/2022]
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12
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Ma W, Mayr C. A Membraneless Organelle Associated with the Endoplasmic Reticulum Enables 3'UTR-Mediated Protein-Protein Interactions. Cell 2018; 175:1492-1506.e19. [PMID: 30449617 DOI: 10.1016/j.cell.2018.10.007] [Citation(s) in RCA: 205] [Impact Index Per Article: 34.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 07/23/2018] [Accepted: 09/29/2018] [Indexed: 01/05/2023]
Abstract
Approximately half of human genes generate mRNAs with alternative 3' untranslated regions (3'UTRs). Through 3'UTR-mediated protein-protein interactions, alternative 3'UTRs enable multi-functionality of proteins with identical amino acid sequence. While studying how information on protein features is transferred from 3'UTRs to proteins, we discovered that the broadly expressed RNA-binding protein TIS11B forms a membraneless organelle, called TIS granule, that enriches membrane protein-encoding mRNAs with multiple AU-rich elements. TIS granules form a reticular meshwork intertwined with the endoplasmic reticulum (ER). The association between TIS granules and the ER creates a subcellular compartment-the TIGER domain-with a biophysically and biochemically distinct environment from the cytoplasm. This compartment promotes 3'UTR-mediated interaction of SET with membrane proteins, thus allowing increased surface expression and functional diversity of proteins, including CD47 and PD-L1. The TIGER domain is a subcellular compartment that enables formation of specific and functionally relevant protein-protein interactions that cannot be established outside.
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Affiliation(s)
- Weirui Ma
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Christine Mayr
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
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13
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Ramirez SA, Leidy C. Effect of the Organization of Rhodopsin on the Association between Transducin and a Photoactivated Receptor. J Phys Chem B 2018; 122:8872-8879. [PMID: 30156842 DOI: 10.1021/acs.jpcb.8b07401] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
After photoactivation, rhodopsin (R), a G-protein-coupled receptor, rapidly activates multiple transducin G-proteins (G) in an initial amplification step of phototransduction. G-protein activation requires diffusion-mediated association with an active rhodopsin (R*) at the rod disk membrane. Different organizations of R within the membrane have been revealded by several microscopy studies, including static and freely diffusing situations. However, it is unclear how such different scenarios influence the activation rate of G proteins. Through Monte Carlo simulations, we study the association reaction between a photoactivated rhodopsin and transducin under different reported receptor organizations including (a) R monomers diffusing freely, (b) R forming static dispersed crystalline domains made of rows of dimers, and (c) R arranged in static tracks formed by two adjacent rows of dimers. A key parameter in our simulations is the probability of binding following a collision ( p). For high p, the association rate between R* and G is higher in the freely diffusive system than in the static organizations, but for low collision efficiencies, the static organizations can result in faster association rates than the mobile system. We also observe that with low p, increasing the concentration of R increases the association rate significantly in the dispersed crystals configuration and just slightly in the free diffusive system. In summary, the lateral organization of rhodopsin influences the association rate between R* and G in a manner strongly dependent on the collision efficiency.
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Affiliation(s)
- Samuel A Ramirez
- Department of Pharmacology , University of North Carolina at Chapel Hill , Chapel Hill , North Carolina 27599 ; United States
| | - Chad Leidy
- Department of Physics , Universidad de los Andes , Bogotá 111711 , Colombia
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14
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Wilson DB, Byrne H, Bruna M. Reactions, diffusion, and volume exclusion in a conserved system of interacting particles. Phys Rev E 2018; 97:062137. [PMID: 30011580 DOI: 10.1103/physreve.97.062137] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Indexed: 11/07/2022]
Abstract
Complex biological and physical transport processes are often described through systems of interacting particles. The effect of excluded volume on these transport processes has been well studied; however, the interplay between volume exclusion and reactions between heterogenous particles is less well studied. In this paper we develop a framework for modeling reaction-diffusion processes which directly incorporates volume exclusion. We consider simple reactions (unimolecular and bimolecular) that conserve the total number of particles. From an off-lattice microscopic individual-based model we use the Fokker-Planck equation and the method of matched asymptotic expansions to derive a low-dimensional macroscopic system of nonlinear partial differential equations describing the evolution of the particles. A biologically motivated, hybrid model of chemotaxis with volume exclusion is explored, where reactions occur at rates dependent upon the chemotactic environment. Further, we show that for reactions that require particle contact the appropriate reaction term in the macroscopic model is of lower order in the asymptotic expansion than the nonlinear diffusion term. However, we find that the next reaction term in the expansion is needed to ensure good agreement with simulations of the microscopic model. Our macroscopic model allows for more direct parametrization to experimental data than existing models.
