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Kaushik S, Hung TI, Chang CA. Molecular mechanics studies of factors affecting overall rate in cascade reactions: Multi-enzyme colocalization and environment. Protein Sci 2024; 33:e5175. [PMID: 39276014 PMCID: PMC11401055 DOI: 10.1002/pro.5175] [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: 02/01/2024] [Revised: 08/27/2024] [Accepted: 08/29/2024] [Indexed: 09/16/2024]
Abstract
Millions of years of evolution have optimized many biosynthetic pathways by use of multi-step catalysis. In addition, multi-step metabolic pathways are commonly found in and on membrane-bound organelles in eukaryotic biochemistry. The fundamental mechanisms that facilitate these reaction processes provide strategies to bioengineer metabolic pathways in synthetic chemistry. Using Brownian dynamics simulations, here we modeled intermediate substrate transportation of colocalized yeast-ester biosynthesis enzymes on the membrane. The substrate acetate ion traveled from the pocket of aldehyde dehydrogenase to its target enzyme acetyl-CoA synthetase, then the substrate acetyl CoA diffused from Acs1 to the active site of the next enzyme, alcohol-O-acetyltransferase. Arranging two enzymes with the smallest inter-enzyme distance of 60 Å had the fastest average substrate association time as compared with anchoring enzymes with larger inter-enzyme distances. When the off-target side reactions were turned on, most substrates were lost, which suggests that native localization is necessary for efficient final product synthesis. We also evaluated the effects of intermolecular interactions, local substrate concentrations, and membrane environment to bring mechanistic insights into the colocalization pathways. The computation work demonstrates that creating spatially organized multi-enzymes on membranes can be an effective strategy to increase final product synthesis in bioengineering systems.
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Affiliation(s)
- Shivansh Kaushik
- Department of ChemistryUniversity of California RiversideRiversideCaliforniaUSA
| | - Ta I Hung
- Department of ChemistryUniversity of California RiversideRiversideCaliforniaUSA
| | - Chia‐en A. Chang
- Department of ChemistryUniversity of California RiversideRiversideCaliforniaUSA
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2
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Xie Y, Minteer SD, Banta S, Barton SC. Markov State Study of Electrostatic Channeling within the Tricarboxylic Acid Cycle Supercomplex. ACS NANOSCIENCE AU 2022; 2:414-421. [PMID: 37102132 PMCID: PMC10125334 DOI: 10.1021/acsnanoscienceau.2c00011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The high efficiency of cascade reactions in supramolecular enzyme nanoassemblies, known as metabolons, has attracted substantial attention in various fields ranging from fundamental biochemistry and molecular biology to recent applications in biofuel cells, biosensors, and chemical synthesis. One reason for the high efficiency of metabolons is the structures formed by sequential enzymes that allow the direct transport of intermediates between consecutive active sites. The supercomplex of malate dehydrogenase (MDH) and citrate synthase (CS) is an ideal example of the controlled transport of intermediates via electrostatic channeling. Here, using a combination of molecular dynamics (MD) simulations and a Markov state model (MSM), we examined the transport process of the intermediate oxaloacetate (OAA) from MDH to CS. The MSM enables the identification of the dominant transport pathways of OAA from MDH to CS. Analysis of all pathways using a hub score approach reveals a small set of residues that control OAA transport. This set includes an arginine residue previously identified experimentally. MSM analysis of a mutated complex, where the identified arginine is replaced by alanine, led to a 2-fold decrease in transfer efficiency, also consistent with experimental results. This work provides a molecular-level understanding of the electrostatic channeling mechanism and will enable the further design of catalytic nanostructures utilizing electrostatic channeling.
