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Ojha AA, Votapka LW, Amaro RE. QMrebind: incorporating quantum mechanical force field reparameterization at the ligand binding site for improved drug-target kinetics through milestoning simulations. Chem Sci 2023; 14:13159-13175. [PMID: 38023523 PMCID: PMC10664576 DOI: 10.1039/d3sc04195f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 10/22/2023] [Indexed: 12/01/2023] Open
Abstract
Understanding the interaction of ligands with biomolecules is an integral component of drug discovery and development. Challenges for computing thermodynamic and kinetic quantities for pharmaceutically relevant receptor-ligand complexes include the size and flexibility of the ligands, large-scale conformational rearrangements of the receptor, accurate force field parameters, simulation efficiency, and sufficient sampling associated with rare events. Our recently developed multiscale milestoning simulation approach, SEEKR2 (Simulation Enabled Estimation of Kinetic Rates v.2), has demonstrated success in predicting unbinding (koff) kinetics by employing molecular dynamics (MD) simulations in regions closer to the binding site. The MD region is further subdivided into smaller Voronoi tessellations to improve the simulation efficiency and parallelization. To date, all MD simulations are run using general molecular mechanics (MM) force fields. The accuracy of calculations can be further improved by incorporating quantum mechanical (QM) methods into generating system-specific force fields through reparameterizing ligand partial charges in the bound state. The force field reparameterization process modifies the potential energy landscape of the bimolecular complex, enabling a more accurate representation of the intermolecular interactions and polarization effects at the bound state. We present QMrebind (Quantum Mechanical force field reparameterization at the receptor-ligand binding site), an ORCA-based software that facilitates reparameterizing the potential energy function within the phase space representing the bound state in a receptor-ligand complex. With SEEKR2 koff estimates and experimentally determined kinetic rates, we compare and interpret the receptor-ligand unbinding kinetics obtained using the newly reparameterized force fields for model host-guest systems and HSP90-inhibitor complexes. This method provides an opportunity to achieve higher accuracy in predicting receptor-ligand koff rate constants.
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Affiliation(s)
- Anupam Anand Ojha
- Department of Chemistry and Biochemistry, University of California San Diego La Jolla California 92093 USA
| | - Lane William Votapka
- Department of Chemistry and Biochemistry, University of California San Diego La Jolla California 92093 USA
| | - Rommie Elizabeth Amaro
- Department of Molecular Biology, University of California San Diego La Jolla California 92093 USA
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2
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Hock MT, Teitgen AE, McCabe KJ, Hirakis SP, Huber GA, Regnier M, Amaro RE, McCammon JA, McCulloch AD. Multiscale computational modeling of the effects of 2'-deoxy-ATP on cardiac muscle calcium handling. JOURNAL OF APPLIED PHYSICS 2023; 134:074905. [PMID: 37601331 PMCID: PMC10435275 DOI: 10.1063/5.0157935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 07/27/2023] [Indexed: 08/22/2023]
Abstract
2'-Deoxy-ATP (dATP), a naturally occurring near analog of ATP, is a well-documented myosin activator that has been shown to increase contractile force, improve pump function, and enhance lusitropy in the heart. Calcium transients in cardiomyocytes with elevated levels of dATP show faster calcium decay compared with cardiomyocytes with basal levels of dATP, but the mechanisms behind this are unknown. Here, we design and utilize a multiscale computational modeling framework to test the hypothesis that dATP acts on the sarcoendoplasmic reticulum calcium-ATPase (SERCA) pump to accelerate calcium re-uptake into the sarcoplasmic reticulum during cardiac relaxation. Gaussian accelerated molecular dynamics simulations of human cardiac SERCA2A in the E1 apo, ATP-bound and dATP-bound states showed that dATP forms more stable contacts in the nucleotide binding pocket of SERCA and leads to increased closure of cytosolic domains. These structural changes ultimately lead to changes in calcium binding, which we assessed using Brownian dynamics simulations. We found that dATP increases calcium association rate constants to SERCA and that dATP binds to apo SERCA more rapidly than ATP. Using a compartmental ordinary differential equation model of human cardiomyocyte excitation-contraction coupling, we found that these increased association rate constants contributed to the accelerated rates of calcium transient decay observed experimentally. This study provides clear mechanistic evidence of enhancements in cardiac SERCA2A pump function due to interactions with dATP.
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Affiliation(s)
- Marcus T. Hock
- Department of Bioengineering, University of California San Diego, La Jolla, California 92093, USA
| | - Abigail E. Teitgen
- Department of Bioengineering, University of California San Diego, La Jolla, California 92093, USA
| | - Kimberly J. McCabe
- Department of Computational Physiology, Simula Resesarch Laboratory, Oslo 0164, Norway
| | - Sophia P. Hirakis
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, USA
| | - Gary A. Huber
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, USA
| | - Michael Regnier
- Department of Bioengineering, University of Washington, Seattle, Washington 98109, USA
| | - Rommie E. Amaro
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, USA
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3
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Tworek JW, Elcock AH. Orientationally Averaged Version of the Rotne-Prager-Yamakawa Tensor Provides a Fast but Still Accurate Treatment of Hydrodynamic Interactions in Brownian Dynamics Simulations of Biological Macromolecules. J Chem Theory Comput 2023; 19:5099-5111. [PMID: 37409946 PMCID: PMC10413861 DOI: 10.1021/acs.jctc.3c00476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Indexed: 07/07/2023]
Abstract
The Brownian dynamics (BD) simulation technique is widely used to model the diffusive and conformational dynamics of complex systems comprising biological macromolecules. For the diffusive properties of macromolecules to be described correctly by BD simulations, it is necessary to include hydrodynamic interactions (HIs). When modeled at the Rotne-Prager-Yamakawa (RPY) level of theory, for example, the translational and rotational diffusion coefficients of isolated macromolecules can be accurately reproduced; when HIs are neglected, however, diffusion coefficients can be underestimated by an order of magnitude or more. The principal drawback to the inclusion of HIs in BD simulations is their computational expense, and several previous studies have sought to accelerate their modeling by developing fast approximations for the calculation of the correlated random displacements. Here, we explore the use of an alternative way to accelerate the calculation of HIs, i.e., by replacing the full RPY tensor with an orientationally averaged (OA) version which retains the distance dependence of the HIs but averages out their orientational dependence. We seek here to determine whether such an approximation can be justified in application to the modeling of typical proteins and RNAs. We show that the use of an OA-RPY tensor allows translational diffusion of macromolecules to be modeled with very high accuracy at the cost of rotational diffusion being underestimated by ∼25%. We show that this finding is independent of the type of macromolecule simulated and the level of structural resolution employed in the models. We also show, however, that these results are critically dependent on the inclusion of a non-zero term that describes the divergence of the diffusion tensor: when this term is omitted from simulations that use the OA-RPY model, unfolded macromolecules undergo rapid collapse. Our results indicate that the orientationally averaged RPY tensor is likely to be a useful, fast, approximate way of including HIs in BD simulations of intermediate-scale systems.
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Affiliation(s)
- John W. Tworek
- Department of Biochemistry
& Molecular Biology, University of Iowa, Iowa City, Iowa 52242, United States
| | - Adrian H. Elcock
- Department of Biochemistry
& Molecular Biology, University of Iowa, Iowa City, Iowa 52242, United States
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4
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Wong CF. 15 Years of molecular simulation of drug-binding kinetics. Expert Opin Drug Discov 2023; 18:1333-1348. [PMID: 37789731 PMCID: PMC10926948 DOI: 10.1080/17460441.2023.2264770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 09/26/2023] [Indexed: 10/05/2023]
Abstract
INTRODUCTION Drug-binding kinetics has been increasingly recognized as an important factor to be considered in drug discovery. Long residence time could prolong the action of some drugs while produce toxicity on others. Early evaluation of the binding kinetics of drug candidates could reduce attrition rate late in the drug discovery process. Computational prediction of drug-binding kinetics is useful as compounds can be evaluated even before they are made. However, simulation of drug-binding kinetics is a challenging problem because of the long-time scale involved. Nevertheless, significant progress has been made. AREAS COVERED This review illustrates the rapid evolution of qualitative to quantitative molecular dynamics-based methods that have been developed over the last 15 years. EXPERT OPINION The development of new methods based on molecular dynamics simulations now enables computation of absolute association/dissociation rate constants. Cheaper methods capable of identifying candidates with fast or slow binding kinetics, or rank-ordering rate constants are also available. Together, these methods have generated useful insights into the molecular mechanisms of drug-binding kinetics, and the design of drug candidates with therapeutically favorable kinetics. Although predicting absolute rate constants is still expensive and challenging, rapid improvement is expected in the coming years with the continuing refinement of current technologies, development of new methodologies, and the utilization of machine learning.
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Affiliation(s)
- Chung F Wong
- Department of Chemistry and Biochemistry, University of Missouri-St. Louis, St. Louis, MO, USA
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5
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Kim SH, Kearns FL, Rosenfeld MA, Votapka L, Casalino L, Papanikolas M, Amaro RE, Freeman R. SARS-CoV-2 evolved variants optimize binding to cellular glycocalyx. CELL REPORTS. PHYSICAL SCIENCE 2023; 4:101346. [PMID: 37077408 PMCID: PMC10080732 DOI: 10.1016/j.xcrp.2023.101346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 02/07/2023] [Accepted: 03/07/2023] [Indexed: 05/03/2023]
Abstract
Viral variants of concern continue to arise for SARS-CoV-2, potentially impacting both methods for detection and mechanisms of action. Here, we investigate the effect of an evolving spike positive charge in SARS-CoV-2 variants and subsequent interactions with heparan sulfate and the angiotensin converting enzyme 2 (ACE2) in the glycocalyx. We show that the positively charged Omicron variant evolved enhanced binding rates to the negatively charged glycocalyx. Moreover, we discover that while the Omicron spike-ACE2 affinity is comparable to that of the Delta variant, the Omicron spike interactions with heparan sulfate are significantly enhanced, giving rise to a ternary complex of spike-heparan sulfate-ACE2 with a large proportion of double-bound and triple-bound ACE2. Our findings suggest that SARS-CoV-2 variants evolve to be more dependent on heparan sulfate in viral attachment and infection. This discovery enables us to engineer a second-generation lateral-flow test strip that harnesses both heparin and ACE2 to reliably detect all variants of concern, including Omicron.