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Affiliation(s)
- Daniel B Wilson
- Mathematical Institute, University of Oxford, Radcliffe Observatory Quarter, Woodstock Road, Oxford OX2 6GG, United Kingdom
| | - Helen Byrne
- Mathematical Institute, University of Oxford, Radcliffe Observatory Quarter, Woodstock Road, Oxford OX2 6GG, United Kingdom
| | - Maria Bruna
- Mathematical Institute, University of Oxford, Radcliffe Observatory Quarter, Woodstock Road, Oxford OX2 6GG, United Kingdom
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15
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Roa R, Siegl T, Kim WK, Dzubiella J. Product interactions and feedback in diffusion-controlled reactions. J Chem Phys 2018; 148:064705. [PMID: 29448770 DOI: 10.1063/1.5016608] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Steric or attractive interactions among reactants or between reactants and inert crowders can substantially influence the total rate of a diffusion-influenced reaction in the liquid phase. However, the role of the product species, which has typically different physical properties than the reactant species, has been disregarded so far. Here we study the effects of reactant-product and product-product interactions as well as asymmetric diffusion properties on the rate of diffusion-controlled reactions in the classical Smoluchowski-setup for chemical transformations at a perfect catalytic sphere. For this, we solve the diffusion equation with appropriate boundary conditions coupled by a mean-field approach on the second virial level to account for the particle interactions. We find that all particle spatial distributions and the total rate can change significantly, depending on the diffusion and interaction properties of the accumulated products. Complex competing and self-regulating (homeostatic) or self-amplifying effects are observed for the system, leading to both decrease and increase in the rates, as the presence of interacting products feeds back to the reactant flux and thus the rate with which the products are generated.
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Affiliation(s)
- Rafael Roa
- Física Aplicada I, Facultad de Ciencias, Universidad de Málaga, 29071 Málaga, Spain
| | - Toni Siegl
- Institut für Weiche Materie und Funktionale Materialien, Helmholtz-Zentrum Berlin für Materialien und Energie, 14109 Berlin, Germany
| | - Won Kyu Kim
- Institut für Weiche Materie und Funktionale Materialien, Helmholtz-Zentrum Berlin für Materialien und Energie, 14109 Berlin, Germany
| | - Joachim Dzubiella
- Institut für Weiche Materie und Funktionale Materialien, Helmholtz-Zentrum Berlin für Materialien und Energie, 14109 Berlin, Germany
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16
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Macias-Medri AE, Liendo JA, Silva RJ. An electrostatic and probabilistic simulation model to describe neurosecretion at the synaptic scale. NETWORK (BRISTOL, ENGLAND) 2017; 28:53-73. [PMID: 29120672 DOI: 10.1080/0954898x.2017.1386806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
A hybrid simulation model (macro-molecular dynamics and Monte Carlo method) is proposed to reproduce neurosecretion and exocytosis. A theory has been developed for vesicular dynamics based on quasi-static electric interactions and a simple transition-state model for the vesicular fusion. Under the non-equilibrium electric conditions in an electrolytic fluid, it is considered that the motion of each synaptic vesicle is influenced by electrostatic forces exerted by the membranes of the synaptic bouton, other vesicles, the intracellular and intravesicular fluids, and external elements to the neuron. In addition, friction between each vesicle and its surrounding intracellular fluid is included in the theory, resulting in a drift type movement. To validate the vesicle equations of motion, a molecular dynamics method has been implemented, where the synaptic pool was replaced by a straight angle parallelepiped, the vesicles were represented by spheres and the fusion between each vesicle and the presynaptic membrane was simulated by a Monte Carlo type probabilistic change of state. Density profiles showing clusters of preferential activity as well as fusion distributions similar to the Poisson distributions associated with miniature end-plate potentials were obtained in the simulations.
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Affiliation(s)
- A E Macias-Medri
- a Departamento de Física , Universidade Federal do Paraná , Curitiba , Brazil
| | - Jacinto A Liendo
- b Physics Department , Simón Bolívar University , Baruta , Venezuela
| | - Ricardo J Silva
- c Instituto Montenegro para la Investigación y Desarrollo de las Neurociencias Cognitivas , Unidad Médica I de la Clínica San Francisco , Guayaquil , Ecuador
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17
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Feig M, Yu I, Wang PH, Nawrocki G, Sugita Y. Crowding in Cellular Environments at an Atomistic Level from Computer Simulations. J Phys Chem B 2017; 121:8009-8025. [PMID: 28666087 PMCID: PMC5582368 DOI: 10.1021/acs.jpcb.7b03570] [Citation(s) in RCA: 115] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
![]()
The
effects of crowding in biological environments on biomolecular
structure, dynamics, and function remain not well understood. Computer
simulations of atomistic models of concentrated peptide and protein
systems at different levels of complexity are beginning to provide
new insights. Crowding, weak interactions with other macromolecules
and metabolites, and altered solvent properties within cellular environments
appear to remodel the energy landscape of peptides and proteins in
significant ways including the possibility of native state destabilization.
Crowding is also seen to affect dynamic properties, both conformational
dynamics and diffusional properties of macromolecules. Recent simulations
that address these questions are reviewed here and discussed in the
context of relevant experiments.
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Affiliation(s)
- Michael Feig
- Department of Biochemistry and Molecular Biology, Michigan State University , East Lansing, Michigan, United States.,Quantitative Biology Center, RIKEN , Kobe, Japan
| | - Isseki Yu
- Theoretical Molecular Science Laboratory, RIKEN , Wako, Japan.,iTHES Research Group, RIKEN , Wako, Japan
| | - Po-Hung Wang
- Theoretical Molecular Science Laboratory, RIKEN , Wako, Japan
| | - Grzegorz Nawrocki
- Department of Biochemistry and Molecular Biology, Michigan State University , East Lansing, Michigan, United States
| | - Yuji Sugita
- Quantitative Biology Center, RIKEN , Kobe, Japan.,Theoretical Molecular Science Laboratory, RIKEN , Wako, Japan.,iTHES Research Group, RIKEN , Wako, Japan.,Advanced Institute for Computational Science, RIKEN , Kobe, Japan
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18
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Abbina S, Vappala S, Kumar P, Siren EMJ, La CC, Abbasi U, Brooks DE, Kizhakkedathu JN. Hyperbranched polyglycerols: recent advances in synthesis, biocompatibility and biomedical applications. J Mater Chem B 2017; 5:9249-9277. [DOI: 10.1039/c7tb02515g] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Hyperbranched polyglycerol is one of the most widely studied biocompatible dendritic polymer and showed promising applications. Here, we summarized the recent advancements in the field.
