1
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Pyrris Y, Papadaki GF, Mikros E, Diallinas G. The last two transmembrane helices in the APC-type FurE transporter act as an intramolecular chaperone essential for concentrative ER-exit. MICROBIAL CELL (GRAZ, AUSTRIA) 2024; 11:1-15. [PMID: 38225947 PMCID: PMC10788122 DOI: 10.15698/mic2024.01.811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 10/31/2023] [Accepted: 11/13/2023] [Indexed: 01/17/2024]
Abstract
FurE is a H+ symporter specific for the cellular uptake of uric acid, allantoin, uracil, and toxic nucleobase analogues in the fungus Aspergillus nidulans. Being member of the NCS1 protein family, FurE is structurally related to the APC-superfamily of transporters. APC-type transporters are characterised by a 5+5 inverted repeat fold made of ten transmembrane segments (TMS1-10) and function through the rocking-bundle mechanism. Most APC-type transporters possess two extra C-terminal TMS segments (TMS11-12), the function of which remains elusive. Here we present a systematic mutational analysis of TMS11-12 of FurE and show that two specific aromatic residues in TMS12, Trp473 and Tyr484, are essential for ER-exit and trafficking to the plasma membrane (PM). Molecular modeling shows that Trp473 and Tyr484 might be essential through dynamic interactions with residues in TMS2 (Leu91), TMS3 (Phe111), TMS10 (Val404, Asp406) and other aromatic residues in TMS12. Genetic analysis confirms the essential role of Phe111, Asp406 and TMS12 aromatic residues in FurE ER-exit. We further show that co-expression of FurE-Y484F or FurE-W473A with wild-type FurE leads to a dominant negative phenotype, compatible with the concept that FurE molecules oligomerize or partition in specific microdomains to achieve concentrative ER-exit and traffic to the PM. Importantly, truncated FurE versions lacking TMS11-12 are unable to reproduce a negative effect on the trafficking of co-expressed wild-type FurE. Overall, we show that TMS11-12 acts as an intramolecular chaperone for proper FurE folding, which seems to provide a structural code for FurE partitioning in ER-exit sites.
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Affiliation(s)
- Yiannis Pyrris
- Department of Biology, National and Kapodistrian University of Athens, Panepistimioupolis, Athens, 15784, Greece
| | - Georgia F. Papadaki
- Department of Biology, National and Kapodistrian University of Athens, Panepistimioupolis, Athens, 15784, Greece
| | - Emmanuel Mikros
- Department of Pharmacy, National and Kapodistrian University of Athens, Panepistimioupolis, Athens, 15771, Greece
| | - George Diallinas
- Department of Biology, National and Kapodistrian University of Athens, Panepistimioupolis, Athens, 15784, Greece
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology, Heraklion, 70013, Greece
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2
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Hellemann E, Durrant JD. Worth the Weight: Sub-Pocket EXplorer (SubPEx), a Weighted Ensemble Method to Enhance Binding-Pocket Conformational Sampling. J Chem Theory Comput 2023; 19:5677-5689. [PMID: 37585617 PMCID: PMC10500992 DOI: 10.1021/acs.jctc.3c00478] [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: 08/18/2023]
Abstract
Structure-based virtual screening (VS) is an effective method for identifying potential small-molecule ligands, but traditional VS approaches consider only a single binding-pocket conformation. Consequently, they struggle to identify ligands that bind to alternate conformations. Ensemble docking helps address this issue by incorporating multiple conformations into the docking process, but it depends on methods that can thoroughly explore pocket flexibility. We here introduce Sub-Pocket EXplorer (SubPEx), an approach that uses weighted ensemble (WE) path sampling to accelerate binding-pocket sampling. As proof of principle, we apply SubPEx to three proteins relevant to drug discovery: heat shock protein 90, influenza neuraminidase, and yeast hexokinase 2. SubPEx is available free of charge without registration under the terms of the open-source MIT license: http://durrantlab.com/subpex/.
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Affiliation(s)
- Erich Hellemann
- Department of Biological
Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Jacob D. Durrant
- Department of Biological
Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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3
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Hellemann E, Durrant JD. Worth the weight: Sub-Pocket EXplorer (SubPEx), a weighted-ensemble method to enhance binding-pocket conformational sampling. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.03.539330. [PMID: 37251500 PMCID: PMC10214482 DOI: 10.1101/2023.05.03.539330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Structure-based virtual screening (VS) is an effective method for identifying potential small-molecule ligands, but traditional VS approaches consider only a single binding-pocket conformation. Consequently, they struggle to identify ligands that bind to alternate conformations. Ensemble docking helps address this issue by incorporating multiple conformations into the docking process, but it depends on methods that can thoroughly explore pocket flexibility. We here introduce Sub-Pocket EXplorer (SubPEx), an approach that uses weighted ensemble (WE) path sampling to accelerate binding-pocket sampling. As proof of principle, we apply SubPEx to three proteins relevant to drug discovery: heat shock protein 90, influenza neuraminidase, and yeast hexokinase 2. SubPEx is available free of charge without registration under the terms of the open-source MIT license: http://durrantlab.com/subpex/.
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Affiliation(s)
- Erich Hellemann
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, 15260, United States
| | - Jacob D. Durrant
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, 15260, United States
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4
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Aristoff D, Copperman J, Simpson G, Webber RJ, Zuckerman DM. Weighted ensemble: Recent mathematical developments. J Chem Phys 2023; 158:014108. [PMID: 36610976 PMCID: PMC9822651 DOI: 10.1063/5.0110873] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Accepted: 12/04/2022] [Indexed: 12/12/2022] Open
Abstract
Weighted ensemble (WE) is an enhanced sampling method based on periodically replicating and pruning trajectories generated in parallel. WE has grown increasingly popular for computational biochemistry problems due, in part, to improved hardware and accessible software implementations. Algorithmic and analytical improvements have played an important role, and progress has accelerated in recent years. Here, we discuss and elaborate on the WE method from a mathematical perspective, highlighting recent results that enhance the computational efficiency. The mathematical theory reveals a new strategy for optimizing trajectory management that approaches the best possible variance while generalizing to systems of arbitrary dimension.