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Affiliation(s)
- Sang Hoon Kim
- Department of Applied Physical Sciences, University of North Carolina - Chapel Hill, 1112 Murray Hall, CB#3050, Chapel Hill, NC 27599-2100, USA
| | - Fiona L Kearns
- Department of Chemistry and Biochemistry, University of California, San Diego, 4238 Urey Hall, MC-0340, La Jolla, CA 92093-0340, USA
| | - Mia A Rosenfeld
- Department of Chemistry and Biochemistry, University of California, San Diego, 4238 Urey Hall, MC-0340, La Jolla, CA 92093-0340, USA
| | - Lane Votapka
- Department of Chemistry and Biochemistry, University of California, San Diego, 4238 Urey Hall, MC-0340, La Jolla, CA 92093-0340, USA
| | - Lorenzo Casalino
- Department of Chemistry and Biochemistry, University of California, San Diego, 4238 Urey Hall, MC-0340, La Jolla, CA 92093-0340, USA
| | - Micah Papanikolas
- Department of Applied Physical Sciences, University of North Carolina - Chapel Hill, 1112 Murray Hall, CB#3050, Chapel Hill, NC 27599-2100, USA
| | - Rommie E Amaro
- Department of Chemistry and Biochemistry, University of California, San Diego, 4238 Urey Hall, MC-0340, La Jolla, CA 92093-0340, USA
| | - Ronit Freeman
- Department of Applied Physical Sciences, University of North Carolina - Chapel Hill, 1112 Murray Hall, CB#3050, Chapel Hill, NC 27599-2100, USA
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6
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Ojha AA, Srivastava A, Votapka LW, Amaro RE. Selectivity and Ranking of Tight-Binding JAK-STAT Inhibitors Using Markovian Milestoning with Voronoi Tessellations. J Chem Inf Model 2023; 63:2469-2482. [PMID: 37023323 PMCID: PMC10131228 DOI: 10.1021/acs.jcim.2c01589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/08/2023]
Abstract
Janus kinases (JAK), a group of proteins in the nonreceptor tyrosine kinase (NRTKs) family, play a crucial role in growth, survival, and angiogenesis. They are activated by cytokines through the Janus kinase-signal transducer and activator of a transcription (JAK-STAT) signaling pathway. JAK-STAT signaling pathways have significant roles in the regulation of cell division, apoptosis, and immunity. Identification of the V617F mutation in the Janus homology 2 (JH2) domain of JAK2 leading to myeloproliferative disorders has stimulated great interest in the drug discovery community to develop JAK2-specific inhibitors. However, such inhibitors should be selective toward JAK2 over other JAKs and display an extended residence time. Recently, novel JAK2/STAT5 axis inhibitors (N-(1H-pyrazol-3-yl)pyrimidin-2-amino derivatives) have displayed extended residence times (hours or longer) on target and adequate selectivity excluding JAK3. To facilitate a deeper understanding of the kinase-inhibitor interactions and advance the development of such inhibitors, we utilize a multiscale Markovian milestoning with Voronoi tessellations (MMVT) approach within the Simulation-Enabled Estimation of Kinetic Rates v.2 (SEEKR2) program to rank order these inhibitors based on their kinetic properties and further explain the selectivity of JAK2 inhibitors over JAK3. Our approach investigates the kinetic and thermodynamic properties of JAK-inhibitor complexes in a user-friendly, fast, efficient, and accurate manner compared to other brute force and hybrid-enhanced sampling approaches.
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Affiliation(s)
- Anupam Anand Ojha
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Ambuj Srivastava
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Lane William Votapka
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Rommie E Amaro
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
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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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8
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Muñiz‐Chicharro A, Votapka LW, Amaro RE, Wade RC. Brownian dynamics simulations of biomolecular diffusional association processes. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2022. [DOI: 10.1002/wcms.1649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Abraham Muñiz‐Chicharro
- Molecular and Cellular Modeling Group Heidelberg Institute for Theoretical Studies (HITS) Heidelberg Germany
- Faculty of Biosciences and Heidelberg Graduate School of Mathematical and Computational Methods for the Sciences (HGS MathComp) Heidelberg University Heidelberg Germany
| | | | | | - Rebecca C. Wade
- Molecular and Cellular Modeling Group Heidelberg Institute for Theoretical Studies (HITS) Heidelberg Germany
- Center for Molecular Biology (ZMBH), DKFZ‐ZMBH Alliance, and Interdisciplinary Center for Scientific Computing (IWR) Heidelberg University Heidelberg Germany
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9
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Ahn SH, Huber GA, McCammon JA. Investigating Intrinsically Disordered Proteins With Brownian Dynamics. Front Mol Biosci 2022; 9:898838. [PMID: 35755809 PMCID: PMC9213797 DOI: 10.3389/fmolb.2022.898838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 05/17/2022] [Indexed: 11/30/2022] Open
Abstract
Intrinsically disordered proteins (IDPs) have recently become systems of great interest due to their involvement in modulating many biological processes and their aggregation being implicated in many diseases. Since IDPs do not have a stable, folded structure, however, they cannot be easily studied with experimental techniques. Hence, conducting a computational study of these systems can be helpful and be complementary with experimental work to elucidate their mechanisms. Thus, we have implemented the coarse-grained force field for proteins (COFFDROP) in Browndye 2.0 to study IDPs using Brownian dynamics (BD) simulations, which are often used to study large-scale motions with longer time scales and diffusion-limited molecular associations. Specifically, we have checked our COFFDROP implementation with eight naturally occurring IDPs and have investigated five (Glu-Lys)25 IDP sequence variants. From measuring the hydrodynamic radii of eight naturally occurring IDPs, we found the ideal scaling factor of 0.786 for non-bonded interactions. We have also measured the entanglement indices (average Cα distances to the other chain) between two (Glu-Lys)25 IDP sequence variants, a property related to molecular association. We found that entanglement indices decrease for all possible pairs at excess salt concentration, which is consistent with long-range interactions of these IDP sequence variants getting weaker at increasing salt concentration.
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Affiliation(s)
- Surl-Hee Ahn
- Department of Chemistry and Biochemistry, University of California, San Diego, San Diego, CA, United States
| | - Gary A Huber
- Department of Chemistry and Biochemistry, University of California, San Diego, San Diego, CA, United States.,Department of Pharmacology, University of California, San Diego, San Diego, CA, United States
| | - J Andrew McCammon
- Department of Chemistry and Biochemistry, University of California, San Diego, San Diego, CA, United States.,Department of Pharmacology, University of California, San Diego, San Diego, CA, United States
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10
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Cholko T, Kaushik S, Wu KY, Montes R, Chang CEA. GeomBD3: Brownian Dynamics Simulation Software for Biological and Engineered Systems. J Chem Inf Model 2022; 62:2257-2263. [PMID: 35549473 DOI: 10.1021/acs.jcim.1c01387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
GeomBD3 is a robust Brownian dynamics simulation package designed to easily handle natural or engineered systems in diverse environments and arrangements. The software package described herein allows users to design, execute, and analyze BD simulations. The simulations use all-atom, rigid molecular models that diffuse according to overdamped Langevin dynamics and interact through electrostatic, Lennard-Jones, and ligand desolvation potentials. The program automatically calculates molecular association rates, surface residence times, and association statistics for any number of user-defined association criteria. Users can also extract molecular association pathways, diffusion coefficients, intermolecular interaction energies, intermolecular contact probability maps, and more using the provided supplementary analysis scripts. We detail the use of the package from start to finish and apply it to a protein-ligand system and a large nucleic acid biosensor. GeomBD3 provides a versatile tool for researchers from various disciplines that can aid in rational design of engineered systems or play an explanatory role as a complement to experiments. GeomBD version 3 is available on our website at http://chemcha-gpu0.ucr.edu/geombd3/ and KBbox at https://kbbox.h-its.org/toolbox/methods/molecular-simulation/geombd/.
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Affiliation(s)
- Timothy Cholko
- Department of Chemistry, University of California, Riverside, Riverside, California 92521, United States
| | - Shivansh Kaushik
- Department of Chemistry, University of California, Riverside, Riverside, California 92521, United States
| | - Kingsley Y Wu
- Department of Chemistry, University of California, Riverside, Riverside, California 92521, United States
| | - Ruben Montes
- Department of Chemistry, University of California, Riverside, Riverside, California 92521, United States
| | - Chia-En A Chang
- Department of Chemistry, University of California, Riverside, Riverside, California 92521, United States
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11
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Huang YMM. Multiscale computational study of ligand binding pathways: Case of p38 MAP kinase and its inhibitors. Biophys J 2021; 120:3881-3892. [PMID: 34453922 PMCID: PMC8511166 DOI: 10.1016/j.bpj.2021.08.026] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Revised: 06/07/2021] [Accepted: 08/20/2021] [Indexed: 01/09/2023] Open
Abstract
Protein kinases are one of the most important drug targets in the past 10 years. Understanding the inhibitor association processes will profoundly impact new binder designs with preferred binding kinetics. However, after more than a decade of effort, a complete atomistic-level study of kinase inhibitor binding pathways is still lacking. As all kinases share a similar scaffold, we used p38 kinase as a model system to investigate the conformational dynamics and free energy transition of inhibitor binding toward kinases. Two major kinase conformations, Asp-Phe-Gly (DFG)-in and DFG-out, and three types of inhibitors, type I, II, and III, were thoroughly investigated in this work. We performed Brownian dynamics simulations and up to 340 μs Gaussian-accelerated molecular dynamics simulations to capture the inhibitor binding paths and a series of conformational transitions of the p38 kinase from its apo to inhibitor-bound form. Eighteen successful binding trajectories, including all types of inhibitors, are reported herein. Our simulations suggest a mechanism of inhibitor recruitment, a faster ligand association step to a pre-existing DFG-in/DFG-out p38 protein, followed by a slower molecular rearrangement step to adjust the protein-ligand conformation followed by a shift in the energy landscape to reach the final bound state. The ligand association processes also reflect the energetic favor of type I and type II/III inhibitor binding through ATP and allosteric channels, respectively. These different binding routes are directly responsible for the fast (type I binders) and slow (type II/III binders) kinetics of different types of p38 inhibitors. Our findings also echo the recent study of p38 inhibitor dissociation, implying that ligand unbinding could undergo a reverse path of binding, and both processes share similar metastates. This study deepens the understanding of molecular and energetic features of kinase inhibitor-binding processes and will inspire future drug development from a kinetic point of view.
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Affiliation(s)
- Yu-Ming M Huang
- Department of Physics and Astronomy, Wayne State University, Detroit, Michigan.
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12
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Cool AM, Lindert S. Computational Methods Elucidate Consequences of Mutations and Post-translational Modifications on Troponin I Effective Concentration to Troponin C. J Phys Chem B 2021; 125:7388-7396. [PMID: 34213339 DOI: 10.1021/acs.jpcb.1c03844] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Ca2+ binding to cardiac troponin C (cTnC) causes a conformational shift that exposes a hydrophobic patch (cTnCHP) for binding of the cTnI switch peptide (cTnISP), ultimately resulting in contraction of the heart. The inhibitory peptide (cTnIIP), attached at the N-terminal end of the cTnISP, serves as a tether for the cTnISP to the rest of the troponin complex. Due to this tethered nature, the cTnISP remains within proximity of the hydrophobic patch region, resulting in the cTnCHP experiencing an elevated "effective concentration" of the cTnISP. Mutations to the cTnIIP region have been hypothesized to cause disease by affecting the ability of the cTnISP to "find" the hydrophobic patch, resulting in alterations to the heart's ability to contract normally. We tested this hypothesis using molecular dynamics (MD) simulations of the troponin complex using a model that contained all three subunits of troponin: C, I, and T. We developed methods that allowed us to quantitatively measure the effective concentration of the cTnISP from the simulations. A significant reduction in the cTnISP effective concentration was observed when the cTnIIP was removed from the system, showcasing the importance of a tethered cTnISP. Through accelerated MD methods, we proposed the minimum effective concentration of a tethered cTnISP to be approximately 21 mM. Modification of the cTnIIP via PKC-mediated phosphorylation of T143 was shown to significantly increase the estimated effective concentration of cTnISP, help the cTnISP find the cTnCHP more effectively, and maintain the relative shape of the cTnIIP when compared to the native model. All of these data indicate that pT143 may be able to help promote binding of cTnISP to the cTnCHP. We then tested six mutations within the cTnIIP region that are known cTnC Ca2+-sensitizing mutations and have been linked with cardiomyopathy. We did not observe a significant reduction in the effective concentration upon the introduction of these mutations; however, we did observe increased variability in the flexibility and dynamics of the cTnIIP region when compared to native. Our observations led us to hypothesize that the mechanism by which these cardiomyopathic mutations affect Ca2+ sensitivity is by altering the off rate of cTnISP from the hydrophobic patch.