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Affiliation(s)
- Srinivas Abbina
- Department of Pathology and Laboratory Medicine
- University of British Columbia
- Vancouver
- Canada
- Center for Blood Research
| | - Sreeparna Vappala
- Department of Pathology and Laboratory Medicine
- University of British Columbia
- Vancouver
- Canada
- Center for Blood Research
| | - Prashant Kumar
- Center for Blood Research
- University of British Columbia
- Vancouver
- Canada
- Department of Chemistry
| | - Erika M. J. Siren
- Center for Blood Research
- University of British Columbia
- Vancouver
- Canada
- Department of Chemistry
| | - Chanel C. La
- Center for Blood Research
- University of British Columbia
- Vancouver
- Canada
- Department of Chemistry
| | - Usama Abbasi
- Department of Pathology and Laboratory Medicine
- University of British Columbia
- Vancouver
- Canada
- Center for Blood Research
| | - Donald E. Brooks
- Department of Pathology and Laboratory Medicine
- University of British Columbia
- Vancouver
- Canada
- Center for Blood Research
| | - Jayachandran N. Kizhakkedathu
- Department of Pathology and Laboratory Medicine
- University of British Columbia
- Vancouver
- Canada
- Center for Blood Research
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19
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Bellesia G, Bales BB. Population dynamics, information transfer, and spatial organization in a chemical reaction network under spatial confinement and crowding conditions. Phys Rev E 2016; 94:042306. [PMID: 27841639 DOI: 10.1103/physreve.94.042306] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2016] [Indexed: 11/07/2022]
Abstract
We investigate, via Brownian dynamics simulations, the reaction dynamics of a generic, nonlinear chemical network under spatial confinement and crowding conditions. In detail, the Willamowski-Rossler chemical reaction system has been "extended" and considered as a prototype reaction-diffusion system. Our results are potentially relevant to a number of open problems in biophysics and biochemistry, such as the synthesis of primitive cellular units (protocells) and the definition of their role in the chemical origin of life and the characterization of vesicle-mediated drug delivery processes. More generally, the computational approach presented in this work makes the case for the use of spatial stochastic simulation methods for the study of biochemical networks in vivo where the "well-mixed" approximation is invalid and both thermal and intrinsic fluctuations linked to the possible presence of molecular species in low number copies cannot be averaged out.
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Affiliation(s)
- Giovanni Bellesia
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - Benjamin B Bales
- Department of Computer Science, University of California Santa Barbara, Santa Barbara, California 93106, USA
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20
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Chien W, Chen YL. Abnormal polymer transport in crowded attractive micropost arrays. SOFT MATTER 2016; 12:7969-7976. [PMID: 27714308 DOI: 10.1039/c6sm01488g] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
We investigate polymer diffusion in a quasi-two-dimensional environment decorated with attractive cylindrical posts using Langevin dynamics simulation. We find that the polymer diffusivity has non-monotonic dependence on the post array density. This diffusive behavior strongly depends on the adsorption-desorption transition and the critical adsorption strength εc. For ε < εc, the polymer undergoes normal diffusion and the diffusivity decreases as the post density increases due to the reduction of the void volume. For ε > εc, polymer dynamics is strongly mediated by post adsorption, and we observe a regime where the polymer diffusivity increases as the post density increases. The polymer diffusivity reaches a maximum, which can be attributed to cross-post translation enabled by large polymer conformation fluctuations. We find both cross-post transport and polymer conformation fluctuations strongly depend on the post absorption strength and the chain length.
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Affiliation(s)
- Wei Chien
- Department of Physics, National Taiwan University, Taipei, Taiwan and Institute of Physics, Academia Sinica, Taipei, Taiwan
| | - Yeng-Long Chen
- Department of Physics, National Taiwan University, Taipei, Taiwan and Institute of Physics, Academia Sinica, Taipei, Taiwan and Department of Chemical Engineering, National Tsing-Hua University, Hsinchu, Taiwan.
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21
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22
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Kelkar AV, Franses EI, Corti DS. Non-ideal diffusion effects, short-range ordering, and unsteady-state effects strongly influence Brownian aggregation rates in concentrated dispersions of interacting spheres. J Chem Phys 2015; 143:074706. [PMID: 26298147 DOI: 10.1063/1.4928505] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Aniruddha V. Kelkar
- School of Chemical Engineering, Purdue University, 480 Stadium Mall Drive, West Lafayette, Indiana 47907-2100, USA
| | - Elias I. Franses
- School of Chemical Engineering, Purdue University, 480 Stadium Mall Drive, West Lafayette, Indiana 47907-2100, USA
| | - David S. Corti
- School of Chemical Engineering, Purdue University, 480 Stadium Mall Drive, West Lafayette, Indiana 47907-2100, USA
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23
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What macromolecular crowding can do to a protein. Int J Mol Sci 2014; 15:23090-140. [PMID: 25514413 PMCID: PMC4284756 DOI: 10.3390/ijms151223090] [Citation(s) in RCA: 355] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Revised: 12/04/2014] [Accepted: 12/05/2014] [Indexed: 01/17/2023] Open
Abstract
The intracellular environment represents an extremely crowded milieu, with a limited amount of free water and an almost complete lack of unoccupied space. Obviously, slightly salted aqueous solutions containing low concentrations of a biomolecule of interest are too simplistic to mimic the “real life” situation, where the biomolecule of interest scrambles and wades through the tightly packed crowd. In laboratory practice, such macromolecular crowding is typically mimicked by concentrated solutions of various polymers that serve as model “crowding agents”. Studies under these conditions revealed that macromolecular crowding might affect protein structure, folding, shape, conformational stability, binding of small molecules, enzymatic activity, protein-protein interactions, protein-nucleic acid interactions, and pathological aggregation. The goal of this review is to systematically analyze currently available experimental data on the variety of effects of macromolecular crowding on a protein molecule. The review covers more than 320 papers and therefore represents one of the most comprehensive compendia of the current knowledge in this exciting area.