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Affiliation(s)
- D. Aristoff
- Mathematics, Colorado State University, Fort Collins, CO 80521 USA
| | - J. Copperman
- Biomedical Engineering, Oregon Health and Science University, Portland, OR 97239 USA
| | - G. Simpson
- Mathematics, Drexel University, Philadelphia, Pennsylvania 19104 USA
| | - R. J. Webber
- Computing and Mathematical Sciences, California Institute of Technology, Pasadena, California 91125 USA
| | - D. M. Zuckerman
- Biomedical Engineering, Oregon Health and Science University, Portland, OR 97239 USA
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5
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del Alamo D, DeSousa L, Nair RM, Rahman S, Meiler J, Mchaourab HS. Integrated AlphaFold2 and DEER investigation of the conformational dynamics of a pH-dependent APC antiporter. Proc Natl Acad Sci U S A 2022; 119:e2206129119. [PMID: 35969794 PMCID: PMC9407458 DOI: 10.1073/pnas.2206129119] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 07/08/2022] [Indexed: 11/18/2022] Open
Abstract
The Amino Acid-Polyamine-Organocation (APC) transporter GadC contributes to the survival of pathogenic bacteria under extreme acid stress by exchanging extracellular glutamate for intracellular γ-aminobutyric acid (GABA). Its structure, determined in an inward-facing conformation at alkaline pH, consists of the canonical LeuT-fold with a conserved five-helix inverted repeat, thereby resembling functionally divergent transporters such as the serotonin transporter SERT and the glucose-sodium symporter SGLT1. However, despite this structural similarity, it is unclear if the conformational dynamics of antiporters such as GadC follow the blueprint of these or other LeuT-fold transporters. Here, we used double electron-electron resonance (DEER) spectroscopy to monitor the conformational dynamics of GadC in lipid bilayers in response to acidification and substrate binding. To guide experimental design and facilitate the interpretation of the DEER data, we generated an ensemble of structural models in multiple conformations using a recently introduced modification of AlphaFold2 . Our experimental results reveal acid-induced conformational changes that dislodge the Cterminus from the permeation pathway coupled with rearrangement of helices that enables isomerization between inward- and outward-facing states. The substrate glutamate, but not GABA, modulates the dynamics of an extracellular thin gate without shifting the equilibrium between inward- and outward-facing conformations. In addition to introducing an integrated methodology for probing transporter conformational dynamics, the congruence of the DEER data with patterns of structural rearrangements deduced from ensembles of AlphaFold2 models illuminates the conformational cycle of GadC underpinning transport and exposes yet another example of the divergence between the dynamics of different families in the LeuT-fold.
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Affiliation(s)
- Diego del Alamo
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 37212
- Department of Chemistry, Vanderbilt University, Nashville, TN 37212
| | - Lillian DeSousa
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 37212
| | - Rahul M. Nair
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 37212
| | - Suhaila Rahman
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 37212
| | - Jens Meiler
- Department of Chemistry, Vanderbilt University, Nashville, TN 37212
- Institute for Drug Discovery, Leipzig University, Leipzig, Germany 04109
| | - Hassane S. Mchaourab
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 37212
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6
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Meshkin H, Zhu F. Toward Convergence in Free Energy Calculations for Protein Conformational Changes: A Case Study on the Thin Gate of Mhp1 Transporter. J Chem Theory Comput 2021; 17:6583-6596. [PMID: 34523931 DOI: 10.1021/acs.jctc.1c00585] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
It has been challenging to obtain reliable free energies for protein conformational changes from all-atom molecular dynamics simulations, despite the availability of many enhanced sampling techniques. To alleviate the difficulties associated with the enormous complexity of the conformational space, here we propose a few practical strategies for such calculations, including (1) a stringent method to examine convergence by comparing independent simulations starting from different initial coordinates, (2) adoption of multistep schemes in which the complete conformational change consists of multiple transition steps, each sampled using a distinct reaction coordinate, and (3) application of boundary restraints to simplify the conformational space. We demonstrate these strategies on the conformational changes between the outward-facing and outward-occluded states of the Mhp1 membrane transporter, obtaining the equilibrium thermodynamics of the relevant metastable states, the kinetic rates between these states, and the reactive trajectories that reveal the atomic details of spontaneous transitions. Our approaches thus promise convergent and reliable calculations to examine intuition-based hypotheses and to eventually elucidate the underlying molecular mechanisms of reversible conformational changes in complex protein systems.
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Affiliation(s)
- Hamed Meshkin
- Department of Physics, Indiana University Purdue University Indianapolis, 402 N. Blackford Street, Indianapolis, Indiana 46202, United States
| | - Fangqiang Zhu
- Department of Physics, Indiana University Purdue University Indianapolis, 402 N. Blackford Street, Indianapolis, Indiana 46202, United States
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7
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Fairweather SJ, Shah N, Brӧer S. Heteromeric Solute Carriers: Function, Structure, Pathology and Pharmacology. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 21:13-127. [PMID: 33052588 DOI: 10.1007/5584_2020_584] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Solute carriers form one of three major superfamilies of membrane transporters in humans, and include uniporters, exchangers and symporters. Following several decades of molecular characterisation, multiple solute carriers that form obligatory heteromers with unrelated subunits are emerging as a distinctive principle of membrane transporter assembly. Here we comprehensively review experimentally established heteromeric solute carriers: SLC3-SLC7 amino acid exchangers, SLC16 monocarboxylate/H+ symporters and basigin/embigin, SLC4A1 (AE1) and glycophorin A exchanger, SLC51 heteromer Ost α-Ost β uniporter, and SLC6 heteromeric symporters. The review covers the history of the heteromer discovery, transporter physiology, structure, disease associations and pharmacology - all with a focus on the heteromeric assembly. The cellular locations, requirements for complex formation, and the functional role of dimerization are extensively detailed, including analysis of the first complete heteromer structures, the SLC7-SLC3 family transporters LAT1-4F2hc, b0,+AT-rBAT and the SLC6 family heteromer B0AT1-ACE2. We present a systematic analysis of the structural and functional aspects of heteromeric solute carriers and conclude with common principles of their functional roles and structural architecture.
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Affiliation(s)
- Stephen J Fairweather
- Research School of Biology, Australian National University, Canberra, ACT, Australia. .,Resarch School of Chemistry, Australian National University, Canberra, ACT, Australia.
| | - Nishank Shah
- Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - Stefan Brӧer
- Research School of Biology, Australian National University, Canberra, ACT, Australia.
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8
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Sharpe DJ, Wales DJ. Efficient and exact sampling of transition path ensembles on Markovian networks. J Chem Phys 2020; 153:024121. [DOI: 10.1063/5.0012128] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Affiliation(s)
- Daniel J. Sharpe
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - David J. Wales
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
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9
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Bisignano P, Lee MA, George A, Zuckerman DM, Grabe M, Rosenberg JM. A kinetic mechanism for enhanced selectivity of membrane transport. PLoS Comput Biol 2020; 16:e1007789. [PMID: 32614861 PMCID: PMC7331977 DOI: 10.1371/journal.pcbi.1007789] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 03/13/2020] [Indexed: 01/06/2023] Open
Abstract
Membrane transport is generally thought to occur via an alternating access mechanism in which the transporter adopts at least two states, accessible from two different sides of the membrane to exchange substrates from the extracellular environment and the cytoplasm or from the cytoplasm and the intracellular matrix of the organelles (only in eukaryotes). In recent years, a number of high resolution structures have supported this general framework for a wide class of transport molecules, although additional states along the transport pathway are emerging as critically important. Given that substrate binding is often weak in order to enhance overall transport rates, there exists the distinct possibility that transporters may transport the incorrect substrate. This is certainly the case for many pharmaceutical compounds that are absorbed in the gut or cross the blood brain barrier through endogenous transporters. Docking studies on the bacterial sugar transporter vSGLT reveal that many highly toxic compounds are compatible with binding to the orthosteric site, further motivating the selective pressure for additional modes of selectivity. Motivated by recent work in which we observed failed substrate delivery in a molecular dynamics simulation where the energized ion still goes down its concentration gradient, we hypothesize that some transporters evolved to harness this 'slip' mechanism to increase substrate selectivity and reduce the uptake of toxic molecules. Here, we test this idea by constructing and exploring a kinetic transport model that includes a slip pathway. While slip reduces the overall productive flux, when coupled with a second toxic molecule that is more prone to slippage, the overall substrate selectivity dramatically increases, suppressing the accumulation of the incorrect compound. We show that the mathematical framework for increased substrate selectivity in our model is analogous to the classic proofreading mechanism originally proposed for tRNA synthase; however, because the transport cycle is reversible we identified conditions in which the selectivity is essentially infinite and incorrect substrates are exported from the cell in a 'detoxification' mode. The cellular consequences of proofreading and membrane slippage are discussed as well as the impact on future drug development.