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Affiliation(s)
- Austin M Cool
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Steffen Lindert
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
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13
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Kaushik S, Chang CEA. Molecular Mechanics Study of Flow and Surface Influence in Ligand-Protein Association. Front Mol Biosci 2021; 8:659687. [PMID: 34041265 PMCID: PMC8142692 DOI: 10.3389/fmolb.2021.659687] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 04/06/2021] [Indexed: 11/13/2022] Open
Abstract
Ligand–protein association is the first and critical step for many biological and chemical processes. This study investigated the molecular association processes under different environments. In biology, cells have different compartments where ligand–protein binding may occur on a membrane. In experiments involving ligand–protein binding, such as the surface plasmon resonance and continuous flow biosynthesis, a substrate flow and surface are required in experimental settings. As compared with a simple binding condition, which includes only the ligand, protein, and solvent, the association rate and processes may be affected by additional ligand transporting forces and other intermolecular interactions between the ligand and environmental objects. We evaluated these environmental factors by using a ligand xk263 binding to HIV protease (HIVp) with atomistic details. Using Brownian dynamics simulations, we modeled xk263 and HIVp association time and probability when a system has xk263 diffusion flux and a non-polar self-assembled monolayer surface. We also examined different protein orientations and accessible surfaces for xk263. To allow xk263 to access to the dimer interface of immobilized HIVp, we simulated the system by placing the protein 20Å above the surface because immobilizing HIVp on a surface prevented xk263 from contacting with the interface. The non-specific interactions increased the binding probability while the association time remained unchanged. When the xk263 diffusion flux increased, the effective xk263 concentration around HIVp, xk263–HIVp association time and binding probability decreased non-linearly regardless of interacting with the self-assembled monolayer surface or not. The work sheds light on the effects of the solvent flow and surface environment on ligand–protein associations and provides a perspective on experimental design.
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Affiliation(s)
- Shivansh Kaushik
- Department of Chemistry, University of Chemistry, Riverside, CA, United States
| | - Chia-En A Chang
- Department of Chemistry, University of Chemistry, Riverside, CA, United States
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14
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Zhang Z, Ricci CG, Fan C, Cheng LT, Li B, McCammon JA. Coupling Monte Carlo, Variational Implicit Solvation, and Binary Level-Set for Simulations of Biomolecular Binding. J Chem Theory Comput 2021; 17:2465-2478. [PMID: 33650860 DOI: 10.1021/acs.jctc.0c01109] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
We develop a hybrid approach that combines the Monte Carlo (MC) method, a variational implicit-solvent model (VISM), and a binary level-set method for the simulation of biomolecular binding in an aqueous solvent. The solvation free energy for the biomolecular complex is estimated by minimizing the VISM free-energy functional of all possible solute-solvent interfaces that are used as dielectric boundaries. This functional consists of the solute volumetric, solute-solvent interfacial, solute-solvent van der Waals interaction, and electrostatic free energy. A technique of shifting the dielectric boundary is used to accurately predict the electrostatic part of the solvation free energy. Minimizing such a functional in each MC move is made possible by our new and fast binary level-set method. This method is based on the approximation of surface area by the convolution of an indicator function with a compactly supported kernel and is implemented by simple flips of numerical grid cells locally around the solute-solvent interface. We apply our approach to the p53-MDM2 system for which the two molecules are approximated by rigid bodies. Our efficient approach captures some of the poses before the final bound state. All-atom molecular dynamics simulations with most of such poses quickly reach the final bound state. Our work is a new step toward realistic simulations of biomolecular interactions. With further improvement of coarse graining and MC sampling, and combined with other models, our hybrid approach can be used to study the free-energy landscape and kinetic pathways of ligand binding to proteins.
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Affiliation(s)
- Zirui Zhang
- Department of Mathematics, University of California, San Diego, La Jolla, California 92093-0112, United States
| | - Clarisse G Ricci
- Department of Chemistry and Biochemistry and Department of Pharmacology, University of California, San Diego, La Jolla, California 92093-0365, United States
| | - Chao Fan
- Department of Mathematics, University of California, San Diego, La Jolla, California 92093-0112, United States
| | - Li-Tien Cheng
- Department of Mathematics, University of California, San Diego, La Jolla, California 92093-0112, United States
| | - Bo Li
- Department of Mathematics and Quantitative Biology Ph.D. Program, University of California, San Diego, La Jolla, California 92093-0112, United States
| | - J Andrew McCammon
- Department of Chemistry and Biochemistry and Department of Pharmacology, University of California, San Diego, La Jolla, California 92093-0365, United States
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15
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Multiscale Simulations Examining Glycan Shield Effects on Drug Binding to Influenza Neuraminidase. Biophys J 2020; 119:2275-2289. [PMID: 33130120 DOI: 10.1016/j.bpj.2020.10.024] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 10/08/2020] [Accepted: 10/21/2020] [Indexed: 12/18/2022] Open
Abstract
Influenza neuraminidase is an important drug target. Glycans are present on neuraminidase and are generally considered to inhibit antibody binding via their glycan shield. In this work, we studied the effect of glycans on the binding kinetics of antiviral drugs to the influenza neuraminidase. We created all-atom in silico systems of influenza neuraminidase with experimentally derived glycoprofiles consisting of four systems with different glycan conformations and one system without glycans. Using Brownian dynamics simulations, we observe a two- to eightfold decrease in the rate of ligand binding to the primary binding site of neuraminidase due to the presence of glycans. These glycans are capable of covering much of the surface area of neuraminidase, and the ligand binding inhibition is derived from glycans sterically occluding the primary binding site on a neighboring monomer. Our work also indicates that drugs preferentially bind to the primary binding site (i.e., the active site) over the secondary binding site, and we propose a binding mechanism illustrating this. These results help illuminate the complex interplay between glycans and ligand binding on the influenza membrane protein neuraminidase.
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16
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McCabe KJ, Aboelkassem Y, Teitgen AE, Huber GA, McCammon JA, Regnier M, McCulloch AD. Predicting the effects of dATP on cardiac contraction using multiscale modeling of the sarcomere. Arch Biochem Biophys 2020; 695:108582. [PMID: 32956632 DOI: 10.1016/j.abb.2020.108582] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 07/30/2020] [Accepted: 09/04/2020] [Indexed: 11/26/2022]
Abstract
2'-deoxy-ATP (dATP) is a naturally occurring small molecule that has shown promise as a therapeutic because it significantly increases cardiac myocyte force development even at low dATP/ATP ratios. To investigate mechanisms by which dATP alters myosin crossbridge dynamics, we used Brownian dynamics simulations to calculate association rates between actin and ADP- or dADP-bound myosin. These rates were then directly incorporated in a mechanistic Monte Carlo Markov Chain model of cooperative sarcomere contraction. A unique combination of increased powerstroke and detachment rates was required to match experimental steady-state and kinetic data for dATP force production in rat cardiac myocytes when the myosin attachment rate in the model was constrained by the results of a Brownian dynamics simulation. Nearest-neighbor cooperativity was seen to contribute to, but not fully explain, the steep relationship between dATP/ATP ratio and steady-state force-development observed at lower dATP concentrations. Dynamic twitch simulations performed using measured calcium transients as inputs showed that the effects of dATP on the crossbridge alone were not sufficient to explain experimentally observed enhancement of relaxation kinetics by dATP treatment. Hence, dATP may also affect calcium handling even at low concentrations. By enabling the effects of dATP on sarcomere mechanics to be predicted, this multi-scale modeling framework may elucidate the molecular mechanisms by which dATP can have therapeutic effects on cardiac contractile dysfunction.
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Affiliation(s)
- Kimberly J McCabe
- Simula Research Laboratory, Department of Computational Physiology, PO Box 134, 1325, Lysaker, Norway.
| | - Yasser Aboelkassem
- San Diego State University, Department of Mechanical Engineering, 5500 Campanile Drive San Diego, CA, 92182, USA
| | - Abigail E Teitgen
- University of California San Diego, Department of Bioengineering, 9500 Gilman Drive MC 0412 La Jolla, CA, 92093, USA
| | - Gary A Huber
- University of California San Diego, Department of Chemistry & Biochemistry, 9500 Gilman Drive, MC 0303 La Jolla, CA, 92093, USA
| | - J Andrew McCammon
- University of California San Diego, Department of Chemistry & Biochemistry, 9500 Gilman Drive, MC 0303 La Jolla, CA, 92093, USA
| | - Michael Regnier
- University of Washington, Department of Bioengineering, Box 355061 Seattle, WA, 98195, USA
| | - Andrew D McCulloch
- University of California San Diego, Department of Bioengineering, 9500 Gilman Drive MC 0412 La Jolla, CA, 92093, USA
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17
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Jagger BR, Ojha AA, Amaro RE. Predicting Ligand Binding Kinetics Using a Markovian Milestoning with Voronoi Tessellations Multiscale Approach. J Chem Theory Comput 2020; 16:5348-5357. [DOI: 10.1021/acs.jctc.0c00495] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Benjamin R. Jagger
- Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Anupam A. Ojha
- Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Rommie E. Amaro
- Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
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18
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Ray D, Andricioaei I. Weighted ensemble milestoning (WEM): A combined approach for rare event simulations. J Chem Phys 2020; 152:234114. [DOI: 10.1063/5.0008028] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Affiliation(s)
- Dhiman Ray
- Department of Chemistry, University of California Irvine, California 92697, USA
| | - Ioan Andricioaei
- Department of Chemistry, University of California Irvine, California 92697, USA
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19
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Aboelkassem Y, McCabe KJ, Huber GA, Regnier M, McCammon JA, McCulloch AD. A Stochastic Multiscale Model of Cardiac Thin Filament Activation Using Brownian-Langevin Dynamics. Biophys J 2019; 117:2255-2272. [PMID: 31547973 PMCID: PMC6990154 DOI: 10.1016/j.bpj.2019.08.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 07/31/2019] [Accepted: 08/02/2019] [Indexed: 11/16/2022] Open
Abstract
We use Brownian-Langevin dynamics principles to derive a coarse-graining multiscale myofilament model that can describe the thin-filament activation process during contraction. The model links atomistic molecular simulations of protein-protein interactions in the thin-filament regulatory unit to sarcomere-level activation dynamics. We first calculate the molecular interaction energy between tropomyosin and actin surface using Brownian dynamics simulations. This energy profile is then generalized to account for the observed tropomyosin transitions between its regulatory stable states. The generalized energy landscape then served as a basis for developing a filament-scale model using Langevin dynamics. This integrated analysis, spanning molecular to thin-filament scales, is capable of tracking the events of the tropomyosin conformational changes as it moves over the actin surface. The tropomyosin coil with flexible overlap regions between adjacent tropomyosins is represented in the model as a system of coupled stochastic ordinary differential equations. The proposed multiscale approach provides a more detailed molecular connection between tropomyosin dynamics, the trompomyosin-actin interaction-energy landscape, and the generated force by the sarcomere.