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24
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Naddaf L, Sayyed-Ahmad A. Intracellular crowding effects on the self-association of the bacterial cell division protein FtsZ. Arch Biochem Biophys 2014; 564:12-9. [DOI: 10.1016/j.abb.2014.08.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Revised: 08/21/2014] [Accepted: 08/26/2014] [Indexed: 11/15/2022]
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25
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Chapanian R, Kwan DH, Constantinescu I, Shaikh FA, Rossi NAA, Withers SG, Kizhakkedathu JN. Enhancement of biological reactions on cell surfaces via macromolecular crowding. Nat Commun 2014; 5:4683. [PMID: 25140641 PMCID: PMC4978540 DOI: 10.1038/ncomms5683] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Accepted: 07/11/2014] [Indexed: 12/18/2022] Open
Abstract
The reaction of macromolecules such as enzymes and antibodies with cell surfaces is often an inefficient process, requiring large amounts of expensive reagent. Here we report a general method based on macromolecular crowding with a range of neutral polymers to enhance such reactions, using red blood cells (RBCs) as a model system. Rates of conversion of type A and B red blood cells to universal O type by removal of antigenic carbohydrates with selective glycosidases are increased up to 400-fold in the presence of crowders. Similar enhancements are seen for antibody binding. We further explore the factors underlying these enhancements using confocal microscopy and fluorescent recovery after bleaching (FRAP) techniques with various fluorescent protein fusion partners. Increased cell-surface concentration due to volume exclusion, along with two-dimensionally confined diffusion of enzymes close to the cell surface, appear to be the major contributing factors.
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Affiliation(s)
- Rafi Chapanian
- 1] Centre for Blood Research, University of British Columbia, 2350 Health Sciences Mall, Life Sciences Centre, Vancouver, British Columbia, Canada V6T 1Z3 [2] Department of Pathology and Laboratory Medicine, University of British Columbia, 2350 Health Sciences Mall, Life Sciences Centre, Vancouver, British Columbia, Canada V6T 1Z3
| | - David H Kwan
- 1] Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia, Canada V6T 1Z1 [2] Centre for High-Throughput Biology, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z3
| | - Iren Constantinescu
- Centre for Blood Research, University of British Columbia, 2350 Health Sciences Mall, Life Sciences Centre, Vancouver, British Columbia, Canada V6T 1Z3
| | - Fathima A Shaikh
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia, Canada V6T 1Z1
| | - Nicholas A A Rossi
- Centre for Blood Research, University of British Columbia, 2350 Health Sciences Mall, Life Sciences Centre, Vancouver, British Columbia, Canada V6T 1Z3
| | - Stephen G Withers
- 1] Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia, Canada V6T 1Z1 [2] Centre for High-Throughput Biology, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z3 [3] Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z3
| | - Jayachandran N Kizhakkedathu
- 1] Centre for Blood Research, University of British Columbia, 2350 Health Sciences Mall, Life Sciences Centre, Vancouver, British Columbia, Canada V6T 1Z3 [2] Department of Pathology and Laboratory Medicine, University of British Columbia, 2350 Health Sciences Mall, Life Sciences Centre, Vancouver, British Columbia, Canada V6T 1Z3 [3] Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia, Canada V6T 1Z1
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26
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Kwon G, Sung BJ, Yethiraj A. Dynamics in Crowded Environments: Is Non-Gaussian Brownian Diffusion Normal? J Phys Chem B 2014; 118:8128-34. [DOI: 10.1021/jp5011617] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Gyemin Kwon
- Department
of Chemistry and Institute for Biological Interfaces, Sogang University, Seoul 121-742, Republic of Korea
| | - Bong June Sung
- Department
of Chemistry and Institute for Biological Interfaces, Sogang University, Seoul 121-742, Republic of Korea
| | - Arun Yethiraj
- Theoretical
Chemistry Institute and Department of Chemistry, University
of Wisconsin, Madison, Wisconsin 53706, United States
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27
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Kelkar AV, Franses EI, Corti DS. Nonideal diffusion effects and short-range ordering lead to higher aggregation rates in concentrated hard-sphere dispersions. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2014; 30:3647-3657. [PMID: 24646405 DOI: 10.1021/la500176t] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Brownian aggregation in concentrated hard-sphere dispersions is studied using models and Brownian dynamics (BD) simulations. Two new theoretical models are presented and compared to several existing approaches and BD simulation results, which serve as benchmarks. The first new model is an improvement over an existing local density approximation (LDA)-based model. The other is based on the more rigorous Fundamental measure theory (FMT) applied to the "liquid-state" dynamic density-functional theory (DDFT). Both models provide significant improvements over the classical Smoluchowski model. The predictions of the new FM-DDFT-based model for aggregation kinetics are in excellent agreement with BD simulation results for dispersions with initial particle volume fractions, ϕ, up to 0.35 (close to the hard-sphere freezing transition at ϕ = 0.494). In contrast to previous approaches, the nonideal particle diffusion effects and the initial and time-dependent short-range ordering in concentrated dispersions due to entropic packing effects are explicitly considered here, in addition to the unsteady-state effects. The greater accuracy of the FM-DDFT-based model compared to that of the LDA-based models indicates that nonlocal contributions to particle diffusion (only accounted for in the former) play important roles in aggregation. At high concentrations, the FM-DDFT-based model predicts aggregation half-times and gelation times that are up to 2 orders of magnitude shorter than those of the Smoluchowski model. Moreover, the FM-DDFT-based model predicts asymmetric cluster-cluster aggregation rate constants, at least for short times. Overall, a rigorous mechanistic understanding of the enhancement of aggregation kinetics in concentrated dispersions is provided.