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Affiliation(s)
- Paola Bisignano
- Cardiovascular Research Institute, Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, United States of America
| | - Michael A. Lee
- Cardiovascular Research Institute, Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, United States of America
| | - August George
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, Oregon, United States of America
| | - Daniel M. Zuckerman
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, Oregon, United States of America
| | - Michael Grabe
- Cardiovascular Research Institute, Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, United States of America
| | - John M. Rosenberg
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
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10
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Li J, Zhao Z, Tajkhorshid E. Locking Two Rigid-body Bundles in an Outward-Facing Conformation: The Ion-coupling Mechanism in a LeuT-fold Transporter. Sci Rep 2019; 9:19479. [PMID: 31862903 PMCID: PMC6925253 DOI: 10.1038/s41598-019-55722-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 12/02/2019] [Indexed: 01/26/2023] Open
Abstract
Secondary active transporters use electrochemical gradient of ions to fuel the "uphill" translocation of the substrate following the alternating-access model. The coupling of ions to conformational dynamics of the protein remains one of the least characterized aspects of the transporter function. We employ extended molecular dynamics (MD) simulations to examine the Na+-binding effects on the structure and dynamics of a LeuT-fold, Na+-coupled secondary transporter (Mhp1) in its major conformational states, i.e., the outward-facing (OF) and inward-facing (IF) states, as well as on the OF ↔ IF state transition. Microsecond-long, unbiased MD simulations illustrate that Na+ stabilizes an OF conformation favorable for substrate association, by binding to a highly conserved site at the interface between the two helical bundles and restraining their relative position and motion. Furthermore, a special-protocol biased simulation for state transition suggests that Na+ binding hinders the OF ↔ IF transition. These synergistic Na+-binding effects allosterically couple the ion and substrate binding sites and modify the kinetics of state transition, collectively increasing the lifetime of an OF conformation with high substrate affinity, thereby facilitating substrate recruitment from a low-concentration environment. Based on the similarity between our findings for Mhp1 and experimental reports on LeuT, we propose that this model may represent a general Na+-coupling mechanism among LeuT-fold transporters.
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Affiliation(s)
- Jing Li
- NIH Center for Macromolecular Modeling and Bioinformatics, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, United States
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, United States
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, United States
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, United States
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, 60637, United States
| | - Zhiyu Zhao
- NIH Center for Macromolecular Modeling and Bioinformatics, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, United States
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, United States
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, United States
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, United States
| | - Emad Tajkhorshid
- NIH Center for Macromolecular Modeling and Bioinformatics, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, United States.
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, United States.
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, United States.
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, United States.
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11
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Cytosolic N- and C-Termini of the Aspergillus nidulans FurE Transporter Contain Distinct Elements that Regulate by Long-Range Effects Function and Specificity. J Mol Biol 2019; 431:3827-3844. [DOI: 10.1016/j.jmb.2019.07.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 07/04/2019] [Accepted: 07/04/2019] [Indexed: 01/05/2023]
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12
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Mostofian B, Zuckerman DM. Statistical Uncertainty Analysis for Small-Sample, High Log-Variance Data: Cautions for Bootstrapping and Bayesian Bootstrapping. J Chem Theory Comput 2019; 15:3499-3509. [PMID: 31002504 PMCID: PMC6754704 DOI: 10.1021/acs.jctc.9b00015] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Recent advances in molecular simulations allow the evaluation of previously unattainable observables, such as rate constants for protein folding. However, these calculations are usually computationally expensive, and even significant computing resources may result in a small number of independent estimates spread over many orders of magnitude. Such small-sample, high "log-variance" data are not readily amenable to analysis using the standard uncertainty (i.e., "standard error of the mean") because unphysical negative limits of confidence intervals result. Bootstrapping, a natural alternative guaranteed to yield a confidence interval within the minimum and maximum values, also exhibits a striking systematic bias of the lower confidence limit in log space. As we show, bootstrapping artifactually assigns high probability to improbably low mean values. A second alternative, the Bayesian bootstrap strategy, does not suffer from the same deficit and is more logically consistent with the type of confidence interval desired. The Bayesian bootstrap provides uncertainty intervals that are more reliable than those from the standard bootstrap method but must be used with caution nevertheless. Neither standard nor Bayesian bootstrapping can overcome the intrinsic challenge of underestimating the mean from small-size, high log-variance samples. Our conclusions are based on extensive analysis of model distributions and reanalysis of multiple independent atomistic simulations. Although we only analyze rate constants, similar considerations will apply to related calculations, potentially including highly nonlinear averages like the Jarzynski relation.
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Affiliation(s)
- Barmak Mostofian
- Department of Biomedical Engineering, School of Medicine, Oregon Health & Science University, Portland, Oregon
| | - Daniel M. Zuckerman
- Department of Biomedical Engineering, School of Medicine, Oregon Health & Science University, Portland, Oregon
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13
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Adhikari U, Mostofian B, Copperman J, Subramanian SR, Petersen AA, Zuckerman DM. Computational Estimation of Microsecond to Second Atomistic Folding Times. J Am Chem Soc 2019; 141:6519-6526. [PMID: 30892023 PMCID: PMC6660137 DOI: 10.1021/jacs.8b10735] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Despite the development of massively parallel computing hardware including inexpensive graphics processing units (GPUs), it has remained infeasible to simulate the folding of atomistic proteins at room temperature using conventional molecular dynamics (MD) beyond the microsecond scale. Here, we report the folding of atomistic, implicitly solvated protein systems with folding times τ ranging from ∼10 μs to ∼100 ms using the weighted ensemble (WE) strategy in combination with GPU computing. Starting from an initial structure or set of structures, WE organizes an ensemble of GPU-accelerated MD trajectory segments via intermittent pruning and replication events to generate statistically unbiased estimates of rate constants for rare events such as folding; no biasing forces are used. Although the variance among atomistic WE folding runs is significant, multiple independent runs are used to reduce and quantify statistical uncertainty. Folding times are estimated directly from WE probability flux and from history-augmented Markov analysis of the WE data. Three systems were examined: NTL9 at low solvent viscosity (yielding τf = 0.8-9 μs), NTL9 at water-like viscosity (τf = 0.2-2 ms), and Protein G at low viscosity (τf = 3-200 ms). In all cases, the folding time, uncertainty, and ensemble properties could be estimated from WE simulation; for Protein G, this characterization required significantly less overall computing than would be required to observe a single folding event with conventional MD simulations. Our results suggest that the use and calibration of force fields and solvent models for precise estimation of kinetic quantities is becoming feasible.