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Affiliation(s)
- Yasser Aboelkassem
- Department of Bioengineering, University of California San Diego, La Jolla, California.
| | - Kimberly J McCabe
- Department of Bioengineering, University of California San Diego, La Jolla, California
| | - Gary A Huber
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California
| | - Michael Regnier
- Department of Bioengineering, University of Washington, Seattle, Washington
| | - J Andrew McCammon
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California
| | - Andrew D McCulloch
- Department of Bioengineering, University of California San Diego, La Jolla, California
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20
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Zewde NT. Multiscale Solutions to Quantitative Systems Biology Models. Front Mol Biosci 2019; 6:119. [PMID: 31737643 PMCID: PMC6831518 DOI: 10.3389/fmolb.2019.00119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 10/14/2019] [Indexed: 11/13/2022] Open
Affiliation(s)
- Nehemiah T Zewde
- Department of Bioengineering, University of California, Riverside, Riverside, CA, United States
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21
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Abstract
Brownian dynamics (BD) is a technique for carrying out computer simulations of physical systems that are driven by thermal fluctuations. Biological systems at the macromolecular and cellular level, while falling in the gap between well-established atomic-level models and continuum models, are especially suitable for such simulations. We present a brief history, examples of important biological processes that are driven by thermal motion, and those that have been profitably studied by BD. We also present some of the challenges facing developers of algorithms and software, especially in the attempt to simulate larger systems more accurately and for longer times.
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Affiliation(s)
- Gary A Huber
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093-0340, USA.,Department of Pharmocology, University of California San Diego, La Jolla, CA 92093-0636, USA
| | - J Andrew McCammon
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093-0340, USA.,Department of Pharmocology, University of California San Diego, La Jolla, CA 92093-0636, USA
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22
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Erdemir A, Hunter PJ, Holzapfel GA, Loew LM, Middleton J, Jacobs CR, Nithiarasu P, Löhner R, Wei G, Winkelstein BA, Barocas VH, Guilak F, Ku JP, Hicks JL, Delp SL, Sacks M, Weiss JA, Ateshian GA, Maas SA, McCulloch AD, Peng GCY. Perspectives on Sharing Models and Related Resources in Computational Biomechanics Research. J Biomech Eng 2019; 140:2666967. [PMID: 29247253 DOI: 10.1115/1.4038768] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2017] [Indexed: 12/23/2022]
Abstract
The role of computational modeling for biomechanics research and related clinical care will be increasingly prominent. The biomechanics community has been developing computational models routinely for exploration of the mechanics and mechanobiology of diverse biological structures. As a result, a large array of models, data, and discipline-specific simulation software has emerged to support endeavors in computational biomechanics. Sharing computational models and related data and simulation software has first become a utilitarian interest, and now, it is a necessity. Exchange of models, in support of knowledge exchange provided by scholarly publishing, has important implications. Specifically, model sharing can facilitate assessment of reproducibility in computational biomechanics and can provide an opportunity for repurposing and reuse, and a venue for medical training. The community's desire to investigate biological and biomechanical phenomena crossing multiple systems, scales, and physical domains, also motivates sharing of modeling resources as blending of models developed by domain experts will be a required step for comprehensive simulation studies as well as the enhancement of their rigor and reproducibility. The goal of this paper is to understand current perspectives in the biomechanics community for the sharing of computational models and related resources. Opinions on opportunities, challenges, and pathways to model sharing, particularly as part of the scholarly publishing workflow, were sought. A group of journal editors and a handful of investigators active in computational biomechanics were approached to collect short opinion pieces as a part of a larger effort of the IEEE EMBS Computational Biology and the Physiome Technical Committee to address model reproducibility through publications. A synthesis of these opinion pieces indicates that the community recognizes the necessity and usefulness of model sharing. There is a strong will to facilitate model sharing, and there are corresponding initiatives by the scientific journals. Outside the publishing enterprise, infrastructure to facilitate model sharing in biomechanics exists, and simulation software developers are interested in accommodating the community's needs for sharing of modeling resources. Encouragement for the use of standardized markups, concerns related to quality assurance, acknowledgement of increased burden, and importance of stewardship of resources are noted. In the short-term, it is advisable that the community builds upon recent strategies and experiments with new pathways for continued demonstration of model sharing, its promotion, and its utility. Nonetheless, the need for a long-term strategy to unify approaches in sharing computational models and related resources is acknowledged. Development of a sustainable platform supported by a culture of open model sharing will likely evolve through continued and inclusive discussions bringing all stakeholders at the table, e.g., by possibly establishing a consortium.
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Affiliation(s)
- Ahmet Erdemir
- Department of Biomedical Engineering and Computational Biomodeling (CoBi) Core, Lerner Research Institute, Cleveland Clinic, 9500 Euclid Avenue (ND20), Cleveland, OH 44195 e-mail:
| | - Peter J Hunter
- Auckland Bioengineering Institute, University of Auckland, Auckland 1142, New Zealand
| | - Gerhard A Holzapfel
- Institute of Biomechanics, Graz University of Technology, Graz 8010, Austria.,Faculty of Engineering Science and Technology, Norwegian University of Science and Technology, Trondheim 7491, Norway
| | - Leslie M Loew
- Center for Cell Analysis and Modeling, University of Connecticut School of Medicine, Farmington, CT 06032
| | - John Middleton
- Department of Orthodontics, Biomaterials/Biomechanics Research Centre, School of Dentistry, Cardiff University, Heath Park, Cardiff CF10 3AT, UK
| | | | - Perumal Nithiarasu
- Zienkiewicz Centre for Computational Engineering, Swansea University, Swansea SA1 8EN, UK
| | - Rainlad Löhner
- Department of Physics and Astronomy, Center for Computational Fluid Dynamics, George Mason University, Fairfax, VA 22030
| | - Guowei Wei
- Department of Mathematics, Michigan State University, East Lansing, MI 48824
| | - Beth A Winkelstein
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104
| | - Victor H Barocas
- Department of Bioengineering, University of Minnesota, Minneapolis, MN 55455
| | - Farshid Guilak
- Department of Orthopaedic Surgery, Shriners Hospitals for Children, Washington University, St. Louis, MO 63130
| | - Joy P Ku
- Department of Bioengineering, Stanford University, Stanford, CA 94305
| | - Jennifer L Hicks
- Department of Bioengineering, Stanford University, Stanford, CA 94305
| | - Scott L Delp
- Department of Bioengineering, Stanford University, Stanford, CA 94305.,Department of Mechanical Engineering, Stanford University, Stanford, CA 94305
| | - Michael Sacks
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX 78712
| | - Jeffrey A Weiss
- Department of Bioengineering, University of Utah, Salt Lake City, UT 84112
| | - Gerard A Ateshian
- Department of Mechanical Engineering, Columbia University, New York, NY 10027
| | - Steve A Maas
- Department of Bioengineering, University of Utah, Salt Lake City, UT 84112
| | - Andrew D McCulloch
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093
| | - Grace C Y Peng
- National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892
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23
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Powers JD, Yuan CC, McCabe KJ, Murray JD, Childers MC, Flint GV, Moussavi-Harami F, Mohran S, Castillo R, Zuzek C, Ma W, Daggett V, McCulloch AD, Irving TC, Regnier M. Cardiac myosin activation with 2-deoxy-ATP via increased electrostatic interactions with actin. Proc Natl Acad Sci U S A 2019; 116:11502-11507. [PMID: 31110001 PMCID: PMC6561254 DOI: 10.1073/pnas.1905028116] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
The naturally occurring nucleotide 2-deoxy-adenosine 5'-triphosphate (dATP) can be used by cardiac muscle as an alternative energy substrate for myosin chemomechanical activity. We and others have previously shown that dATP increases contractile force in normal hearts and models of depressed systolic function, but the structural basis of these effects has remained unresolved. In this work, we combine multiple techniques to provide structural and functional information at the angstrom-nanometer and millisecond time scales, demonstrating the ability to make both structural measurements and quantitative kinetic estimates of weak actin-myosin interactions that underpin sarcomere dynamics. Exploiting dATP as a molecular probe, we assess how small changes in myosin structure translate to electrostatic-based changes in sarcomere function to augment contractility in cardiac muscle. Through Brownian dynamics simulation and computational structural analysis, we found that deoxy-hydrolysis products [2-deoxy-adenosine 5'-diphosphate (dADP) and inorganic phosphate (Pi)] bound to prepowerstroke myosin induce an allosteric restructuring of the actin-binding surface on myosin to increase the rate of cross-bridge formation. We then show experimentally that this predicted effect translates into increased electrostatic interactions between actin and cardiac myosin in vitro. Finally, using small-angle X-ray diffraction analysis of sarcomere structure, we demonstrate that the proposed increased electrostatic affinity of myosin for actin causes a disruption of the resting conformation of myosin motors, resulting in their repositioning toward the thin filament before activation. The dATP-mediated structural alterations in myosin reported here may provide insight into an improved criterion for the design or selection of small molecules to be developed as therapeutic agents to treat systolic dysfunction.