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Affiliation(s)
- Aniruddha V Kelkar
- School of Chemical Engineering, Purdue University , West Lafayette, Indiana 47907, United States
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28
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Kim JS, Szleifer I. Crowding-induced formation and structural alteration of nuclear compartments: insights from computer simulations. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2014; 307:73-108. [PMID: 24380593 DOI: 10.1016/b978-0-12-800046-5.00004-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/09/2022]
Abstract
Our understanding of the structural and dynamical characteristics of nuclear structures such as chromosomes and nuclear bodies (NBs) has increased significantly in recent days owing to advances in biophysical and biochemical techniques. These techniques include the use of computer simulations, which have provided further physical insights complementary to findings from experiments. In this chapter, we review recent computer simulation studies on the structural alteration of chromosome subcompartments and the formation and maintenance of NBs in the highly crowded cell nucleus. It is found that because of macromolecular crowding, the degree of chromosome compaction changes significantly and the formation of NBs is facilitated. We further discuss the physical consequences of these phenomena, which may be of critical importance in understanding genome processes.
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Affiliation(s)
- Jun Soo Kim
- Department of Chemistry and Nano Science, Global Top5 Research Program, Ewha Womans University, Seoul, Republic of Korea.
| | - Igal Szleifer
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois, USA; Department of Chemistry, Northwestern University, Evanston, Illinois, USA; Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois, USA
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29
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30
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Höfling F, Franosch T. Anomalous transport in the crowded world of biological cells. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2013; 76:046602. [PMID: 23481518 DOI: 10.1088/0034-4885/76/4/046602] [Citation(s) in RCA: 580] [Impact Index Per Article: 52.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
A ubiquitous observation in cell biology is that the diffusive motion of macromolecules and organelles is anomalous, and a description simply based on the conventional diffusion equation with diffusion constants measured in dilute solution fails. This is commonly attributed to macromolecular crowding in the interior of cells and in cellular membranes, summarizing their densely packed and heterogeneous structures. The most familiar phenomenon is a sublinear, power-law increase of the mean-square displacement (MSD) as a function of the lag time, but there are other manifestations like strongly reduced and time-dependent diffusion coefficients, persistent correlations in time, non-Gaussian distributions of spatial displacements, heterogeneous diffusion and a fraction of immobile particles. After a general introduction to the statistical description of slow, anomalous transport, we summarize some widely used theoretical models: Gaussian models like fractional Brownian motion and Langevin equations for visco-elastic media, the continuous-time random walk model, and the Lorentz model describing obstructed transport in a heterogeneous environment. Particular emphasis is put on the spatio-temporal properties of the transport in terms of two-point correlation functions, dynamic scaling behaviour, and how the models are distinguished by their propagators even if the MSDs are identical. Then, we review the theory underlying commonly applied experimental techniques in the presence of anomalous transport like single-particle tracking, fluorescence correlation spectroscopy (FCS) and fluorescence recovery after photobleaching (FRAP). We report on the large body of recent experimental evidence for anomalous transport in crowded biological media: in cyto- and nucleoplasm as well as in cellular membranes, complemented by in vitro experiments where a variety of model systems mimic physiological crowding conditions. Finally, computer simulations are discussed which play an important role in testing the theoretical models and corroborating the experimental findings. The review is completed by a synthesis of the theoretical and experimental progress identifying open questions for future investigation.
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Affiliation(s)
- Felix Höfling
- Max-Planck-Institut für Intelligente Systeme, Heisenbergstraße 3, 70569 Stuttgart, and Institut für Theoretische Physik IV, Universität Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany
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31
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Cho EJ, Kim JS. Crowding effects on the formation and maintenance of nuclear bodies: insights from molecular-dynamics simulations of simple spherical model particles. Biophys J 2013; 103:424-433. [PMID: 22947858 DOI: 10.1016/j.bpj.2012.07.007] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2012] [Revised: 06/28/2012] [Accepted: 07/05/2012] [Indexed: 12/01/2022] Open
Abstract
The physics of structure formation and maintenance of nuclear bodies (NBs), such as nucleoli, Cajal bodies, promyelocytic leukemia bodies, and speckles, in a crowded nuclear environment remains largely unknown. We investigate the role of macromolecular crowding in the formation and maintenance of NBs using computer simulations of a simple spherical model, called Lennard-Jones (LJ) particles. LJ particles form a one-phase, dilute fluid when the intermolecular interaction is weaker than a critical value, above which they phase separate and form a condensed domain. We find that when volume-exclusive crowders exist in significant concentrations, domain formation is induced even for weaker intermolecular interactions, and the effect is more pronounced with increasing crowder concentration. Simulation results show that a previous experimental finding that promyelocytic leukemia bodies disappear in the less-crowded condition and reassemble in the normal crowded condition can be interpreted as a consequence of the increased intermolecular interactions between NB proteins due to crowding. Based on further analysis of the simulation results, we discuss the acceleration of macromolecular associations that occur within NBs, and the delay of diffusive transport of macromolecules within and out of NBs when the crowder concentration increases. This study suggests that in a polydisperse nuclear environment that is enriched with a variety of macromolecules, macromolecular crowding not only plays an important role in the formation and maintenance of NBs, but also may perform some regulatory functions in response to alterations in the crowding conditions.