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Affiliation(s)
- Yan Xie
- Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, Michigan 48824, United States
| | - Shelley D. Minteer
- Department of Chemistry, The University of Utah, Salt Lake City, Utah 84112, United States
| | - Scott Banta
- Department of Chemical Engineering, Columbia University, New York, New York 10027, United States
| | - Scott Calabrese Barton
- Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, Michigan 48824, United States
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3
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Rahmaninejad H, Pace T, Bhatt S, Sun B, Kekenes-Huskey P. Co-localization and confinement of ecto-nucleotidases modulate extracellular adenosine nucleotide distributions. PLoS Comput Biol 2020; 16:e1007903. [PMID: 32584811 PMCID: PMC7316229 DOI: 10.1371/journal.pcbi.1007903] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 04/22/2020] [Indexed: 12/30/2022] Open
Abstract
Nucleotides comprise small molecules that perform critical signaling roles in biological systems. Adenosine-based nucleotides, including adenosine tri-, di-, and mono-phosphate, are controlled through their rapid degradation by diphosphohydrolases and ecto-nucleotidases (NDAs). The interplay between nucleotide signaling and degradation is especially important in synapses formed between cells, which create signaling 'nanodomains'. Within these 'nanodomains', charged nucleotides interact with densely-packed membranes and biomolecules. While the contributions of electrostatic and steric interactions within such nanodomains are known to shape diffusion-limited reaction rates, less is understood about how these factors control the kinetics of nucleotidase activity. To quantify these factors, we utilized reaction-diffusion numerical simulations of 1) adenosine triphosphate (ATP) hydrolysis into adenosine monophosphate (AMP) and 2) AMP into adenosine (Ado) via two representative nucleotidases, CD39 and CD73. We evaluate these sequentially-coupled reactions in nanodomain geometries representative of extracellular synapses, within which we localize the nucleotidases. With this model, we find that 1) nucleotidase confinement reduces reaction rates relative to an open (bulk) system, 2) the rates of AMP and ADO formation are accelerated by restricting the diffusion of substrates away from the enzymes, and 3) nucleotidase co-localization and the presence of complementary (positive) charges to ATP enhance reaction rates, though the impact of these contributions on nucleotide pools depends on the degree to which the membrane competes for substrates. As a result, these contributions integratively control the relative concentrations and distributions of ATP and its metabolites within the junctional space. Altogether, our studies suggest that CD39 and CD73 nucleotidase activity within junctional spaces can exploit their confinement and favorable electrostatic interactions to finely control nucleotide signaling.
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Affiliation(s)
- Hadi Rahmaninejad
- Department of Physics and Astronomy, University of Kentucky, Lexington, Kentucky, United States of America
| | - Tom Pace
- Department of Physics and Astronomy, University of Kentucky, Lexington, Kentucky, United States of America
| | - Shashank Bhatt
- Paul Laurence Dunbar High School, Lexington, Kentucky, United States of America
| | - Bin Sun
- Department of Chemistry, University of Kentucky, Lexington, Kentucky, United States of America
| | - Peter Kekenes-Huskey
- Department of Cell & Molecular Physiology, Loyola University Chicago, Chicago, Illinois, United States of America
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4
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Kekenes-Huskey PM, Eun C, McCammon JA. Enzyme localization, crowding, and buffers collectively modulate diffusion-influenced signal transduction: Insights from continuum diffusion modeling. J Chem Phys 2016; 143:094103. [PMID: 26342355 DOI: 10.1063/1.4929528] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Biochemical reaction networks consisting of coupled enzymes connect substrate signaling events with biological function. Substrates involved in these reactions can be strongly influenced by diffusion "barriers" arising from impenetrable cellular structures and macromolecules, as well as interactions with biomolecules, especially within crowded environments. For diffusion-influenced reactions, the spatial organization of diffusion barriers arising from intracellular structures, non-specific crowders, and specific-binders (buffers) strongly controls the temporal and spatial reaction kinetics. In this study, we use two prototypical biochemical reactions, a Goodwin oscillator, and a reaction with a periodic source/sink term to examine how a diffusion barrier that partitions substrates controls reaction behavior. Namely, we examine how conditions representative of a densely packed cytosol, including reduced accessible volume fraction, non-specific interactions, and buffers, impede diffusion over nanometer length-scales. We find that diffusion barriers can modulate the frequencies and amplitudes of coupled diffusion-influenced reaction networks, as well as give rise to "compartments" of decoupled reactant populations. These effects appear to be intensified in the presence of buffers localized to the diffusion barrier. These findings have strong implications for the role of the cellular environment in tuning the dynamics of signaling pathways.