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Affiliation(s)
- Joseph D Powers
- Department of Bioengineering, University of Washington, Seattle, WA 98109;
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093
| | - Chen-Ching Yuan
- Department of Bioengineering, University of Washington, Seattle, WA 98109
| | - Kimberly J McCabe
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093
| | - Jason D Murray
- Department of Bioengineering, University of Washington, Seattle, WA 98109
- Department of Physiology and Biophysics, University of Washington, Seattle, WA 98109
| | | | - Galina V Flint
- Department of Bioengineering, University of Washington, Seattle, WA 98109
| | - Farid Moussavi-Harami
- Division of Cardiology, Department of Medicine, University of Washington, Seattle, WA 98109
| | - Saffie Mohran
- Department of Bioengineering, University of Washington, Seattle, WA 98109
| | - Romi Castillo
- Department of Bioengineering, University of Washington, Seattle, WA 98109
| | - Carla Zuzek
- Department of Bioengineering, University of Washington, Seattle, WA 98109
| | - Weikang Ma
- Department of Biological Sciences, Illinois Institute of Technology, Chicago, IL 60616
| | - Valerie Daggett
- Department of Bioengineering, University of Washington, Seattle, WA 98109
| | - Andrew D McCulloch
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093
| | - Thomas C Irving
- Department of Biological Sciences, Illinois Institute of Technology, Chicago, IL 60616
| | - Michael Regnier
- Department of Bioengineering, University of Washington, Seattle, WA 98109;
- Department of Physiology and Biophysics, University of Washington, Seattle, WA 98109
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24
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Harrison RES, Morikis D. Molecular Mechanisms of Macular Degeneration Associated with the Complement Factor H Y402H Mutation. Biophys J 2018; 116:215-226. [PMID: 30616835 DOI: 10.1016/j.bpj.2018.12.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 10/24/2018] [Accepted: 12/07/2018] [Indexed: 01/02/2023] Open
Abstract
A single nucleotide polymorphism, tyrosine at position 402 to histidine (Y402H), within the gene encoding complement factor H (FH) predisposes individuals to acquiring age-related macular degeneration (AMD) after aging. This polymorphism occurs in short consensus repeat (SCR) 7 of FH and results in decreased binding affinity of SCR6-8 for heparin. As FH is responsible for regulating the complement system, decreased affinity for heparin results in decreased regulation on surfaces of self. To understand the involvement of the Y402H polymorphism in AMD, we leverage methods from bioinformatics and computational biophysics to quantify structural and dynamical differences between SCR7 isoforms that contribute to decreased pattern recognition in SCR7H402. Our data from molecular and Brownian dynamics simulations suggest a revised mechanism for decreased heparin binding. In this model, transient contacts not observed in structures for SCR7 are predicted to occur in molecular dynamics simulations between coevolved residues Y402 and I412, stabilizing SCR7Y402 in a conformation that promotes association with heparin. H402 in the risk isoform is less likely to form a contact with I412 and samples a larger conformational space than Y402. We observe energy minima for sidechains of Y402 and R404 from SCR7Y402 that are predicted to associate with heparin at a rate constant faster than energy minima for sidechains of H402 and R404 from SCR7H402. As both carbohydrate density and degree of sulfation decrease with age in Bruch's membrane of the macula, the decreased heparin recognition of SCR7H402 may contribute to the pathogenesis of AMD.
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Affiliation(s)
- Reed E S Harrison
- Department of Bioengineering, University of California, Riverside, Riverside, California
| | - Dimitrios Morikis
- Department of Bioengineering, University of California, Riverside, Riverside, California.
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25
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Campeggio J, Polimeno A, Zerbetto M. DiTe2: Calculating the diffusion tensor for flexible molecules. J Comput Chem 2018; 40:697-705. [DOI: 10.1002/jcc.25742] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Revised: 10/06/2018] [Accepted: 10/09/2018] [Indexed: 01/29/2023]
Affiliation(s)
| | - Antonino Polimeno
- Department of Chemical SciencesUniversity of Padua Padova 35131 Italy
| | - Mirco Zerbetto
- Department of Chemical SciencesUniversity of Padua Padova 35131 Italy
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26
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Sun B, Cook EC, Creamer TP, Kekenes-Huskey PM. Electrostatic control of calcineurin's intrinsically-disordered regulatory domain binding to calmodulin. Biochim Biophys Acta Gen Subj 2018; 1862:2651-2659. [PMID: 30071273 PMCID: PMC6317854 DOI: 10.1016/j.bbagen.2018.07.027] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Revised: 07/13/2018] [Accepted: 07/24/2018] [Indexed: 12/26/2022]
Abstract
Calcineurin (CaN) is a serine/threonine phosphatase that regulates a variety of physiological and pathophysiological processes in mammalian tissue. The calcineurin (CaN) regulatory domain (RD) is responsible for regulating the enzyme's phosphatase activity, and is believed to be highly-disordered when inhibiting CaN, but undergoes a disorder-to-order transition upon diffusion-limited binding with the regulatory protein calmodulin (CaM). The prevalence of polar and charged amino acids in the regulatory domain (RD) suggests electrostatic interactions are involved in mediating calmodulin (CaM) binding, yet the lack of atomistic-resolution data for the bound complex has stymied efforts to probe how the RD sequence controls its conformational ensemble and long-range attractions contribute to target protein binding. In the present study, we investigated via computational modeling the extent to which electrostatics and structural disorder facilitate CaM/CaN association kinetics. Specifically, we examined several RD constructs that contain the CaM binding region (CAMBR) to characterize the roles of electrostatics versus conformational diversity in controlling diffusion-limited association rates, via microsecond-scale molecular dynamics (MD) and Brownian dynamic (BD) simulations. Our results indicate that the RD amino acid composition and sequence length influence both the dynamic availability of conformations amenable to CaM binding, as well as long-range electrostatic interactions to steer association. These findings provide intriguing insight into the interplay between conformational diversity and electrostatically-driven protein-protein association involving CaN, which are likely to extend to wide-ranging diffusion-limited processes regulated by intrinsically-disordered proteins.
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Affiliation(s)
- Bin Sun
- Department of Chemistry, University of Kentucky, 505 Rose St., Chemistry-Physics Building, Lexington, KY, USA 40506
| | - Erik C Cook
- Department of Molecular and Cellular Biochemistry, University of Kentucky, 741 South Limestone, St. Lexington, KY, USA 40536
| | - Trevor P Creamer
- Department of Molecular and Cellular Biochemistry, University of Kentucky, 741 South Limestone, St. Lexington, KY, USA 40536
| | - Peter M Kekenes-Huskey
- Department of Chemistry, University of Kentucky, 505 Rose St., Chemistry-Physics Building, Lexington, KY, USA 40506.
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27
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Amaro RE, Ieong PU, Huber G, Dommer A, Steven AC, Bush RM, Durrant JD, Votapka LW. A Computational Assay that Explores the Hemagglutinin/Neuraminidase Functional Balance Reveals the Neuraminidase Secondary Site as a Novel Anti-Influenza Target. ACS CENTRAL SCIENCE 2018; 4:1570-1577. [PMID: 30555910 PMCID: PMC6276040 DOI: 10.1021/acscentsci.8b00666] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Indexed: 05/09/2023]
Abstract
Studies of pathogen-host specificity, virulence, and transmissibility are critical for basic research as well as for assessing the pandemic potential of emerging infectious diseases. This is especially true for viruses such as influenza, which continue to affect millions of people annually through both seasonal and occasional pandemic events. Although the influenza virus has been fairly well studied for decades, our understanding of host-cell binding and its relation to viral transmissibility and infection is still incomplete. Assessing the binding mechanisms of complex biological systems with atomic-scale detail is challenging given current experimental limitations. Much remains to be learned, for example, about how the terminal residue of influenza-binding host-cell receptors (sialic acid) interacts with the viral surface. Here, we present an integrative structural-modeling and physics-based computational assay that reveals the sialic acid association rate constants (k on) to three influenza sites: the hemagglutinin (HA), neuraminidase (NA) active, and NA secondary binding sites. We developed a series of highly detailed (atomic-resolution) structural models of fully intact influenza viral envelopes. Brownian dynamics simulations of these systems showed how structural properties, such as stalk height and secondary-site binding, affect sialic acid k on values. Comparing the k on values of the three sialic acid binding sites across different viral strains suggests a detailed model of encounter-complex formation and indicates that the secondary NA binding site may play a compensatory role in host-cell receptor binding. Our method elucidates the competition among these sites, all present on the same virion, and provides a new technology for directly studying the functional balance between HA and NA.
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Affiliation(s)
- Rommie E. Amaro
- Department
of Chemistry and Biochemistry, University
of California, San Diego, La Jolla, California, United States
- E-mail: . (R.E.A.)
| | - Pek U Ieong
- Department
of Chemistry and Biochemistry, University
of California, San Diego, La Jolla, California, United States
| | - Gary Huber
- Department
of Chemistry and Biochemistry, University
of California, San Diego, La Jolla, California, United States
| | - Abigail Dommer
- Department
of Chemistry and Biochemistry, University
of California, San Diego, La Jolla, California, United States
| | - Alasdair C. Steven
- Structural
Biology Laboratory, National Institutes
of Health, Bethesda, Maryland, United States
| | - Robin M. Bush
- Department
of Ecology and Evolutionary Biology, University
of California, Irvine, Irvine, California, United States
| | - Jacob D. Durrant
- Department
of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States
- E-mail: . (J.D.D.)
| | - Lane W. Votapka
- Department
of Chemistry, Point Loma Nazarene University, San Diego, California, United States
- E-mail: . (L.W.V.)
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28
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Jagger BR, Lee CT, Amaro RE. Quantitative Ranking of Ligand Binding Kinetics with a Multiscale Milestoning Simulation Approach. J Phys Chem Lett 2018; 9:4941-4948. [PMID: 30070844 PMCID: PMC6443090 DOI: 10.1021/acs.jpclett.8b02047] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Efficient prediction and ranking of small molecule binders by their kinetic ( kon and koff) and thermodynamic ( Δ G) properties can be a valuable metric for drug lead optimization, as these quantities are often indicators of in vivo efficacy. We have previously described a hybrid molecular dynamics, Brownian dynamics, and milestoning model, Simulation Enabled Estimation of Kinetic Rates (SEEKR), that can predict kon's, koff's, and Δ G's. Here we demonstrate the effectiveness of this approach for ranking a series of seven small molecule compounds for the model system, β-cyclodextrin, based on predicted kon's and koff's. We compare our results using SEEKR to experimentally determined rates as well as rates calculated using long time scale molecular dynamics simulations and show that SEEKR can effectively rank the compounds by koff and Δ G with reduced computational cost. We also provide a discussion of convergence properties and sensitivities of calculations with SEEKR to establish "best practices" for its future use.
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Affiliation(s)
- Benjamin R Jagger
- Department of Chemistry and Biochemistry , University of California, San Diego , 9500 Gilman Drive , La Jolla , California 92093-0340 , United States
| | - Christopher T Lee
- Department of Chemistry and Biochemistry , University of California, San Diego , 9500 Gilman Drive , La Jolla , California 92093-0340 , United States
| | - Rommie E Amaro
- Department of Chemistry and Biochemistry , University of California, San Diego , 9500 Gilman Drive , La Jolla , California 92093-0340 , United States
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29
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Gui S, Khan D, Wang Q, Yan DM, Lu BZ. Frontiers in biomolecular mesh generation and molecular visualization systems. Vis Comput Ind Biomed Art 2018; 1:7. [PMID: 32240387 PMCID: PMC7099538 DOI: 10.1186/s42492-018-0007-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2018] [Accepted: 07/01/2018] [Indexed: 11/25/2022] Open
Abstract
With the development of biomolecular modeling and simulation, especially implicit solvent modeling, higher requirements are set for the stability, efficiency and mesh quality of molecular mesh generation software. In this review, we summarize the recent works in biomolecular mesh generation and molecular visualization. First, we introduce various definitions of molecular surface and corresponding meshing software. Second, as the mesh quality significantly influences biomolecular simulation, we investigate some remeshing methods in the fields of computer graphics and molecular modeling. Then, we show the application of biomolecular mesh in the boundary element method (BEM) and the finite element method (FEM). Finally, to conveniently visualize the numerical results based on the mesh, we present two types of molecular visualization systems.