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Affiliation(s)
- Eun Jin Cho
- Department of Chemistry and Applied Chemistry, Hanyang University, Kyeonggi-do, Republic of Korea
| | - Jun Soo Kim
- Department of Chemistry and Nano Science, Ewha Womans University, Seoul, Republic of Korea.
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32
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Frazier Z, Alber F. A computational approach to increase time scales in Brownian dynamics-based reaction-diffusion modeling. J Comput Biol 2012; 19:606-18. [PMID: 22697237 DOI: 10.1089/cmb.2012.0027] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Particle-based Brownian dynamics simulations offer the opportunity to not only simulate diffusion of particles but also the reactions between them. They therefore provide an opportunity to integrate varied biological data into spatially explicit models of biological processes, such as signal transduction or mitosis. However, particle based reaction-diffusion methods often are hampered by the relatively small time step needed for accurate description of the reaction-diffusion framework. Such small time steps often prevent simulation times that are relevant for biological processes. It is therefore of great importance to develop reaction-diffusion methods that tolerate larger time steps while maintaining relatively high accuracy. Here, we provide an algorithm, which detects potential particle collisions prior to a BD-based particle displacement and at the same time rigorously obeys the detailed balance rule of equilibrium reactions. We can show that for reaction-diffusion processes of particles mimicking proteins, the method can increase the typical BD time step by an order of magnitude while maintaining similar accuracy in the reaction diffusion modelling.
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Affiliation(s)
- Zachary Frazier
- Program in Molecular and Computational Biology, University of Southern California, Los Angeles, CA, USA
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33
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Three-dimensional stochastic off-lattice model of binding chemistry in crowded environments. PLoS One 2012; 7:e30131. [PMID: 22272286 PMCID: PMC3260218 DOI: 10.1371/journal.pone.0030131] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2011] [Accepted: 12/14/2011] [Indexed: 01/01/2023] Open
Abstract
Molecular crowding is one of the characteristic features of the intracellular environment, defined by a dense mixture of varying kinds of proteins and other molecules. Interaction with these molecules significantly alters the rates and equilibria of chemical reactions in the crowded environment. Numerous fundamental activities of a living cell are strongly influenced by the crowding effect, such as protein folding, protein assembly and disassembly, enzyme activity, and signal transduction. Quantitatively predicting how crowding will affect any particular process is, however, a very challenging problem because many physical and chemical parameters act synergistically in ways that defy easy analysis. To build a more realistic model for this problem, we extend a prior stochastic off-lattice model from two-dimensional (2D) to three-dimensional (3D) space and examine how the 3D results compare to those found in 2D. We show that both models exhibit qualitatively similar crowding effects and similar parameter dependence, particularly with respect to a set of parameters previously shown to act linearly on total reaction equilibrium. There are quantitative differences between 2D and 3D models, although with a generally gradual nonlinear interpolation as a system is extended from 2D to 3D. However, the additional freedom of movement allowed to particles as thickness of the simulation box increases can produce significant quantitative change as a system moves from 2D to 3D. Simulation results over broader parameter ranges further show that the impact of molecular crowding is highly dependent on the specific reaction system examined.
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Abstract
Biological cells accomplish their physiological functions using interconnected networks of genes, proteins, and other biomolecules. Most interactions in biological signaling networks, such as bimolecular association or covalent modification, can be modeled in a physically realistic manner using elementary reaction kinetics. However, the size and combinatorial complexity of such reaction networks have hindered such a mechanistic approach, leading many to conclude that it is premature and to adopt alternative statistical or phenomenological approaches. The recent development of rule-based modeling languages, such as BioNetGen (BNG) and Kappa, enables the precise and succinct encoding of large reaction networks. Coupled with complementary advances in simulation methods, these languages circumvent the combinatorial barrier and allow mechanistic modeling on a much larger scale than previously possible. These languages are also intuitive to the biologist and accessible to the novice modeler. In this chapter, we provide a self-contained tutorial on modeling signal transduction networks using the BNG Language and related software tools. We review the basic syntax of the language and show how biochemical knowledge can be articulated using reaction rules, which can be used to capture a broad range of biochemical and biophysical phenomena in a concise and modular way. A model of ligand-activated receptor dimerization is examined, with a detailed treatment of each step of the modeling process. Sections discussing modeling theory, implicit and explicit model assumptions, and model parameterization are included, with special focus on retaining biophysical realism and avoiding common pitfalls. We also discuss the more advanced case of compartmental modeling using the compartmental extension to BioNetGen. In addition, we provide a comprehensive set of example reaction rules that cover the various aspects of signal transduction, from signaling at the membrane to gene regulation. The reader can modify these reaction rules to model their own systems of interest.