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Affiliation(s)
| | - Changsun Eun
- Howard Hughes Medical Institute, University of California San Diego, La Jolla, California 92093-0365, USA
| | - J A McCammon
- Howard Hughes Medical Institute, University of California San Diego, La Jolla, California 92093-0365, USA
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5
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Zhang YHP. Production of biofuels and biochemicals by in vitro synthetic biosystems: Opportunities and challenges. Biotechnol Adv 2015; 33:1467-83. [DOI: 10.1016/j.biotechadv.2014.10.009] [Citation(s) in RCA: 116] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2014] [Revised: 10/09/2014] [Accepted: 10/19/2014] [Indexed: 12/20/2022]
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Metzger VT, Eun C, Kekenes-Huskey PM, Huber G, McCammon JA. Electrostatic channeling in P. falciparum DHFR-TS: Brownian dynamics and Smoluchowski modeling. Biophys J 2015; 107:2394-402. [PMID: 25418308 DOI: 10.1016/j.bpj.2014.09.039] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Revised: 09/15/2014] [Accepted: 09/19/2014] [Indexed: 11/15/2022] Open
Abstract
We perform Brownian dynamics simulations and Smoluchowski continuum modeling of the bifunctional Plasmodium falciparum dihydrofolate reductase-thymidylate synthase (P. falciparum DHFR-TS) with the objective of understanding the electrostatic channeling of dihydrofolate generated at the TS active site to the DHFR active site. The results of Brownian dynamics simulations and Smoluchowski continuum modeling suggest that compared to Leishmania major DHFR-TS, P. falciparum DHFR-TS has a lower but significant electrostatic-mediated channeling efficiency (?15-25%) at physiological pH (7.0) and ionic strength (150 mM). We also find that removing the electric charges from key basic residues located between the DHFR and TS active sites significantly reduces the channeling efficiency of P. falciparum DHFR-TS. Although several protozoan DHFR-TS enzymes are known to have similar tertiary and quaternary structure, subtle differences in structure, active-site geometry, and charge distribution appear to influence both electrostatic-mediated and proximity-based substrate channeling.
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Affiliation(s)
- Vincent T Metzger
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California.
| | - Changsun Eun
- Howard Hughes Medical Institute, University of California San Diego, La Jolla, California.
| | | | - Gary Huber
- Howard Hughes Medical Institute, University of California San Diego, La Jolla, California
| | - J Andrew McCammon
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California; Howard Hughes Medical Institute, University of California San Diego, La Jolla, California; Department of Pharmacology, University of California San Diego, La Jolla, California
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7
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Kekenes-Huskey PM, Gillette AK, McCammon JA. Predicting the influence of long-range molecular interactions on macroscopic-scale diffusion by homogenization of the Smoluchowski equation. J Chem Phys 2015; 140:174106. [PMID: 24811624 DOI: 10.1063/1.4873382] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The macroscopic diffusion constant for a charged diffuser is in part dependent on (1) the volume excluded by solute "obstacles" and (2) long-range interactions between those obstacles and the diffuser. Increasing excluded volume reduces transport of the diffuser, while long-range interactions can either increase or decrease diffusivity, depending on the nature of the potential. We previously demonstrated [P. M. Kekenes-Huskey et al., Biophys. J. 105, 2130 (2013)] using homogenization theory that the configuration of molecular-scale obstacles can both hinder diffusion and induce diffusional anisotropy for small ions. As the density of molecular obstacles increases, van der Waals (vdW) and electrostatic interactions between obstacle and a diffuser become significant and can strongly influence the latter's diffusivity, which was neglected in our original model. Here, we extend this methodology to include a fixed (time-independent) potential of mean force, through homogenization of the Smoluchowski equation. We consider the diffusion of ions in crowded, hydrophilic environments at physiological ionic strengths and find that electrostatic and vdW interactions can enhance or depress effective diffusion rates for attractive or repulsive forces, respectively. Additionally, we show that the observed diffusion rate may be reduced independent of non-specific electrostatic and vdW interactions by treating obstacles that exhibit specific binding interactions as "buffers" that absorb free diffusers. Finally, we demonstrate that effective diffusion rates are sensitive to distribution of surface charge on a globular protein, Troponin C, suggesting that the use of molecular structures with atomistic-scale resolution can account for electrostatic influences on substrate transport. This approach offers new insight into the influence of molecular-scale, long-range interactions on transport of charged species, particularly for diffusion-influenced signaling events occurring in crowded cellular environments.