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Affiliation(s)
- Sheng Gui
- LSEC, NCMIS, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing, 100190, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Dawar Khan
- National Laboratory of Pattern Recognition, Institute of Automation, Chinese Academy of Sciences, Beijing, 100190, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qin Wang
- LSEC, NCMIS, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing, 100190, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Dong-Ming Yan
- National Laboratory of Pattern Recognition, Institute of Automation, Chinese Academy of Sciences, Beijing, 100190, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ben-Zhuo Lu
- LSEC, NCMIS, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing, 100190, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
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30
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Shaping Substrate Selectivity in a Broad-Spectrum Metallo-β-Lactamase. Antimicrob Agents Chemother 2018; 62:AAC.02079-17. [PMID: 29358299 DOI: 10.1128/aac.02079-17] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 01/18/2018] [Indexed: 11/20/2022] Open
Abstract
Metallo-β-lactamases (MBLs) are the major group of carbapenemases produced by bacterial pathogens. The design of MBL inhibitors has been limited by, among other issues, incomplete knowledge about how these enzymes modulate substrate recognition. While most MBLs are broad-spectrum enzymes, B2 MBLs are exclusive carbapenemases. This narrower substrate profile has been attributed to a sequence insertion present in B2 enzymes that limits accessibility to the active site. In this work, we evaluate the role of sequence insertions naturally occurring in the B2 enzyme Sfh-I and in the broad-spectrum B1 enzyme SPM-1. We engineered a chimeric protein in which the sequence insertion of SPM-1 was replaced by the one present in Sfh-I. The chimeric variant is a selective cephalosporinase, revealing that the substrate profile of MBLs can be further tuned depending on the protein context. These results also show that the stable scaffold of MBLs allows a modular engineering much richer than the one observed in nature.
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31
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Huang YMM, Huber GA, Wang N, Minteer SD, McCammon JA. Brownian dynamic study of an enzyme metabolon in the TCA cycle: Substrate kinetics and channeling. Protein Sci 2017; 27:463-471. [PMID: 29094409 DOI: 10.1002/pro.3338] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Revised: 10/23/2017] [Accepted: 10/29/2017] [Indexed: 01/08/2023]
Abstract
Malate dehydrogenase (MDH) and citrate synthase (CS) are two pacemaking enzymes involved in the tricarboxylic acid (TCA) cycle. Oxaloacetate (OAA) molecules are the intermediate substrates that are transferred from the MDH to CS to carry out sequential catalysis. It is known that, to achieve a high flux of intermediate transport and reduce the probability of substrate leaking, a MDH-CS metabolon forms to enhance the OAA substrate channeling. In this study, we aim to understand the OAA channeling within possible MDH-CS metabolons that have different structural orientations in their complexes. Three MDH-CS metabolons from native bovine, wild-type porcine, and recombinant sources, published in recent work, were selected to calculate OAA transfer efficiency by Brownian dynamics (BD) simulations and to study, through electrostatic potential calculations, a possible role of charges that drive the substrate channeling. Our results show that an electrostatic channel is formed in the metabolons of native bovine and recombinant porcine enzymes, which guides the oppositely charged OAA molecules passing through the channel and enhances the transfer efficiency. However, the channeling probability in a suggested wild-type porcine metabolon conformation is reduced due to an extended diffusion length between the MDH and CS active sites, implying that the corresponding arrangements of MDH and CS result in the decrease of electrostatic steering between substrates and protein surface and then reduce the substrate transfer efficiency from one active site to another.
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Affiliation(s)
- Yu-Ming M Huang
- Department of Pharmacology, University of California, San Diego, La Jolla, California, 92093
| | - Gary A Huber
- Howard Hughes Medical Institute, University of California, San Diego, La Jolla, California, 92093
| | - Nuo Wang
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California, 92093
| | - Shelley D Minteer
- Department of Chemistry, The University of Utah, Salt Lake City, Utah, 84112
| | - J Andrew McCammon
- Department of Pharmacology, University of California, San Diego, La Jolla, California, 92093.,Howard Hughes Medical Institute, University of California, San Diego, La Jolla, California, 92093.,Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California, 92093
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32
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Jurrus E, Engel D, Star K, Monson K, Brandi J, Felberg LE, Brookes DH, Wilson L, Chen J, Liles K, Chun M, Li P, Gohara DW, Dolinsky T, Konecny R, Koes DR, Nielsen JE, Head-Gordon T, Geng W, Krasny R, Wei GW, Holst MJ, McCammon JA, Baker NA. Improvements to the APBS biomolecular solvation software suite. Protein Sci 2017; 27:112-128. [PMID: 28836357 DOI: 10.1002/pro.3280] [Citation(s) in RCA: 1165] [Impact Index Per Article: 166.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 08/21/2017] [Accepted: 08/22/2017] [Indexed: 12/11/2022]
Abstract
The Adaptive Poisson-Boltzmann Solver (APBS) software was developed to solve the equations of continuum electrostatics for large biomolecular assemblages that have provided impact in the study of a broad range of chemical, biological, and biomedical applications. APBS addresses the three key technology challenges for understanding solvation and electrostatics in biomedical applications: accurate and efficient models for biomolecular solvation and electrostatics, robust and scalable software for applying those theories to biomolecular systems, and mechanisms for sharing and analyzing biomolecular electrostatics data in the scientific community. To address new research applications and advancing computational capabilities, we have continually updated APBS and its suite of accompanying software since its release in 2001. In this article, we discuss the models and capabilities that have recently been implemented within the APBS software package including a Poisson-Boltzmann analytical and a semi-analytical solver, an optimized boundary element solver, a geometry-based geometric flow solvation model, a graph theory-based algorithm for determining pKa values, and an improved web-based visualization tool for viewing electrostatics.
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Affiliation(s)
| | - Dave Engel
- Pacific Northwest National Laboratory, Richland, Washington
| | - Keith Star
- Pacific Northwest National Laboratory, Richland, Washington
| | - Kyle Monson
- Pacific Northwest National Laboratory, Richland, Washington
| | - Juan Brandi
- Pacific Northwest National Laboratory, Richland, Washington
| | | | | | | | - Jiahui Chen
- Southern Methodist University, Dallas, Texas
| | - Karina Liles
- Pacific Northwest National Laboratory, Richland, Washington
| | - Minju Chun
- Pacific Northwest National Laboratory, Richland, Washington
| | - Peter Li
- Pacific Northwest National Laboratory, Richland, Washington
| | | | | | - Robert Konecny
- University of California San Diego, San Diego, California
| | - David R Koes
- University of Pittsburgh, Pittsburgh, Pennsylvania
| | | | | | - Weihua Geng
- Southern Methodist University, Dallas, Texas
| | | | - Guo-Wei Wei
- Michigan State University, East Lansing, Michigan
| | | | | | - Nathan A Baker
- Pacific Northwest National Laboratory, Richland, Washington.,Brown University, Providence, Rhode Island
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33
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Hirakis SP, Malmstrom RD, Amaro RE. Molecular Simulations Reveal an Unresolved Conformation of the Type IA Protein Kinase A Regulatory Subunit and Suggest Its Role in the cAMP Regulatory Mechanism. Biochemistry 2017; 56:3885-3888. [PMID: 28661131 PMCID: PMC5751417 DOI: 10.1021/acs.biochem.7b00461] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
We identify a previously unresolved, unrecognized, and highly stable conformation of the protein kinase A (PKA) regulatory subunit RIα. This conformation, which we term the "Flipback" structure, bridges conflicting characteristics in crystallographic structures and solution experiments of the PKA RIα heterotetramer. Our simulations reveal a hinge residue, G235, in the B/C helix that is conserved through all isoforms of RI. Brownian dynamics simulations suggest that the Flipback conformation plays a role in cAMP association to the A domain of the R subunit.
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Affiliation(s)
- Sophia P. Hirakis
- Department of Chemistry and Biochemistry and National Biomedical Computational Resource, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0304
| | - Robert D. Malmstrom
- Department of Chemistry and Biochemistry and National Biomedical Computational Resource, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0304
| | - Rommie E. Amaro
- Department of Chemistry and Biochemistry and National Biomedical Computational Resource, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0304
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34
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Votapka LW, Jagger BR, Heyneman AL, Amaro RE. SEEKR: Simulation Enabled Estimation of Kinetic Rates, A Computational Tool to Estimate Molecular Kinetics and Its Application to Trypsin-Benzamidine Binding. J Phys Chem B 2017; 121:3597-3606. [PMID: 28191969 PMCID: PMC5562489 DOI: 10.1021/acs.jpcb.6b09388] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
We present the Simulation Enabled Estimation of Kinetic Rates (SEEKR) package, a suite of open-source scripts and tools designed to enable researchers to perform multiscale computation of the kinetics of molecular binding, unbinding, and transport using a combination of molecular dynamics, Brownian dynamics, and milestoning theory. To demonstrate its utility, we compute the kon, koff, and ΔGbind for the protein trypsin with its noncovalent binder, benzamidine, and examine the kinetics and other results generated in the context of the new software, and compare our findings to previous studies performed on the same system. We compute a kon estimate of (2.1 ± 0.3) × 107 M-1 s-1, a koff estimate of 83 ± 14 s-1, and a ΔGbind of -7.4 ± 0.1 kcal·mol-1, all of which compare closely to the experimentally measured values of 2.9 × 107 M-1 s-1, 600 ± 300 s-1, and -6.71 ± 0.05 kcal·mol-1, respectively.
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Affiliation(s)
- Lane W. Votapka
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794
- University of California San Diego, 9500 Gilman Dr., La Jolla, CA 92093
| | | | | | - Rommie E. Amaro
- University of California San Diego, 9500 Gilman Dr., La Jolla, CA 92093
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35
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Poshyvailo L, von Lieres E, Kondrat S. Does metabolite channeling accelerate enzyme-catalyzed cascade reactions? PLoS One 2017; 12:e0172673. [PMID: 28234973 PMCID: PMC5325314 DOI: 10.1371/journal.pone.0172673] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Accepted: 02/08/2017] [Indexed: 12/30/2022] Open
Abstract
Metabolite or substrate channeling is a direct transfer of metabolites from one enzyme to the next enzyme in a cascade. Among many potential advantages of substrate channeling, acceleration of the total reaction rate is considered as one of the most important and self-evident. However, using a simple model, supported by stochastic simulations, we show that it is not always the case; particularly at long times (i.e. in steady state) and high substrate concentrations, a channeled reaction cannot be faster, and can even be slower, than the original non-channeled cascade reaction. In addition we show that increasing the degree of channeling may lead to an increase of the metabolite pool size. We substantiate that the main advantage of channeling likely lies in protecting metabolites from degradation or competing side reactions.