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Affiliation(s)
- John A P Sekar
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
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35
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Bruna M, Chapman SJ. Excluded-volume effects in the diffusion of hard spheres. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2012; 85:011103. [PMID: 22400508 DOI: 10.1103/physreve.85.011103] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2010] [Revised: 09/15/2011] [Indexed: 05/31/2023]
Abstract
Excluded-volume effects can play an important role in determining transport properties in diffusion of particles. Here, the diffusion of finite-sized hard-core interacting particles in two or three dimensions is considered systematically using the method of matched asymptotic expansions. The result is a nonlinear diffusion equation for the one-particle distribution function, with excluded-volume effects enhancing the overall collective diffusion rate. An expression for the effective (collective) diffusion coefficient is obtained. Stochastic simulations of the full particle system are shown to compare well with the solution of this equation for two examples.
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Affiliation(s)
- Maria Bruna
- University of Oxford, Mathematical Institute, 24-29 St. Giles', Oxford OX1 3LB, United Kingdom
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36
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Lee B, Leduc PR, Schwartz R. Unified regression model of binding equilibria in crowded environments. Sci Rep 2011; 1:97. [PMID: 22355615 PMCID: PMC3239167 DOI: 10.1038/srep00097] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2011] [Accepted: 09/05/2011] [Indexed: 01/08/2023] Open
Abstract
Molecular crowding is a critical feature distinguishing intracellular environments
from idealized solution-based environments and is essential to understanding
numerous biochemical reactions, from protein folding to signal transduction. Many
biochemical reactions are dramatically altered by crowding, yet it is extremely
difficult to predict how crowding will quantitatively affect any particular reaction
systems. We previously developed a novel stochastic off-lattice model to efficiently
simulate binding reactions across wide parameter ranges in various crowded
conditions. We now show that a polynomial regression model can incorporate several
interrelated parameters influencing chemistry under crowded conditions. The unified
model of binding equilibria accurately reproduces the results of particle
simulations over a broad range of variation of six physical parameters that
collectively yield a complicated, non-linear crowding effect. The work represents an
important step toward the long-term goal of computationally tractable predictive
models of reaction chemistry in the cellular environment.
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Affiliation(s)
- Byoungkoo Lee
- Department of Biological Sciences and Lane Center for Computational Biology, Carnegie Mellon University, 654 Mellon Institute, 4400 Fifth Avenue., Pittsburgh, PA, USA
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37
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Długosz M, Trylska J. Diffusion in crowded biological environments: applications of Brownian dynamics. BMC BIOPHYSICS 2011; 4:3. [PMID: 21595998 PMCID: PMC3093676 DOI: 10.1186/2046-1682-4-3] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 02/09/2011] [Accepted: 03/02/2011] [Indexed: 01/10/2023]
Abstract
Biochemical reactions in living systems occur in complex, heterogeneous media with total concentrations of macromolecules in the range of 50 - 400 mgml. Molecular species occupy a significant fraction of the immersing medium, up to 40% of volume. Such complex and volume-occupied environments are generally termed 'crowded' and/or 'confined'. In crowded conditions non-specific interactions between macromolecules may hinder diffusion - a major process determining metabolism, transport, and signaling. Also, the crowded media can alter, both qualitatively and quantitatively, the reactions in vivo in comparison with their in vitro counterparts. This review focuses on recent developments in particle-based Brownian dynamics algorithms, their applications to model diffusive transport in crowded systems, and their abilities to reproduce and predict the behavior of macromolecules under in vivo conditions.
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Affiliation(s)
- Maciej Długosz
- Interdisciplinary Centre for Mathematical and Computational Modeling, University of Warsaw, Żwirki i Wigury 93, 02-089 Warsaw, Poland
| | - Joanna Trylska
- Interdisciplinary Centre for Mathematical and Computational Modeling, University of Warsaw, Żwirki i Wigury 93, 02-089 Warsaw, Poland
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38
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Rincón V, Bocanegra R, Rodríguez-Huete A, Rivas G, Mateu MG. Effects of macromolecular crowding on the inhibition of virus assembly and virus-cell receptor recognition. Biophys J 2011; 100:738-746. [PMID: 21281589 PMCID: PMC3030154 DOI: 10.1016/j.bpj.2010.12.3714] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2010] [Revised: 11/22/2010] [Accepted: 12/15/2010] [Indexed: 10/18/2022] Open
Abstract
Biological fluids contain a very high total concentration of macromolecules that leads to volume exclusion by one molecule to another. Theory and experiment have shown that this condition, termed macromolecular crowding, can have significant effects on molecular recognition. However, the influence of molecular crowding on recognition events involving virus particles, and their inhibition by antiviral compounds, is virtually unexplored. Among these processes, capsid self-assembly during viral morphogenesis and capsid-cell receptor recognition during virus entry into cells are receiving increasing attention as targets for the development of new antiviral drugs. In this study, we have analyzed the effect of macromolecular crowding on the inhibition of these two processes by peptides. Macromolecular crowding led to a significant reduction in the inhibitory activity of: 1), a capsid-binding peptide and a small capsid protein domain that interfere with assembly of the human immunodeficiency virus capsid, and 2), a RGD-containing peptide able to block the interaction between foot-and-mouth disease virus and receptor molecules on the host cell membrane (in this case, the effect was dependent on the conditions used). The results, discussed in the light of macromolecular crowding theory, are relevant for a quantitative understanding of molecular recognition processes during virus infection and its inhibition.