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Affiliation(s)
- Upendra Adhikari
- Department of Biomedical Engineering, School of Medicine, Oregon Health & Science University, Portland, OR 97239
| | - Barmak Mostofian
- Department of Biomedical Engineering, School of Medicine, Oregon Health & Science University, Portland, OR 97239
| | - Jeremy Copperman
- Department of Biomedical Engineering, School of Medicine, Oregon Health & Science University, Portland, OR 97239
| | | | - Andrew A. Petersen
- NCSU Data Science Resources, North Carolina State University, Raleigh, NC 27695
| | - Daniel M. Zuckerman
- Department of Biomedical Engineering, School of Medicine, Oregon Health & Science University, Portland, OR 97239
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14
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Nunes-Alves A, Zuckerman DM, Arantes GM. Escape of a Small Molecule from Inside T4 Lysozyme by Multiple Pathways. Biophys J 2019. [PMID: 29539393 DOI: 10.1016/j.bpj.2018.01.014] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
The T4 lysozyme L99A mutant is often used as a model system to study small-molecule binding to proteins, but pathways for ligand entry and exit from the buried binding site and the associated protein conformational changes have not been fully resolved. Here, molecular dynamics simulations were employed to model benzene exit from its binding cavity using the weighted ensemble (WE) approach to enhance sampling of low-probability unbinding trajectories. Independent WE simulations revealed four pathways for benzene exit, which correspond to transient tunnels spontaneously formed in previous simulations of apo T4 lysozyme. Thus, benzene unbinding occurs through multiple pathways partially created by intrinsic protein structural fluctuations. Motions of several α-helices and side chains were involved in ligand escape from metastable microstates. WE simulations also provided preliminary estimates of rate constants for each exit pathway. These results complement previous works and provide a semiquantitative characterization of pathway heterogeneity for binding of small molecules to proteins.
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Affiliation(s)
- Ariane Nunes-Alves
- Department of Biochemistry, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Daniel M Zuckerman
- Department of Biomedical Engineering, School of Medicine, Oregon Health & Science University, Portland, Oregon.
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15
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Patching SG. Recent developments in nucleobase cation symporter-1 (NCS1) family transport proteins from bacteria, archaea, fungi and plants. J Biosci 2018; 43:797-815. [PMID: 30207323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The nucleobase cation symporter-1 (NCS1) family of secondary active transport proteins comprises over 2500 sequenced members from bacteria, archaea, fungi and plants. NCS1 proteins use a proton or sodium gradient to drive inward cellular transport of purine and pyrimidine nucleobases and nucleosides, hydantoins and related compounds. The structural organization, substrate binding residues and molecular mechanism of NCS1 proteins are defined by crystal structures of sodium-coupled hydantoin transporter, Mhp1. Plant proteins are most closely related to bacterial/archaeal proteins and the distinct Fur-type and Fcy-type fungal proteins and plant proteins originated through independent horizontal transfers from prokaryotes. Analyses of 25 experimentally characterized proteins reveal high substrate specificity in bacterial proteins, distinct non-overlapping specificities in Fur-type and Fcy-type fungal proteins and broad specificity in plant proteins. Possible structural explanations are identified for differences in substrate specificity between bacterial proteins, whilst specificities of other proteins cannot be predicted by simple sequence comparisons. Specificity appears to be species specific and determined by combinations of effects dictated by multiple residues in the major substrate binding site and gating domains. This is an exploratory research review of evolutionary relationships, function and structural organization, molecular mechanism and origins of substrate specificity in NCS1 proteins and avenues of future direction.
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Affiliation(s)
- Simon G Patching
- School of Biomedical Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK,
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16
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Patching SG. Recent developments in nucleobase cation symporter-1 (NCS1) family transport proteins from bacteria, archaea, fungi and plants. J Biosci 2018. [DOI: 10.1007/s12038-018-9780-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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17
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Substrate Specificity of the FurE Transporter Is Determined by Cytoplasmic Terminal Domain Interactions. Genetics 2017; 207:1387-1400. [PMID: 28978674 DOI: 10.1534/genetics.117.300327] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 10/03/2017] [Indexed: 12/17/2022] Open
Abstract
FurE, a member of the Nucleobase Cation Symporter 1 transporter family in Aspergillus nidulans, is specific for allantoin, uric acid (UA), uracil, and related analogs. Herein, we show that C- or N-terminally-truncated FurE transporters (FurE-ΔC or FurE-ΔΝ) present increased protein stability, but also an inability for UA transport. To better understand the role of cytoplasmic terminal regions, we characterized genetic suppressors that restore FurE-ΔC-mediated UA transport. Suppressors map in the periphery of the substrate-binding site [Thr133 in transmembrane segment (TMS)3 and Val343 in TMS8], an outward-facing gate (Ser296 in TMS7, Ile371 in TMS9, and Tyr392 and Leu394 in TMS10), or in flexible loops (Asp26 in LN, Gly222 in L5, and Asn308 in L7). Selected suppressors were also shown to restore the wild-type specificity of FurE-ΔΝ, suggesting that both C- and/or N-terminal domains are involved in intramolecular dynamics critical for substrate selection. A direct, substrate-sensitive interaction of C- and/or N-terminal domains was supported by bimolecular fluorescence complementation assays. To our knowledge, this is the first case where not only the function, but also the specificity, of a eukaryotic transporter is regulated by its terminal cytoplasmic regions.
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18
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Calabrese AN, Jackson SM, Jones LN, Beckstein O, Heinkel F, Gsponer J, Sharples D, Sans M, Kokkinidou M, Pearson AR, Radford SE, Ashcroft AE, Henderson PJF. Topological Dissection of the Membrane Transport Protein Mhp1 Derived from Cysteine Accessibility and Mass Spectrometry. Anal Chem 2017; 89:8844-8852. [PMID: 28726379 PMCID: PMC5588088 DOI: 10.1021/acs.analchem.7b01310] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2017] [Accepted: 07/20/2017] [Indexed: 01/01/2023]
Abstract
Cys accessibility and quantitative intact mass spectrometry (MS) analyses have been devised to study the topological transitions of Mhp1, the membrane protein for sodium-linked transport of hydantoins from Microbacterium liquefaciens. Mhp1 has been crystallized in three forms (outward-facing open, outward-facing occluded with substrate bound, and inward-facing open). We show that one natural cysteine residue, Cys327, out of three, has an enhanced solvent accessibility in the inward-facing (relative to the outward-facing) form. Reaction of the purified protein, in detergent, with the thiol-reactive N-ethylmalemide (NEM), results in modification of Cys327, suggesting that Mhp1 adopts predominantly inward-facing conformations. Addition of either sodium ions or the substrate 5-benzyl-l-hydantoin (L-BH) does not shift this conformational equilibrium, but systematic co-addition of the two results in an attenuation of labeling, indicating a shift toward outward-facing conformations that can be interpreted using conventional enzyme kinetic analyses. Such measurements can afford the Km for each ligand as well as the stoichiometry of ion-substrate-coupled conformational changes. Mutations that perturb the substrate binding site either result in the protein being unable to adopt outward-facing conformations or in a global destabilization of structure. The methodology combines covalent labeling, mass spectrometry, and kinetic analyses in a straightforward workflow applicable to a range of systems, enabling the interrogation of changes in a protein's conformation required for function at varied concentrations of substrates, and the consequences of mutations on these conformational transitions.