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Affiliation(s)
- P M Kekenes-Huskey
- Department of Pharmacology, University of California San Diego, La Jolla, California 92093-0636, USA
| | - A K Gillette
- Department of Mathematics, University of Arizona, Tucson, Arizona 85721-0089, USA
| | - J A McCammon
- Department of Pharmacology, University of California San Diego, La Jolla, California 92093-0636, USA
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8
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Eun C, Kekenes-Huskey PM, Metzger VT, McCammon JA. A model study of sequential enzyme reactions and electrostatic channeling. J Chem Phys 2014; 140:105101. [PMID: 24628210 DOI: 10.1063/1.4867286] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We study models of two sequential enzyme-catalyzed reactions as a basic functional building block for coupled biochemical networks. We investigate the influence of enzyme distributions and long-range molecular interactions on reaction kinetics, which have been exploited in biological systems to maximize metabolic efficiency and signaling effects. Specifically, we examine how the maximal rate of product generation in a series of sequential reactions is dependent on the enzyme distribution and the electrostatic composition of its participant enzymes and substrates. We find that close proximity between enzymes does not guarantee optimal reaction rates, as the benefit of decreasing enzyme separation is countered by the volume excluded by adjacent enzymes. We further quantify the extent to which the electrostatic potential increases the efficiency of transferring substrate between enzymes, which supports the existence of electrostatic channeling in nature. Here, a major finding is that the role of attractive electrostatic interactions in confining intermediate substrates in the vicinity of the enzymes can contribute more to net reactive throughput than the directional properties of the electrostatic fields. These findings shed light on the interplay of long-range interactions and enzyme distributions in coupled enzyme-catalyzed reactions, and their influence on signaling in biological systems.
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Affiliation(s)
- Changsun Eun
- Howard Hughes Medical Institute, University of California, San Diego, La Jolla, California 92093, USA
| | - Peter M Kekenes-Huskey
- Department of Pharmacology, University of California, San Diego, La Jolla, California 92093, USA
| | - Vincent T Metzger
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, USA
| | - J Andrew McCammon
- Howard Hughes Medical Institute, University of California, San Diego, La Jolla, California 92093, USA
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9
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Multi-core CPU or GPU-accelerated Multiscale Modeling for Biomolecular Complexes. COMPUTATIONAL AND MATHEMATICAL BIOPHYSICS 2013; 1. [PMID: 24352481 DOI: 10.2478/mlbmb-2013-0009] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Multi-scale modeling plays an important role in understanding the structure and biological functionalities of large biomolecular complexes. In this paper, we present an efficient computational framework to construct multi-scale models from atomic resolution data in the Protein Data Bank (PDB), which is accelerated by multi-core CPU and programmable Graphics Processing Units (GPU). A multi-level summation of Gaus-sian kernel functions is employed to generate implicit models for biomolecules. The coefficients in the summation are designed as functions of the structure indices, which specify the structures at a certain level and enable a local resolution control on the biomolecular surface. A method called neighboring search is adopted to locate the grid points close to the expected biomolecular surface, and reduce the number of grids to be analyzed. For a specific grid point, a KD-tree or bounding volume hierarchy is applied to search for the atoms contributing to its density computation, and faraway atoms are ignored due to the decay of Gaussian kernel functions. In addition to density map construction, three modes are also employed and compared during mesh generation and quality improvement to generate high quality tetrahedral meshes: CPU sequential, multi-core CPU parallel and GPU parallel. We have applied our algorithm to several large proteins and obtained good results.