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Affiliation(s)
- Verónica Rincón
- Centro de Biología Molecular "Severo Ochoa" (Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid), Universidad Autónoma de Madrid, Madrid, Spain
| | - Rebeca Bocanegra
- Centro de Biología Molecular "Severo Ochoa" (Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid), Universidad Autónoma de Madrid, Madrid, Spain
| | - Alicia Rodríguez-Huete
- Centro de Biología Molecular "Severo Ochoa" (Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid), Universidad Autónoma de Madrid, Madrid, Spain
| | - Germán Rivas
- Centro de Investigaciones Biológicas (Consejo Superior de Investigaciones Científicas), Madrid, Spain
| | - Mauricio G Mateu
- Centro de Biología Molecular "Severo Ochoa" (Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid), Universidad Autónoma de Madrid, Madrid, Spain.
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39
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Kim JS, Yethiraj A. Crowding effects on protein association: effect of interactions between crowding agents. J Phys Chem B 2010; 115:347-53. [PMID: 21166404 DOI: 10.1021/jp107123y] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The cell cytoplasm is a dense environment where the presence of inert cosolutes can significantly alter the rates of protein folding and protein association reactions. Most theoretical studies focus on hard sphere crowding agents and quantify the effect of excluded volume on reaction rates. In this work the effect of interactions between the crowding agents on the thermodynamics of protein association is studied using computer simulation. Three cases are considered, where the crowding agents are (i) hard spheres, (ii) hard spheres with additional attractive or repulsive interactions, and (iii) chains of hard spheres. Reactants and products of the protein association are modeled as hard spheres. Although crowding effects are sensitive to the shape of the reaction product, in most cases the excess free energy difference between the product and reactants (nonideality factor) is insensitive to the interactions between crowding agents, due to a cancellation of effects. The simulations therefore suggest that the hard sphere model of crowding agents has a surprisingly large regime of validity and should be sufficient for a qualitative understanding of the thermodynamics of crowding effects when the interactions of associating proteins with crowding agents other than excluded volume interactions are not significant.
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Affiliation(s)
- Jun Soo Kim
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin, Madison, Wisconsin 53706, USA
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40
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Dorsaz N, De Michele C, Piazza F, De Los Rios P, Foffi G. Diffusion-limited reactions in crowded environments. PHYSICAL REVIEW LETTERS 2010; 105:120601. [PMID: 20867619 DOI: 10.1103/physrevlett.105.120601] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2010] [Indexed: 05/29/2023]
Abstract
Diffusion-limited reactions are usually described within the Smoluchowski theory, which neglects interparticle interactions. We propose a simple way to incorporate excluded-volume effects building on simulations of hard sphere in the presence of a sink. For large values of the sink-to-particle size ratio R(s), the measured encounter rate is in good agreement with a simple generalization of the Smoluchowski equation at high densities. Reducing R(s), the encounter rate is substantially depressed and becomes even nonmonotonic for R(s)<<1. Concurrently with the saturation of the rate, stationary density waves set in close to the sink. A mean-field analysis helps to shed light on the subtle link between such ordering and the slowing down of the encounter dynamics. Finally, we show how an infinitesimal amount of nonreacting impurities can equally slow down dramatically the reaction.
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Affiliation(s)
- N Dorsaz
- University of Fribourg, Adolphe Merkle Institute, CH-1723 Marly 1, Switzerland
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41
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Tsourkas PK, Raychaudhuri S. Monte Carlo investigation of diffusion of receptors and ligands that bind across opposing surfaces. Ann Biomed Eng 2010; 39:427-42. [PMID: 20811955 PMCID: PMC3010212 DOI: 10.1007/s10439-010-0143-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2010] [Accepted: 08/05/2010] [Indexed: 01/22/2023]
Abstract
Studies of receptor diffusion on a cell surface show a variety of behaviors, such as diffusive, sub-diffusive, or super-diffusive motion. However, most studies to date focus on receptor molecules diffusing on a single cell surface. We have previously studied receptor diffusion to probe the molecular mechanism of receptor clustering at the cell–cell junction between two opposing cell surfaces. Here, we characterize the diffusion of receptors and ligands that bind to each other across two opposing cell surfaces, as in cell–cell and cell–bilayer interactions. We use a Monte Carlo method, where receptors and ligands are simulated as independent agents that bind and diffuse probabilistically. We vary receptor–ligand binding affinity and plot the molecule-averaged mean square displacement (MSD) of ligand molecules as a function of time. Our results show that MSD plots are qualitatively different for flat and curved interfaces, as well as between the cases of presence and absence of directed transport of receptor–ligand complexes toward a specific location on the interface. Receptor–ligand binding across two opposing surfaces leads to transient sub-diffusive motion at early times provided the interface is flat. This effect is entirely absent if the interface is curved, however, in this instance we observe sub-diffusive motion. In addition, a decrease in the equilibrium value of the MSD occurs as affinity increases, something which is absent for a flat interface. In the presence of directed transport of receptor–ligand complexes, we observe super-diffusive motion at early times for a flat interface. Super-diffusive motion is absent for a curved interface, however, in this case we observe a transient decrease in MSD with time prior to equilibration for high-affinity values.
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Affiliation(s)
- Philippos K Tsourkas
- Department of Biomedical Engineering, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
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