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Affiliation(s)
| | | | | | - Oliver Beckstein
- Department of Physics, Arizona State University , Tempe, Arizona 85287-1504, United States
| | - Florian Heinkel
- Centre for High-Throughput Biology, University of British Columbia , Vancouver, British Columbia, Canada V6T 1Z4
| | - Joerg Gsponer
- Centre for High-Throughput Biology, University of British Columbia , Vancouver, British Columbia, Canada V6T 1Z4
| | | | - Marta Sans
- Hamburg Centre for Ultrafast Imaging, Institute for Nanostructure and Solid State Physics, Universität Hamburg , Hamburg 22761, Germany
| | - Maria Kokkinidou
- Hamburg Centre for Ultrafast Imaging, Institute for Nanostructure and Solid State Physics, Universität Hamburg , Hamburg 22761, Germany
| | - Arwen R Pearson
- Hamburg Centre for Ultrafast Imaging, Institute for Nanostructure and Solid State Physics, Universität Hamburg , Hamburg 22761, Germany
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19
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Mechanism of Substrate Translocation in an Alternating Access Transporter. Cell 2017; 169:96-107.e12. [PMID: 28340354 DOI: 10.1016/j.cell.2017.03.010] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Revised: 01/15/2017] [Accepted: 03/03/2017] [Indexed: 12/11/2022]
Abstract
Transporters shuttle molecules across cell membranes by alternating among distinct conformational states. Fundamental questions remain about how transporters transition between states and how such structural rearrangements regulate substrate translocation. Here, we capture the translocation process by crystallography and unguided molecular dynamics simulations, providing an atomic-level description of alternating access transport. Simulations of a SWEET-family transporter initiated from an outward-open, glucose-bound structure reported here spontaneously adopt occluded and inward-open conformations. Strikingly, these conformations match crystal structures, including our inward-open structure. Mutagenesis experiments further validate simulation predictions. Our results reveal that state transitions are driven by favorable interactions formed upon closure of extracellular and intracellular "gates" and by an unfavorable transmembrane helix configuration when both gates are closed. This mechanism leads to tight allosteric coupling between gates, preventing them from opening simultaneously. Interestingly, the substrate appears to take a "free ride" across the membrane without causing major structural rearrangements in the transporter.
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20
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Abstract
The weighted ensemble (WE) methodology orchestrates quasi-independent parallel simulations run with intermittent communication that can enhance sampling of rare events such as protein conformational changes, folding, and binding. The WE strategy can achieve superlinear scaling-the unbiased estimation of key observables such as rate constants and equilibrium state populations to greater precision than would be possible with ordinary parallel simulation. WE software can be used to control any dynamics engine, such as standard molecular dynamics and cell-modeling packages. This article reviews the theoretical basis of WE and goes on to describe successful applications to a number of complex biological processes-protein conformational transitions, (un)binding, and assembly processes, as well as cell-scale processes in systems biology. We furthermore discuss the challenges that need to be overcome in the next phase of WE methodological development. Overall, the combined advances in WE methodology and software have enabled the simulation of long-timescale processes that would otherwise not be practical on typical computing resources using standard simulation.
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Affiliation(s)
- Daniel M Zuckerman
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, Oregon 97239;
| | - Lillian T Chong
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260;
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21
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Song HD, Zhu F. Finite Temperature String Method with Umbrella Sampling: Application on a Side Chain Flipping in Mhp1 Transporter. J Phys Chem B 2016; 121:3376-3386. [PMID: 27959537 DOI: 10.1021/acs.jpcb.6b08568] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Protein conformational change is of central importance in molecular biology. Here we demonstrate a computational approach to characterize the transition between two metastable conformations in all-atom simulations. Our approach is based on the finite temperature string method, and the implementation is essentially a generalization of umbrella sampling simulations with Hamiltonian replica exchange. We represent the transition pathway by a curve in the conformational space, with the curve parameter taken as the reaction coordinate. Our approach can efficiently refine a transition pathway and compute a one-dimensional free energy as a function of the reaction coordinate. A diffusion model can then be used to calculate the forward and backward transition rates, the major kinetic quantities for the transition. We applied the approach on a local transition in the ligand-free Mhp1 transporter, between its outward-facing conformation and an intermediate conformation with the side chain of Phe305 flipped to the outside of the protein. Our simulations predict that the flipped-out position of this side chain has a free energy 6.5 kcal/mol higher than the original position in the crystal structure, and that the forward and backward transition rates are in the millisecond and submicrosecond time scales, respectively.
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Affiliation(s)
- Hyun Deok Song
- Department of Physics, Indiana University - Purdue University Indianapolis , Indianapolis, Indiana 46202, United States
| | - Fangqiang Zhu
- Department of Physics, Indiana University - Purdue University Indianapolis , Indianapolis, Indiana 46202, United States
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22
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Path-sampling strategies for simulating rare events in biomolecular systems. Curr Opin Struct Biol 2016; 43:88-94. [PMID: 27984811 DOI: 10.1016/j.sbi.2016.11.019] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2016] [Revised: 11/18/2016] [Accepted: 11/21/2016] [Indexed: 12/20/2022]
Abstract
Despite more than three decades of effort with molecular dynamics simulations, long-timescale (ms and beyond) biologically relevant phenomena remain out of reach in most systems of interest. This is largely because important transitions, such as conformational changes and (un)binding events, tend to be rare for conventional simulations (<10μs). That is, conventional simulations will predominantly dwell in metastable states instead of making large transitions in complex biomolecular energy landscapes. In contrast, path sampling approaches focus computing effort specifically on transitions of interest. Such approaches have been in use for nearly 20 years in biomolecular systems and enabled the generation of pathways and calculation of rate constants for ms processes, including large protein conformational changes, protein folding, and protein (un)binding.
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23
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Abstract
The structures of transport proteins have been steadily revealed in the last few decades, and yet the conversion of this information into molecular-level understanding of their function is still lagging behind. In this study, we try to elucidate how the action of the archaeal sodium/proton antiporter MjNhaP1 depends on its structure-energy relationship. To this end, we calculate the binding energies of its substrates and evaluate the conformational change barrier, focusing on the rotation of the catalytic residue D161. We find that sodium ions and protons compete against a common binding site and that the accessibility of this binding site is restricted to either the inside or outside of the cell. We suggest that the rotation of D161 χ1 angle correlates with the conformational change and is energetically unfavorable when D161 does not bind any substrate. This restriction ensures coupling between the sodium ions and the protons, allowing MjNhaP1 and probably other similar transporters to exchange substrates with minimal leak. Using Monte Carlo simulations we demonstrate the feasibility of our model. Overall we present a complete picture that reproduces the electroneutral (at 1:1 substrate ratio) and coupled transport activity of MjNhaP1 including the energetic basis for the criteria provided by Jardetzky half a century ago.
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Affiliation(s)
- Raphael Alhadeff
- Department of Chemistry, University of Southern California , SGM 418, 3620 McClintock Avenue, Los Angeles, California 90089, United States
| | - Arieh Warshel
- Department of Chemistry, University of Southern California , SGM 418, 3620 McClintock Avenue, Los Angeles, California 90089, United States
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24
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Adelman JL, Grabe M. Simulating Current-Voltage Relationships for a Narrow Ion Channel Using the Weighted Ensemble Method. J Chem Theory Comput 2016; 11:1907-18. [PMID: 26392816 DOI: 10.1021/ct501134s] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Ion channels are responsible for a myriad of fundamental biological processes via their role in controlling the flow of ions through water-filled membrane-spanning pores in response to environmental cues. Molecular simulation has played an important role in elucidating the mechanism of ion conduction, but connecting atomistically detailed structural models of the protein to electrophysiological measurements remains a broad challenge due to the computational cost of reaching the necessary time scales. Here, we introduce an enhanced sampling method for simulating the conduction properties of narrow ion channels using the Weighted ensemble (WE) sampling approach. We demonstrate the application of this method to calculate the current–voltage relationship as well as the nonequilibrium ion distribution at steady-state of a simple model ion channel. By direct comparisons with long brute force simulations, we show that the WE simulations rigorously reproduce the correct long-time scale kinetics of the system and are capable of determining these quantities using significantly less aggregate simulation time under conditions where permeation events are rare.