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10
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Kekenes-Huskey PM, Cheng Y, Hake JE, Sachse FB, Bridge JH, Holst MJ, McCammon JA, McCulloch AD, Michailova AP. Modeling effects of L-type ca(2+) current and na(+)-ca(2+) exchanger on ca(2+) trigger flux in rabbit myocytes with realistic T-tubule geometries. Front Physiol 2012; 3:351. [PMID: 23060801 PMCID: PMC3463892 DOI: 10.3389/fphys.2012.00351] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2012] [Accepted: 08/16/2012] [Indexed: 12/26/2022] Open
Abstract
The transverse tubular system of rabbit ventricular myocytes consists of cell membrane invaginations (t-tubules) that are essential for efficient cardiac excitation-contraction coupling. In this study, we investigate how t-tubule micro-anatomy, L-type Ca2+ channel (LCC) clustering, and allosteric activation of Na+/Ca2+ exchanger by L-type Ca2+ current affects intracellular Ca2+ dynamics. Our model includes a realistic 3D geometry of a single t-tubule and its surrounding half-sarcomeres for rabbit ventricular myocytes. The effects of spatially distributed membrane ion-transporters (LCC, Na+/Ca2+ exchanger, sarcolemmal Ca2+ pump, and sarcolemmal Ca2+ leak), and stationary and mobile Ca2+ buffers (troponin C, ATP, calmodulin, and Fluo-3) are also considered. We used a coupled reaction-diffusion system to describe the spatio-temporal concentration profiles of free and buffered intracellular Ca2+. We obtained parameters from voltage-clamp protocols of L-type Ca2+ current and line-scan recordings of Ca2+ concentration profiles in rabbit cells, in which the sarcoplasmic reticulum is disabled. Our model results agree with experimental measurements of global Ca2+ transient in myocytes loaded with 50 μM Fluo-3. We found that local Ca2+ concentrations within the cytosol and sub-sarcolemma, as well as the local trigger fluxes of Ca2+ crossing the cell membrane, are sensitive to details of t-tubule micro-structure and membrane Ca2+ flux distribution. The model additionally predicts that local Ca2+ trigger fluxes are at least threefold to eightfold higher than the whole-cell Ca2+ trigger flux. We found also that the activation of allosteric Ca2+-binding sites on the Na+/Ca2+ exchanger could provide a mechanism for regulating global and local Ca2+ trigger fluxes in vivo. Our studies indicate that improved structural and functional models could improve our understanding of the contributions of L-type and Na+/Ca2+ exchanger fluxes to intracellular Ca2+ dynamics.
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Alves CS, Kairys V, Castanho MARB, Fernandes MX. Interaction of antimicrobial peptides, BP100 and pepR, with model membrane systems as explored by brownian dynamics simulations on a coarse-grained model. Biopolymers 2012. [DOI: 10.1002/bip.22075] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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12
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Bauler P, Huber GA, McCammon JA. Hybrid finite element and Brownian dynamics method for diffusion-controlled reactions. J Chem Phys 2012; 136:164107. [PMID: 22559470 DOI: 10.1063/1.4704808] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Diffusion is often the rate determining step in many biological processes. Currently, the two main computational methods for studying diffusion are stochastic methods, such as Brownian dynamics, and continuum methods, such as the finite element method. This paper proposes a new hybrid diffusion method that couples the strengths of each of these two methods. The method is derived for a general multidimensional system, and is presented using a basic test case for 1D linear and radially symmetric diffusion systems.