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Affiliation(s)
- Liubov Poshyvailo
- Forschungszentrum Jülich, IBG-1: Biotechnology, Jülich, Germany
- Forschungszentrum Jülich, IEK-7: Institute of Energy and Climate Research, Jülich, Germany
| | - Eric von Lieres
- Forschungszentrum Jülich, IBG-1: Biotechnology, Jülich, Germany
| | - Svyatoslav Kondrat
- Forschungszentrum Jülich, IBG-1: Biotechnology, Jülich, Germany
- * E-mail: ,
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36
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Tang Z, Roberts CC, Chang CEA. Understanding ligand-receptor non-covalent binding kinetics using molecular modeling. FRONT BIOSCI-LANDMRK 2017; 22:960-981. [PMID: 27814657 PMCID: PMC5470370 DOI: 10.2741/4527] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Kinetic properties may serve as critical differentiators and predictors of drug efficacy and safety, in addition to the traditionally focused binding affinity. However the quantitative structure-kinetics relationship (QSKR) for modeling and ligand design is still poorly understood. This review provides an introduction to the kinetics of drug binding from a fundamental chemistry perspective. We focus on recent developments of computational tools and their applications to non-covalent binding kinetics.
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Affiliation(s)
- Zhiye Tang
- Department of Chemistry, University of California, Riverside, CA 92521
| | | | - Chia-En A Chang
- Department of Chemistry, University of California, Riverside, CA 92521,
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37
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Ma L, Li X, Liu C. From generalized Langevin equations to Brownian dynamics and embedded Brownian dynamics. J Chem Phys 2016. [DOI: 10.1063/1.4962419] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Lina Ma
- Department of Mathematics, The Pennsylvania State University, University Park, Pennsylvania 16802-6400, USA
| | - Xiantao Li
- Department of Mathematics, The Pennsylvania State University, University Park, Pennsylvania 16802-6400, USA
| | - Chun Liu
- Department of Mathematics, The Pennsylvania State University, University Park, Pennsylvania 16802-6400, USA
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38
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Dewan S, McCabe KJ, Regnier M, McCulloch AD, Lindert S. Molecular Effects of cTnC DCM Mutations on Calcium Sensitivity and Myofilament Activation-An Integrated Multiscale Modeling Study. J Phys Chem B 2016; 120:8264-75. [PMID: 27133568 PMCID: PMC5001916 DOI: 10.1021/acs.jpcb.6b01950] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Mutations in cardiac troponin C (D75Y, E59D, and G159D), a key regulatory protein of myofilament contraction, have been associated with dilated cardiomyopathy (DCM). Despite reports of altered myofilament function in these mutants, the underlying molecular alterations caused by these mutations remain elusive. Here we investigate in silico the intramolecular mechanisms by which these mutations affect myofilament contraction. On the basis of the location of cardiac troponin C (cTnC) mutations, we tested the hypothesis that intramolecular effects can explain the altered myofilament calcium sensitivity of force development for D75Y and E59D cTnC, whereas altered cardiac troponin C-troponin I (cTnC-cTnI) interaction contributes to the reported contractile effects of the G159D mutation. We employed a multiscale approach combining molecular dynamics (MD) and Brownian dynamics (BD) simulations to estimate cTnC calcium association and hydrophobic patch opening. We then integrated these parameters into a Markov model of myofilament activation to compute the steady-state force-pCa relationship. The analysis showed that myofilament calcium sensitivity with D75Y and E59D can be explained by changes in calcium binding affinity of cTnC and the rate of hydrophobic patch opening, if a partial cTnC interhelical opening angle (110°) is sufficient for cTnI switch peptide association to cTnC. In contrast, interactions between cTnC and cTnI within the cardiac troponin complex must also be accounted for to explain contractile alterations due to G159D. In conclusion, this is the first multiscale in silico study to elucidate how direct molecular effects of genetic mutations in cTnC translate to altered myofilament contractile function.
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Affiliation(s)
- Sukriti Dewan
- Department of Bioengineering, University of California at San Diego, La Jolla, CA, 92093
| | - Kimberly J. McCabe
- Department of Bioengineering, University of California at San Diego, La Jolla, CA, 92093
| | - Michael Regnier
- Dept. of Bioengineering, University of Washington, Seattle, WA 98195
- Center for Cardiovascular Biology, University of Washington, Seattle, WA 98109
| | - Andrew D. McCulloch
- Department of Bioengineering, University of California at San Diego, La Jolla, CA, 92093
| | - Steffen Lindert
- Department of Chemistry & Biochemistry, Ohio State University, Columbus, OH, 43210
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39
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Roberts CC, Chang CEA. Analysis of Ligand-Receptor Association and Intermediate Transfer Rates in Multienzyme Nanostructures with All-Atom Brownian Dynamics Simulations. J Phys Chem B 2016; 120:8518-31. [PMID: 27248669 DOI: 10.1021/acs.jpcb.6b02236] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We present the second-generation GeomBD Brownian dynamics software for determining interenzyme intermediate transfer rates and substrate association rates in biomolecular complexes. Substrate and intermediate association rates for a series of enzymes or biomolecules can be compared between the freely diffusing disorganized configuration and various colocalized or complexed arrangements for kinetic investigation of enhanced intermediate transfer. In addition, enzyme engineering techniques, such as synthetic protein conjugation, can be computationally modeled and analyzed to better understand changes in substrate association relative to native enzymes. Tools are provided to determine nonspecific ligand-receptor association residence times, and to visualize common sites of nonspecific association of substrates on receptor surfaces. To demonstrate features of the software, interenzyme intermediate substrate transfer rate constants are calculated and compared for all-atom models of DNA origami scaffold-bound bienzyme systems of glucose oxidase and horseradish peroxidase. Also, a DNA conjugated horseradish peroxidase enzyme was analyzed for its propensity to increase substrate association rates and substrate local residence times relative to the unmodified enzyme. We also demonstrate the rapid determination and visualization of common sites of nonspecific ligand-receptor association by using HIV-1 protease and an inhibitor, XK263. GeomBD2 accelerates simulations by precomputing van der Waals potential energy grids and electrostatic potential grid maps, and has a flexible and extensible support for all-atom and coarse-grained force fields. Simulation software is written in C++ and utilizes modern parallelization techniques for potential grid preparation and Brownian dynamics simulation processes. Analysis scripts, written in the Python scripting language, are provided for quantitative simulation analysis. GeomBD2 is applicable to the fields of biophysics, bioengineering, and enzymology in both predictive and explanatory roles.
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Affiliation(s)
- Christopher C Roberts
- Department of Chemistry, University of California , Riverside, California 92521, United States
| | - Chia-En A Chang
- Department of Chemistry, University of California , Riverside, California 92521, United States
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40
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Abstract
![]()
Electrostatic effects
are ubiquitous in protein interactions and
are found to be pervasive in the complement system as well. The interaction
between complement fragment C3d and complement receptor 2 (CR2) has
evolved to become a link between innate and adaptive immunity. Electrostatic
interactions have been suggested to be the driving factor for the
association of the C3d:CR2 complex. In this study, we investigate
the effects of ionic strength and mutagenesis on the association of
C3d:CR2 through Brownian dynamics simulations. We demonstrate that
the formation of the C3d:CR2 complex is ionic strength-dependent,
suggesting the presence of long-range electrostatic steering that
accelerates the complex formation. Electrostatic steering occurs through
the interaction of an acidic surface patch in C3d and the positively
charged CR2 and is supported by the effects of mutations within the
acidic patch of C3d that slow or diminish association. Our data are
in agreement with previous experimental mutagenesis and binding studies
and computational studies. Although the C3d acidic patch may be locally
destabilizing because of unfavorable Coulombic interactions of like
charges, it contributes to the acceleration of association. Therefore,
acceleration of function through electrostatic steering takes precedence
to stability. The site of interaction between C3d and CR2 has been
the target for delivery of CR2-bound nanoparticle, antibody, and small
molecule biomarkers, as well as potential therapeutics. A detailed
knowledge of the physicochemical basis of C3d:CR2 association may
be necessary to accelerate biomarker and drug discovery efforts.
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Affiliation(s)
- Rohith R Mohan
- Department of Bioengineering, University of California , Riverside, California 92521, United States
| | - Gary A Huber
- Department of Chemistry and Biochemistry, University of California , San Diego, California 92093, United States
| | - Dimitrios Morikis
- Department of Bioengineering, University of California , Riverside, California 92521, United States
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41
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Multiscale method for modeling binding phenomena involving large objects: application to kinesin motor domains motion along microtubules. Sci Rep 2016; 6:23249. [PMID: 26988596 PMCID: PMC4796874 DOI: 10.1038/srep23249] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 03/03/2016] [Indexed: 11/30/2022] Open
Abstract
Many biological phenomena involve the binding of proteins to a large object. Because the electrostatic forces that guide binding act over large distances, truncating the size of the system to facilitate computational modeling frequently yields inaccurate results. Our multiscale approach implements a computational focusing method that permits computation of large systems without truncating the electrostatic potential and achieves the high resolution required for modeling macromolecular interactions, all while keeping the computational time reasonable. We tested our approach on the motility of various kinesin motor domains. We found that electrostatics help guide kinesins as they walk: N-kinesins towards the plus-end, and C-kinesins towards the minus-end of microtubules. Our methodology enables computation in similar, large systems including protein binding to DNA, viruses, and membranes.
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42
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Votapka LW, Amaro RE. Multiscale Estimation of Binding Kinetics Using Brownian Dynamics, Molecular Dynamics and Milestoning. PLoS Comput Biol 2015; 11:e1004381. [PMID: 26505480 PMCID: PMC4624728 DOI: 10.1371/journal.pcbi.1004381] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Accepted: 06/04/2015] [Indexed: 12/16/2022] Open
Abstract
The kinetic rate constants of binding were estimated for four biochemically relevant molecular systems by a method that uses milestoning theory to combine Brownian dynamics simulations with more detailed molecular dynamics simulations. The rate constants found using this method agreed well with experimentally and theoretically obtained values. We predicted the association rate of a small charged molecule toward both a charged and an uncharged spherical receptor and verified the estimated value with Smoluchowski theory. We also calculated the kon rate constant for superoxide dismutase with its natural substrate, O2-, in a validation of a previous experiment using similar methods but with a number of important improvements. We also calculated the kon for a new system: the N-terminal domain of Troponin C with its natural substrate Ca2+. The kon calculated for the latter two systems closely resemble experimentally obtained values. This novel multiscale approach is computationally cheaper and more parallelizable when compared to other methods of similar accuracy. We anticipate that this methodology will be useful for predicting kinetic rate constants and for understanding the process of binding between a small molecule and a protein receptor.