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25
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Zwier MC, Pratt AJ, Adelman JL, Kaus JW, Zuckerman DM, Chong LT. Efficient Atomistic Simulation of Pathways and Calculation of Rate Constants for a Protein-Peptide Binding Process: Application to the MDM2 Protein and an Intrinsically Disordered p53 Peptide. J Phys Chem Lett 2016; 7:3440-5. [PMID: 27532687 PMCID: PMC5008990 DOI: 10.1021/acs.jpclett.6b01502] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
The characterization of protein binding processes - with all of the key conformational changes - has been a grand challenge in the field of biophysics. Here, we have used the weighted ensemble path sampling strategy to orchestrate molecular dynamics simulations, yielding atomistic views of protein-peptide binding pathways involving the MDM2 oncoprotein and an intrinsically disordered p53 peptide. A total of 182 independent, continuous binding pathways were generated, yielding a kon that is in good agreement with experiment. These pathways were generated in 15 days using 3500 cores of a supercomputer, substantially faster than would be possible with "brute force" simulations. Many of these pathways involve the anchoring of p53 residue F19 into the MDM2 binding cleft when forming the metastable encounter complex, indicating that F19 may be a kinetically important residue. Our study demonstrates that it is now practical to generate pathways and calculate rate constants for protein binding processes using atomistic simulation on typical computing resources.
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Affiliation(s)
- Matthew C. Zwier
- Department of Chemistry, Drake University, Des Moines, Iowa 50311, United States
| | - Adam J. Pratt
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Joshua L. Adelman
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Joseph W. Kaus
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Daniel M. Zuckerman
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Lillian T. Chong
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
- Institute of Biochemistry and Biotechnology, Martin-Luther Universität Halle-Wittenberg, Halle 06120, Germany
- Corresponding Author:
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26
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Zhang JL, Zheng QC, Yu LY, Li ZQ, Zhang HX. Effect of External Electric Field on Substrate Transport of a Secondary Active Transporter. J Chem Inf Model 2016; 56:1539-46. [PMID: 27472561 DOI: 10.1021/acs.jcim.6b00212] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Substrate transport across a membrane accomplished by a secondary active transporter (SAT) is essential to the normal physiological function of living cells. In the present research, a series of all-atom molecular dynamics (MD) simulations under different electric field (EF) strengths was performed to investigate the effect of an external EF on the substrate transport of an SAT. The results show that EF both affects the interaction between substrate and related protein's residues by changing their conformations and tunes the timeline of the transport event, which collectively reduces the height of energy barrier for substrate transport and results in the appearance of two intermediate conformations under the existence of an external EF. Our work spotlights the crucial influence of external EFs on the substrate transport of SATs and could provide a more penetrating understanding of the substrate transport mechanism of SATs.
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Affiliation(s)
- Ji-Long Zhang
- International Joint Research Laboratory of Nano-Micro Architecture Chemistry, Institute of Theoretical Chemistry, Jilin University , Changchun 130023, Jilin, People's Republic of China.,Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, Jilin University , Changchun 130021, Jilin, People's Republic of China.,Department of Chemistry and Supercomputing Institute, University of Minnesota , Minneapolis, Minnesota 55455, United States
| | - Qing-Chuan Zheng
- International Joint Research Laboratory of Nano-Micro Architecture Chemistry, Institute of Theoretical Chemistry, Jilin University , Changchun 130023, Jilin, People's Republic of China
| | - Li-Ying Yu
- International Joint Research Laboratory of Nano-Micro Architecture Chemistry, Institute of Theoretical Chemistry, Jilin University , Changchun 130023, Jilin, People's Republic of China
| | - Zheng-Qiang Li
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, Jilin University , Changchun 130021, Jilin, People's Republic of China
| | - Hong-Xing Zhang
- International Joint Research Laboratory of Nano-Micro Architecture Chemistry, Institute of Theoretical Chemistry, Jilin University , Changchun 130023, Jilin, People's Republic of China
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27
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Maximova T, Moffatt R, Ma B, Nussinov R, Shehu A. Principles and Overview of Sampling Methods for Modeling Macromolecular Structure and Dynamics. PLoS Comput Biol 2016; 12:e1004619. [PMID: 27124275 PMCID: PMC4849799 DOI: 10.1371/journal.pcbi.1004619] [Citation(s) in RCA: 132] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Investigation of macromolecular structure and dynamics is fundamental to understanding how macromolecules carry out their functions in the cell. Significant advances have been made toward this end in silico, with a growing number of computational methods proposed yearly to study and simulate various aspects of macromolecular structure and dynamics. This review aims to provide an overview of recent advances, focusing primarily on methods proposed for exploring the structure space of macromolecules in isolation and in assemblies for the purpose of characterizing equilibrium structure and dynamics. In addition to surveying recent applications that showcase current capabilities of computational methods, this review highlights state-of-the-art algorithmic techniques proposed to overcome challenges posed in silico by the disparate spatial and time scales accessed by dynamic macromolecules. This review is not meant to be exhaustive, as such an endeavor is impossible, but rather aims to balance breadth and depth of strategies for modeling macromolecular structure and dynamics for a broad audience of novices and experts.
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Affiliation(s)
- Tatiana Maximova
- Department of Computer Science, George Mason University, Fairfax, Virginia, United States of America
| | - Ryan Moffatt
- Department of Computer Science, George Mason University, Fairfax, Virginia, United States of America
| | - Buyong Ma
- Basic Science Program, Leidos Biomedical Research, Inc. Cancer and Inflammation Program, National Cancer Institute, Frederick, Maryland, United States of America
| | - Ruth Nussinov
- Basic Science Program, Leidos Biomedical Research, Inc. Cancer and Inflammation Program, National Cancer Institute, Frederick, Maryland, United States of America
- Sackler Institute of Molecular Medicine, Department of Human Genetics and Molecular Medicine, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Amarda Shehu
- Department of Computer Science, George Mason University, Fairfax, Virginia, United States of America
- Department of Biongineering, George Mason University, Fairfax, Virginia, United States of America
- School of Systems Biology, George Mason University, Manassas, Virginia, United States of America
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28
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Ma P, Patching SG, Ivanova E, Baldwin JM, Sharples D, Baldwin SA, Henderson PJF. Allantoin transport protein, PucI, from Bacillus subtilis: evolutionary relationships, amplified expression, activity and specificity. MICROBIOLOGY-SGM 2016; 162:823-836. [PMID: 26967546 DOI: 10.1099/mic.0.000266] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
This work reports the evolutionary relationships, amplified expression, functional characterization and purification of the putative allantoin transport protein, PucI, from Bacillus subtilis. Sequence alignments and phylogenetic analysis confirmed close evolutionary relationships between PucI and membrane proteins of the nucleobase-cation-symport-1 family of secondary active transporters. These include the sodium-coupled hydantoin transport protein, Mhp1, from Microbacterium liquefaciens, and related proteins from bacteria, fungi and plants. Membrane topology predictions for PucI were consistent with 12 putative transmembrane-spanning α-helices with both N- and C-terminal ends at the cytoplasmic side of the membrane. The pucI gene was cloned into the IPTG-inducible plasmid pTTQ18 upstream from an in-frame hexahistidine tag and conditions determined for optimal amplified expression of the PucI(His6) protein in Escherichia coli to a level of about 5 % in inner membranes. Initial rates of inducible PucI-mediated uptake of 14C-allantoin into energized E. coli whole cells conformed to Michaelis-Menten kinetics with an apparent affinity (Kmapp) of 24 ± 3 μM, therefore confirming that PucI is a medium-affinity transporter of allantoin. Dependence of allantoin transport on sodium was not apparent. Competitive uptake experiments showed that PucI recognizes some additional hydantoin compounds, including hydantoin itself, and to a lesser extent a range of nucleobases and nucleosides. PucI(His6) was solubilized from inner membranes using n-dodecyl-β-d-maltoside and purified. The isolated protein contained a substantial proportion of α-helix secondary structure, consistent with the predictions, and a 3D model was therefore constructed on a template of the Mhp1 structure, which aided localization of the potential ligand binding site in PucI.