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Affiliation(s)
- Patricia Bauler
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, USA
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13
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Cheng Y, Kekenes-Huskey P, Hake J, Holst M, McCammon J, Michailova A. Multi-Scale Continuum Modeling of Biological Processes: From Molecular Electro-Diffusion to Sub-Cellular Signaling Transduction. ACTA ACUST UNITED AC 2012; 5. [PMID: 23505398 DOI: 10.1088/1749-4699/5/1/015002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
This article provides a brief review of multi-scale modeling at the molecular to cellular scale, with new results for heart muscle cells. A finite element-based simulation package (SMOL) was used to investigate the signaling transduction at molecular and sub-cellular scales (http://mccammon.ucsd.edu/smol/, http://FETK.org) by numerical solution of time-dependent Smoluchowski equations and a reaction-diffusion system. At the molecular scale, SMOL has yielded experimentally-validated estimates of the diffusion-limited association rates for the binding of acetylcholine to mouse acetylcholinesterase using crystallographic structural data. The predicted rate constants exhibit increasingly delayed steady-state times with increasing ionic strength and demonstrate the role of an enzyme's electrostatic potential in influencing ligand binding. At the sub-cellular scale, an extension of SMOL solves a non-linear, reaction-diffusion system describing Ca2+ ligand buffering and diffusion in experimentally-derived rodent ventricular myocyte geometries. Results reveal the important role for mobile and stationary Ca2+ buffers, including Ca2+ indicator dye. We found that the alterations in Ca2+-binding and dissociation rates of troponin C (TnC) and total TnC concentration modulate subcellular Ca2+ signals. Model predicts that reduced off-rate in whole troponin complex (TnC, TnI, TnT) versus reconstructed thin filaments (Tn, Tm, actin) alters cytosolic Ca2+ dynamics under control conditions or in disease-linked TnC mutations. The ultimate goal of these studies is to develop scalable methods and theories for integration of molecular-scale information into simulations of cellular-scale systems.
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Affiliation(s)
- Y Cheng
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
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15
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Cheng Y, Yu Z, Hoshijima M, Holst MJ, McCulloch AD, McCammon JA, Michailova AP. Numerical analysis of Ca2+ signaling in rat ventricular myocytes with realistic transverse-axial tubular geometry and inhibited sarcoplasmic reticulum. PLoS Comput Biol 2010; 6:e1000972. [PMID: 21060856 PMCID: PMC2965743 DOI: 10.1371/journal.pcbi.1000972] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2009] [Accepted: 09/23/2010] [Indexed: 12/21/2022] Open
Abstract
The t-tubules of mammalian ventricular myocytes are invaginations of the cell membrane that occur at each Z-line. These invaginations branch within the cell to form a complex network that allows rapid propagation of the electrical signal, and hence synchronous rise of intracellular calcium (Ca2+). To investigate how the t-tubule microanatomy and the distribution of membrane Ca2+ flux affect cardiac excitation-contraction coupling we developed a 3-D continuum model of Ca2+ signaling, buffering and diffusion in rat ventricular myocytes. The transverse-axial t-tubule geometry was derived from light microscopy structural data. To solve the nonlinear reaction-diffusion system we extended SMOL software tool (http://mccammon.ucsd.edu/smol/). The analysis suggests that the quantitative understanding of the Ca2+ signaling requires more accurate knowledge of the t-tubule ultra-structure and Ca2+ flux distribution along the sarcolemma. The results reveal the important role for mobile and stationary Ca2+ buffers, including the Ca2+ indicator dye. In agreement with experiment, in the presence of fluorescence dye and inhibited sarcoplasmic reticulum, the lack of detectible differences in the depolarization-evoked Ca2+ transients was found when the Ca2+ flux was heterogeneously distributed along the sarcolemma. In the absence of fluorescence dye, strongly non-uniform Ca2+ signals are predicted. Even at modest elevation of Ca2+, reached during Ca2+ influx, large and steep Ca2+ gradients are found in the narrow sub-sarcolemmal space. The model predicts that the branched t-tubule structure and changes in the normal Ca2+ flux density along the cell membrane support initiation and propagation of Ca2+ waves in rat myocytes. In cardiac muscle cells, calcium (Ca2+) is best known for its role in contraction activation. A remarkable amount of quantitative data on cardiac cell structure, ion-transporting protein distributions and intracellular Ca2+ dynamics has been accumulated. Various alterations in the protein distributions or cell ultra-structure are now recognized to be the primary mechanisms of cardiac dysfunction in a diverse range of common pathologies including cardiac arrhythmias and hypertrophy. Using a 3-D computational model, incorporating more realistic transverse-axial t-tubule geometry and considering geometric irregularities and inhomogeneities in the distribution of ion-transporting proteins, we analyze several important spatial and temporal features of Ca2+ signaling in rat ventricular myocytes. This study demonstrates that the computational models could serve as powerful tools for prediction and analyses of how the Ca2+ dynamics and cardiac excitation-contraction coupling are regulated under normal conditions or certain pathologies. The use of computational and mathematical approaches will help also to better understand aspects of cell functions that are not currently amenable to experimental investigation.