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Affiliation(s)
- Lane W. Votapka
- Department of Chemistry and Biochemistry and National Biomedical Computation Resource, University of California, San Diego, San Diego, California, United States of America
| | - Rommie E. Amaro
- Department of Chemistry and Biochemistry and National Biomedical Computation Resource, University of California, San Diego, San Diego, California, United States of America
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43
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Boras BW, Hirakis SP, Votapka LW, Malmstrom RD, Amaro RE, McCulloch AD. Bridging scales through multiscale modeling: a case study on protein kinase A. Front Physiol 2015; 6:250. [PMID: 26441670 PMCID: PMC4563169 DOI: 10.3389/fphys.2015.00250] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 08/24/2015] [Indexed: 12/21/2022] Open
Abstract
The goal of multiscale modeling in biology is to use structurally based physico-chemical models to integrate across temporal and spatial scales of biology and thereby improve mechanistic understanding of, for example, how a single mutation can alter organism-scale phenotypes. This approach may also inform therapeutic strategies or identify candidate drug targets that might otherwise have been overlooked. However, in many cases, it remains unclear how best to synthesize information obtained from various scales and analysis approaches, such as atomistic molecular models, Markov state models (MSM), subcellular network models, and whole cell models. In this paper, we use protein kinase A (PKA) activation as a case study to explore how computational methods that model different physical scales can complement each other and integrate into an improved multiscale representation of the biological mechanisms. Using measured crystal structures, we show how molecular dynamics (MD) simulations coupled with atomic-scale MSMs can provide conformations for Brownian dynamics (BD) simulations to feed transitional states and kinetic parameters into protein-scale MSMs. We discuss how milestoning can give reaction probabilities and forward-rate constants of cAMP association events by seamlessly integrating MD and BD simulation scales. These rate constants coupled with MSMs provide a robust representation of the free energy landscape, enabling access to kinetic, and thermodynamic parameters unavailable from current experimental data. These approaches have helped to illuminate the cooperative nature of PKA activation in response to distinct cAMP binding events. Collectively, this approach exemplifies a general strategy for multiscale model development that is applicable to a wide range of biological problems.
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Affiliation(s)
- Britton W. Boras
- Department of Bioengineering, University of CaliforniaSan Diego, La Jolla, CA, USA
| | - Sophia P. Hirakis
- Department of Chemistry and Biochemistry, University of CaliforniaSan Diego, La Jolla, CA, USA
| | - Lane W. Votapka
- Department of Chemistry and Biochemistry, University of CaliforniaSan Diego, La Jolla, CA, USA
| | - Robert D. Malmstrom
- National Biomedical Computation Resource, University of CaliforniaSan Diego, La Jolla, CA, USA
| | - Rommie E. Amaro
- Department of Chemistry and Biochemistry, University of CaliforniaSan Diego, La Jolla, CA, USA
- National Biomedical Computation Resource, University of CaliforniaSan Diego, La Jolla, CA, USA
| | - Andrew D. McCulloch
- Department of Bioengineering, University of CaliforniaSan Diego, La Jolla, CA, USA
- National Biomedical Computation Resource, University of CaliforniaSan Diego, La Jolla, CA, USA
- Department of Medicine, University of CaliforniaSan Diego, La Jolla, CA, USA
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44
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Huang YMM, Huber G, McCammon JA. Electrostatic steering enhances the rate of cAMP binding to phosphodiesterase: Brownian dynamics modeling. Protein Sci 2015; 24:1884-9. [PMID: 26346301 DOI: 10.1002/pro.2794] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Revised: 08/20/2015] [Accepted: 08/24/2015] [Indexed: 01/18/2023]
Abstract
Signaling in cells often involves co-localization of the signaling molecules. Most experimental evidence has shown that intracellular compartmentalization restricts the range of action of the second messenger, 3'-5'-cyclic adenosine monophosphate (cAMP), which is degraded by phosphodiesterases (PDEs). The objective of this study is to understand the details of molecular encounter that may play a role in efficient operation of the cAMP signaling apparatus. The results from electrostatic potential calculations and Brownian dynamics simulations suggest that positive potential of the active site from PDE enhances capture of diffusing cAMP molecules. This electrostatic steering between cAMP and the active site of a PDE plays a major role in the enzyme-substrate encounter, an effect that may be of significance in sequestering cAMP released from a nearby binding site or in attracting more freely diffusing cAMP molecules.
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Affiliation(s)
- Yu-ming M Huang
- Department of Pharmacology, University of California, San Diego, La Jolla, California, 92093
| | - Gary Huber
- Howard Hughes Medical Institute, University of California, San Diego, La Jolla, California, 92093
| | - J Andrew McCammon
- Department of Pharmacology, University of California, San Diego, La Jolla, California, 92093.,Howard Hughes Medical Institute, University of California, San Diego, La Jolla, California, 92093.,Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California, 92093
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45
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Martinez M, Bruce NJ, Romanowska J, Kokh DB, Ozboyaci M, Yu X, Öztürk MA, Richter S, Wade RC. SDA 7: A modular and parallel implementation of the simulation of diffusional association software. J Comput Chem 2015; 36:1631-45. [PMID: 26123630 PMCID: PMC4755232 DOI: 10.1002/jcc.23971] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Revised: 05/12/2015] [Accepted: 05/18/2015] [Indexed: 01/22/2023]
Abstract
The simulation of diffusional association (SDA) Brownian dynamics software package has been widely used in the study of biomacromolecular association. Initially developed to calculate bimolecular protein-protein association rate constants, it has since been extended to study electron transfer rates, to predict the structures of biomacromolecular complexes, to investigate the adsorption of proteins to inorganic surfaces, and to simulate the dynamics of large systems containing many biomacromolecular solutes, allowing the study of concentration-dependent effects. These extensions have led to a number of divergent versions of the software. In this article, we report the development of the latest version of the software (SDA 7). This release was developed to consolidate the existing codes into a single framework, while improving the parallelization of the code to better exploit modern multicore shared memory computer architectures. It is built using a modular object-oriented programming scheme, to allow for easy maintenance and extension of the software, and includes new features, such as adding flexible solute representations. We discuss a number of application examples, which describe some of the methods available in the release, and provide benchmarking data to demonstrate the parallel performance.
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Affiliation(s)
- Michael Martinez
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Schloss-Wolfsbrunnenweg 35, 69118, Heidelberg, Germany
| | - Neil J Bruce
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Schloss-Wolfsbrunnenweg 35, 69118, Heidelberg, Germany
| | - Julia Romanowska
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Schloss-Wolfsbrunnenweg 35, 69118, Heidelberg, Germany
| | - Daria B Kokh
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Schloss-Wolfsbrunnenweg 35, 69118, Heidelberg, Germany
| | - Musa Ozboyaci
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Schloss-Wolfsbrunnenweg 35, 69118, Heidelberg, Germany
- Heidelberg Graduate School of Mathematical and Computational Methods for the Sciences (HGS MathComp), Im Neuenheimer Feld 368, 69120, Heidelberg, Germany
| | - Xiaofeng Yu
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Schloss-Wolfsbrunnenweg 35, 69118, Heidelberg, Germany
- Hartmut Hoffmann-Berling International Graduate School of Molecular and Cellular Biology (HBIGS), Im Neuenheimer Feld 501, 69120, Heidelberg, Germany
| | - Mehmet Ali Öztürk
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Schloss-Wolfsbrunnenweg 35, 69118, Heidelberg, Germany
- Hartmut Hoffmann-Berling International Graduate School of Molecular and Cellular Biology (HBIGS), Im Neuenheimer Feld 501, 69120, Heidelberg, Germany
| | - Stefan Richter
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Schloss-Wolfsbrunnenweg 35, 69118, Heidelberg, Germany
| | - Rebecca C Wade
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Schloss-Wolfsbrunnenweg 35, 69118, Heidelberg, Germany
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, 69120, Heidelberg, Germany
- Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University, Im Neuenheimer Feld 368, 69120, Heidelberg, Germany
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46
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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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47
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Wang N, McCammon JA. Substrate channeling between the human dihydrofolate reductase and thymidylate synthase. Protein Sci 2015; 25:79-86. [PMID: 26096018 DOI: 10.1002/pro.2720] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Revised: 06/02/2015] [Accepted: 06/05/2015] [Indexed: 12/17/2022]
Abstract
In vivo, as an advanced catalytic strategy, transient non-covalently bound multi-enzyme complexes can be formed to facilitate the relay of substrates, i. e. substrate channeling, between sequential enzymatic reactions and to enhance the throughput of multi-step enzymatic pathways. The human thymidylate synthase and dihydrofolate reductase catalyze two consecutive reactions in the folate metabolism pathway, and experiments have shown that they are very likely to bind in the same multi-enzyme complex in vivo. While reports on the protozoa thymidylate synthase-dihydrofolate reductase bifunctional enzyme give substantial evidences of substrate channeling along a surface "electrostatic highway," attention has not been paid to whether the human thymidylate synthase and dihydrofolate reductase, if they are in contact with each other in the multi-enzyme complex, are capable of substrate channeling employing surface electrostatics. This work utilizes protein-protein docking, electrostatics calculations, and Brownian dynamics to explore the existence and mechanism of the substrate channeling between the human thymidylate synthase and dihydrofolate reductase. The results show that the bound human thymidylate synthase and dihydrofolate reductase are capable of substrate channeling and the formation of the surface "electrostatic highway." The substrate channeling efficiency between the two can be reasonably high and comparable to that of the protozoa.
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Affiliation(s)
- Nuo Wang
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, 92037
| | - J Andrew McCammon
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, 92037.,Department of Pharmacology, University of California San Diego, La Jolla, California, 92037.,Howard Hughes Medical Institute, University of California San Diego, La Jolla, California, 92037
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48
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Khruschev SS, Abaturova AM, Diakonova AN, Fedorov VA, Ustinin DM, Kovalenko IB, Riznichenko GY, Rubin AB. Brownian-dynamics simulations of protein–protein interactions in the photosynthetic electron transport chain. Biophysics (Nagoya-shi) 2015. [DOI: 10.1134/s0006350915020086] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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49
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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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50
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Gorham RD, Rodriguez W, Morikis D. Molecular analysis of the interaction between staphylococcal virulence factor Sbi-IV and complement C3d. Biophys J 2014; 106:1164-73. [PMID: 24606940 DOI: 10.1016/j.bpj.2014.01.033] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Revised: 12/29/2013] [Accepted: 01/23/2014] [Indexed: 02/07/2023] Open
Abstract
Staphylococcus aureus expresses numerous virulence factors that aid in immune evasion. The four-domain staphylococcal immunoglobulin binding (Sbi) protein interacts with complement component 3 (C3) and its thioester domain (C3d)-containing fragments. Recent structural data suggested two possible modes of binding of Sbi domain IV (Sbi-IV) to C3d, but the physiological binding mode remains unclear. We used a computational approach to provide insight into the C3d-Sbi-IV interaction. Molecular dynamics (MD) simulations showed that the first binding mode (PDB code 2WY8) is more robust than the second (PDB code 2WY7), with more persistent polar and nonpolar interactions, as well as conserved interfacial solvent accessible surface area. Brownian dynamics and steered MD simulations revealed that the first binding mode has faster association kinetics and maintains more stable intermolecular interactions compared to the second binding mode. In light of available experimental and structural data, our data confirm that the first binding mode represents Sbi-IV interaction with C3d (and C3) in a physiological context. Although the second binding mode is inherently less stable, we suggest a possible physiological role. Both binding sites may serve as a template for structure-based design of novel complement therapeutics.
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Affiliation(s)
- Ronald D Gorham
- Department of Bioengineering, University of California, Riverside, California
| | - Wilson Rodriguez
- Department of Bioengineering, University of California, Riverside, California
| | - Dimitrios Morikis
- Department of Bioengineering, University of California, Riverside, California.
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