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Affiliation(s)
- Pikyee Ma
- School of BioMedical Sciences and the Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Simon G Patching
- School of BioMedical Sciences and the Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Ekaterina Ivanova
- School of BioMedical Sciences and the Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Jocelyn M Baldwin
- School of BioMedical Sciences and the Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - David Sharples
- School of BioMedical Sciences and the Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Stephen A Baldwin
- School of BioMedical Sciences and the Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Peter J F Henderson
- School of BioMedical Sciences and the Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
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29
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Bisha I, Magistrato A. The molecular mechanism of secondary sodium symporters elucidated through the lens of the computational microscope. RSC Adv 2016. [DOI: 10.1039/c5ra22131e] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Transport of molecules across cellular membranes is a key biological process for normal cell function. In this review we describe current state-of-the-art knowledge on molecular mechanism of secondary active transporters obtained by molecular simulations studies.
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Affiliation(s)
- Ina Bisha
- Theoretical Chemical Biology and Protein Modelling Group
- Technische Universität München
- 85354 Freising
- Germany
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30
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Song HD, Zhu F. Conformational Changes in Two Inter-Helical Loops of Mhp1 Membrane Transporter. PLoS One 2015; 10:e0133388. [PMID: 26186341 PMCID: PMC4505851 DOI: 10.1371/journal.pone.0133388] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Accepted: 06/26/2015] [Indexed: 12/17/2022] Open
Abstract
Mhp1 is a bacterial secondary transporter with high-resolution crystal structures available for both the outward- and inward-facing conformations. Through molecular dynamics simulations of the ligand-free Mhp1 as well as analysis of its crystal structures, here we show that two inter-helical loops, respectively located at the extra- and intracellular ends of the "hash motif" in the protein, play important roles in the conformational transition. In the outward- and inward-facing states of the protein, the loops adopt different secondary structures, either wrapped to the end of an alpha-helix, or unwrapped to extended conformations. In equilibrium simulations of 100 ns with Mhp1 in explicit lipids and water, the loop conformations remain largely stable. In targeted molecular dynamics simulations with the protein structure driven from one state to the other, the loops exhibit resistance and only undergo abrupt changes when other parts of the protein already approach the target conformation. Free energy calculations on the isolated loops further confirm that the wrapping/unwrapping transitions are associated with substantial energetic barriers, and consist of multiple sequential steps involving the rotation of certain backbone torsion angles. Furthermore, in simulations with the loops driven from one state to the other, a large part of the protein follows the loops to the target conformation. Taken together, our simulations suggest that changes of the loop secondary structures would be among the slow degrees of freedom in the conformational transition of the entire protein. Incorporation of detailed loop structures into the reaction coordinate, therefore, should improve the convergence and relevance of the resulting conformational free energy.
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Affiliation(s)
- Hyun Deok Song
- Department of Physics, Indiana University—Purdue University Indianapolis, Indianapolis, Indiana, United States of America
| | - Fangqiang Zhu
- Department of Physics, Indiana University—Purdue University Indianapolis, Indianapolis, Indiana, United States of America
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31
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Krypotou E, Evangelidis T, Bobonis J, Pittis AA, Gabaldón T, Scazzocchio C, Mikros E, Diallinas G. Origin, diversification and substrate specificity in the family of NCS1/FUR transporters. Mol Microbiol 2015; 96:927-50. [DOI: 10.1111/mmi.12982] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/22/2015] [Indexed: 12/19/2022]
Affiliation(s)
- Emilia Krypotou
- Faculty of Biology; University of Athens; Panepistimioupolis Athens 15784 Greece
| | - Thomas Evangelidis
- Faculty of Pharmacy; University of Athens; Panepistimioupolis Athens 15771 Greece
| | - Jacob Bobonis
- Faculty of Biology; University of Athens; Panepistimioupolis Athens 15784 Greece
| | - Alexandros A. Pittis
- Bioinformatics and Genomics Programme; Centre for Genomic Regulation (CRG); Dr. Aiguader, 88 Barcelona 08003 Spain
- Department of Experimental and Health Sciences; Universitat Pompeu Fabra (UPF); Barcelona 08003 Spain
| | - Toni Gabaldón
- Bioinformatics and Genomics Programme; Centre for Genomic Regulation (CRG); Dr. Aiguader, 88 Barcelona 08003 Spain
- Department of Experimental and Health Sciences; Universitat Pompeu Fabra (UPF); Barcelona 08003 Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA); Pg. Lluís Companys 23 Barcelona 08010 Spain
| | - Claudio Scazzocchio
- Department of Microbiology; Imperial College; London SW7 2AZ UK
- Institut de Génétique et Microbiologie; Université Paris-Sud; France
| | - Emmanuel Mikros
- Faculty of Pharmacy; University of Athens; Panepistimioupolis Athens 15771 Greece
| | - George Diallinas
- Faculty of Biology; University of Athens; Panepistimioupolis Athens 15784 Greece
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32
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Li J, Wen PC, Moradi M, Tajkhorshid E. Computational characterization of structural dynamics underlying function in active membrane transporters. Curr Opin Struct Biol 2015; 31:96-105. [PMID: 25913536 PMCID: PMC4476910 DOI: 10.1016/j.sbi.2015.04.001] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2015] [Revised: 04/06/2015] [Accepted: 04/07/2015] [Indexed: 11/21/2022]
Abstract
Active transport of materials across the cellular membrane is one the most fundamental processes in biology. In order to accomplish this task, membrane transporters rely on a wide range of conformational changes spanning multiple time and size scales. These molecular events govern key functional aspects in membrane transporters, namely, coordinated gating motions underlying the alternating access mode of operation, and coupling of uphill transport of substrate to various sources of energy, for example, transmembrane electrochemical gradients and ATP binding and hydrolysis. Computational techniques such as molecular dynamics simulations and free energy calculations have equipped us with a powerful repertoire of biophysical tools offering unparalleled spatial and temporal resolutions that can effectively complement experimental methodologies, and therefore help fill the gap of knowledge in understanding the molecular basis of function in membrane transporters.