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Affiliation(s)
- Yuhui Cheng
- Department of Bioengineering, University of California San Diego, La Jolla, California, United States of America
| | - Zeyun Yu
- Department of Computer Science, University of Wisconsin, Milwaukee, Wisconsin, United States of America
| | - Masahiko Hoshijima
- Department of Medicine, University of California San Diego, La Jolla, California, United States of America
| | - Michael J. Holst
- Department of Mathematics, University of California San Diego, La Jolla, California, United States of America
| | - Andrew D. McCulloch
- Department of Bioengineering, University of California San Diego, La Jolla, California, United States of America
| | - J. Andrew McCammon
- Department of Chemistry and Biochemistry, Department of Pharmacology, University of California San Diego, La Jolla, California, United States of America
- Howard Hughes Medical Institute, University of California San Diego, La Jolla, California, United States of America
| | - Anushka P. Michailova
- Department of Bioengineering, University of California San Diego, La Jolla, California, United States of America
- * E-mail:
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16
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Eisenberg B. Multiple Scales in the Simulation of Ion Channels and Proteins. THE JOURNAL OF PHYSICAL CHEMISTRY. C, NANOMATERIALS AND INTERFACES 2010; 114:20719-20733. [PMID: 21135913 PMCID: PMC2996618 DOI: 10.1021/jp106760t] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Computation of living processes creates great promise for the everyday life of mankind and great challenges for physical scientists. Simulations molecular dynamics have great appeal to biologists as a natural extension of structural biology. Once a biologist sees a structure, she/he wants to see it move. Molecular biology has shown that a small number of atoms, sometimes even one messenger ion, like Ca(2+), can control biological function on the scale of cells, organs, tissues, and organisms. Enormously concentrated ions-at number densities of ~20 M-in protein channels and enzymes are responsible for many of the characteristics of living systems, just as highly concentrated ions near electrodes are responsible for many of the characteristics of electrochemical systems. Here we confront the reality of the scale differences of ions. We show that the scale differences needed to simulate all the atoms of biological cells are 10(7) in linear dimension, 10(21) in three dimensions, 10(9) in resolution, 10(11) in time, and 10(13) in particle number (to deal with concentrations of Ca(2+)). These scales must be dealt with simultaneously if the simulation is to deal with most biological functions. Biological function extends across all of them, all at once in most cases. We suggest a computational approach using explicit multiscale analysis instead of implicit simulation of all scales. The approach is based on an energy variational principle EnVarA introduced by Chun Liu to deal with complex fluids. Variational methods deal automatically with multiple interacting components and scales. When an additional component is added to the system, the resulting Euler Lagrange field equations change form automatically-by algebra alone-without additional unknown parameters. Multifaceted interactions are solutions of the resulting equations. We suggest that ionic solutions should be viewed as complex fluids with simple components. Highly concentrated solutions-dominated by interactions of components-are easily computed by EnVarA. Successful computation of ions concentrated in special places may be a significant step to understanding the defining characteristics of biological and electrochemical systems. Indeed, computing ions near proteins and nucleic acids may prove as important to molecular biology and chemical technology as computing holes and electrons has been to our semiconductor and digital technology.
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Affiliation(s)
- Bob Eisenberg
- Department of Molecular Biophysics and Physiology, Rush University, Chicago IL 60612
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Bauler P, Huber G, Leyh T, McCammon JA. Channeling by Proximity: The Catalytic Advantages of Active Site Colocalization Using Brownian Dynamics. J Phys Chem Lett 2010; 1:1332-1335. [PMID: 20454551 PMCID: PMC2865391 DOI: 10.1021/jz1002007] [Citation(s) in RCA: 95] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2010] [Accepted: 04/06/2010] [Indexed: 05/22/2023]
Abstract
Nature often colocalizes successive steps in a metabolic pathway. Such organization is predicted to increase the effective concentration of pathway intermediates near their recipient active sites and to enhance catalytic efficiency. Here, the pathway of a two-step reaction is modeled using a simple spherical approximation for the enzymes and substrate particles. Brownian dynamics are used to simulate the trajectory of a substrate particle as it diffuses between the active site zones of two different enzyme spheres. The results approximate distances for the most effective reaction pathways, indicating that the most effective reaction pathway is one in which the active sites are closely aligned. However, when the active sites are too close, the ability of the substrate to react with the first enzyme was hindered, suggesting that even the most efficient orientations can be improved for a system that is allowed to rotate or change orientation to optimize the likelihood of reaction at both sites.
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Affiliation(s)
- Patricia Bauler
- Department of Chemistry and Biochemistry
- Department of Pharmacology
- Center for Theoretical Biological Physics
- Howard Hughes Medical Institute
- To whom correspondence should be addressed. E-mail: ,
| | - Gary Huber
- Department of Chemistry and Biochemistry
- Department of Pharmacology
- Center for Theoretical Biological Physics
- Howard Hughes Medical Institute
- To whom correspondence should be addressed. E-mail: ,
| | - Thomas Leyh
- Department of Microbiology and Immunology, The Albert Einstein College of Medicine, Bronx, New York 10461
| | - J. Andrew McCammon
- Department of Chemistry and Biochemistry
- Department of Pharmacology
- Center for Theoretical Biological Physics
- Howard Hughes Medical Institute
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dos Santos ES, Gritta DS, Taft CA, Almeida PF, Ramos-de-Souza E. Molecular dynamics simulation of the adenylylsulphate reductase from hyperthermophilicArchaeoglobus fulgidus. MOLECULAR SIMULATION 2010. [DOI: 10.1080/08927020903177658] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Fatmi MQ, Ai R, Chang CEA. Synergistic Regulation and Ligand-Induced Conformational Changes of Tryptophan Synthase. Biochemistry 2009; 48:9921-31. [DOI: 10.1021/bi901358j] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- M. Qaiser Fatmi
- Department of Chemistry, University of California, Riverside, California 92521
| | - Rizi Ai
- Department of Chemistry, University of California, Riverside, California 92521
| | - Chia-en A. Chang
- Department of Chemistry, University of California, Riverside, California 92521
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Russel D, Lasker K, Phillips J, Schneidman-Duhovny D, Velázquez-Muriel JA, Sali A. The structural dynamics of macromolecular processes. Curr Opin Cell Biol 2009; 21:97-108. [PMID: 19223165 DOI: 10.1016/j.ceb.2009.01.022] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2008] [Revised: 12/20/2008] [Accepted: 01/20/2009] [Indexed: 12/17/2022]
Abstract
Dynamic processes involving macromolecular complexes are essential to cell function. These processes take place over a wide variety of length scales from nanometers to micrometers, and over time scales from nanoseconds to minutes. As a result, information from a variety of different experimental and computational approaches is required. We review the relevant sources of information and introduce a framework for integrating the data to produce representations of dynamic processes.
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Affiliation(s)
- Daniel Russel
- Department of Bioengineering and Therapeutic Sciences, University of California at San Francisco, 1700 4th Street, San Francisco, CA 94158-2330, USA
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