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Affiliation(s)
- Jing Li
- Department of Biochemistry, Center for Biophysics and Computational Biology, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
| | - Po-Chao Wen
- Department of Biochemistry, Center for Biophysics and Computational Biology, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
| | - Mahmoud Moradi
- Department of Biochemistry, Center for Biophysics and Computational Biology, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
| | - Emad Tajkhorshid
- Department of Biochemistry, Center for Biophysics and Computational Biology, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States.
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33
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Zwier MC, Adelman JL, Kaus JW, Pratt AJ, Wong KF, Rego NB, Suárez E, Lettieri S, Wang DW, Grabe M, Zuckerman DM, Chong LT. WESTPA: an interoperable, highly scalable software package for weighted ensemble simulation and analysis. J Chem Theory Comput 2015; 11:800-9. [PMID: 26392815 PMCID: PMC4573570 DOI: 10.1021/ct5010615] [Citation(s) in RCA: 90] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The weighted ensemble (WE) path sampling approach orchestrates an ensemble of parallel calculations with intermittent communication to enhance the sampling of rare events, such as molecular associations or conformational changes in proteins or peptides. Trajectories are replicated and pruned in a way that focuses computational effort on underexplored regions of configuration space while maintaining rigorous kinetics. To enable the simulation of rare events at any scale (e.g., atomistic, cellular), we have developed an open-source, interoperable, and highly scalable software package for the execution and analysis of WE simulations: WESTPA (The Weighted Ensemble Simulation Toolkit with Parallelization and Analysis). WESTPA scales to thousands of CPU cores and includes a suite of analysis tools that have been implemented in a massively parallel fashion. The software has been designed to interface conveniently with any dynamics engine and has already been used with a variety of molecular dynamics (e.g., GROMACS, NAMD, OpenMM, AMBER) and cell-modeling packages (e.g., BioNetGen, MCell). WESTPA has been in production use for over a year, and its utility has been demonstrated for a broad set of problems, ranging from atomically detailed host–guest associations to nonspatial chemical kinetics of cellular signaling networks. The following describes the design and features of WESTPA, including the facilities it provides for running WE simulations and storing and analyzing WE simulation data, as well as examples of input and output.
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Affiliation(s)
| | - Joshua L. Adelman
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15206
| | - Joseph W. Kaus
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15206
| | - Adam J. Pratt
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15206
| | - Kim F. Wong
- Center for Simulation and Modeling, University of Pittsburgh, Pittsburgh, PA 15206
| | - Nicholas B. Rego
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15206
| | - Ernesto Suárez
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA 15206
| | - Steven Lettieri
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA 15206
| | - David W. Wang
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15206
| | - Michael Grabe
- Cardiovascular Research Institute, Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158
| | - Daniel M. Zuckerman
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA 15206
| | - Lillian T. Chong
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15206
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34
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Zhu F. How does water pass through a sugar transporter? Biophys J 2014; 106:1229-30. [PMID: 24655496 DOI: 10.1016/j.bpj.2014.02.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2014] [Revised: 02/02/2014] [Accepted: 02/04/2014] [Indexed: 10/25/2022] Open
Affiliation(s)
- Fangqiang Zhu
- Department of Physics, Indiana University - Purdue University Indianapolis, Indianapolis, Indiana.
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35
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Abdul-Wahid B, Feng H, Rajan D, Costaouec R, Darve E, Thain D, Izaguirre JA. AWE-WQ: fast-forwarding molecular dynamics using the accelerated weighted ensemble. J Chem Inf Model 2014; 54:3033-43. [PMID: 25207854 PMCID: PMC4210180 DOI: 10.1021/ci500321g] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
A limitation of traditional molecular dynamics (MD) is that reaction rates are difficult to compute. This is due to the rarity of observing transitions between metastable states since high energy barriers trap the system in these states. Recently the weighted ensemble (WE) family of methods have emerged which can flexibly and efficiently sample conformational space without being trapped and allow calculation of unbiased rates. However, while WE can sample correctly and efficiently, a scalable implementation applicable to interesting biomolecular systems is not available. We provide here a GPLv2 implementation called AWE-WQ of a WE algorithm using the master/worker distributed computing WorkQueue (WQ) framework. AWE-WQ is scalable to thousands of nodes and supports dynamic allocation of computer resources, heterogeneous resource usage (such as central processing units (CPU) and graphical processing units (GPUs) concurrently), seamless heterogeneous cluster usage (i.e., campus grids and cloud providers), and support for arbitrary MD codes such as GROMACS, while ensuring that all statistics are unbiased. We applied AWE-WQ to a 34 residue protein which simulated 1.5 ms over 8 months with peak aggregate performance of 1000 ns/h. Comparison was done with a 200 μs simulation collected on a GPU over a similar timespan. The folding and unfolded rates were of comparable accuracy.
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Affiliation(s)
- Badi' Abdul-Wahid
- Department of Computer Science and Engineering, University of Notre Dame , South Bend, Indiana 46556, United States
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36
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Simmons KJ, Jackson SM, Brueckner F, Patching SG, Beckstein O, Ivanova E, Geng T, Weyand S, Drew D, Lanigan J, Sharples DJ, Sansom MSP, Iwata S, Fishwick CWG, Johnson AP, Cameron AD, Henderson PJF. Molecular mechanism of ligand recognition by membrane transport protein, Mhp1. EMBO J 2014; 33:1831-44. [PMID: 24952894 PMCID: PMC4195764 DOI: 10.15252/embj.201387557] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The hydantoin transporter Mhp1 is a sodium-coupled secondary active transport protein of the nucleobase-cation-symport family and a member of the widespread 5-helix inverted repeat superfamily of transporters. The structure of Mhp1 was previously solved in three different conformations providing insight into the molecular basis of the alternating access mechanism. Here, we elucidate detailed events of substrate binding, through a combination of crystallography, molecular dynamics, site-directed mutagenesis, biochemical/biophysical assays, and the design and synthesis of novel ligands. We show precisely where 5-substituted hydantoin substrates bind in an extended configuration at the interface of the bundle and hash domains. They are recognised through hydrogen bonds to the hydantoin moiety and the complementarity of the 5-substituent for a hydrophobic pocket in the protein. Furthermore, we describe a novel structure of an intermediate state of the protein with the external thin gate locked open by an inhibitor, 5-(2-naphthylmethyl)-L-hydantoin, which becomes a substrate when leucine 363 is changed to an alanine. We deduce the molecular events that underlie acquisition and transport of a ligand by Mhp1.
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Affiliation(s)
- Katie J Simmons
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK
| | - Scott M Jackson
- School of Biomedical Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK
| | - Florian Brueckner
- Membrane Protein Laboratory, Diamond Light Source Harwell Science and Innovation Campus, Chilton, Didcot, UK Division of Molecular Biosciences, Membrane Protein Crystallography Group Imperial College, London, UK Rutherford Appleton Laboratory, Research Complex at Harwell, Harwell, Oxford, Didcot, UK
| | - Simon G Patching
- School of Biomedical Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK
| | - Oliver Beckstein
- Department of Physics, Arizona State University, Tempe, AZ, USA Department of Biochemistry, University of Oxford, Oxford, UK
| | - Ekaterina Ivanova
- School of Biomedical Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK
| | - Tian Geng
- Membrane Protein Laboratory, Diamond Light Source Harwell Science and Innovation Campus, Chilton, Didcot, UK Division of Molecular Biosciences, Membrane Protein Crystallography Group Imperial College, London, UK Rutherford Appleton Laboratory, Research Complex at Harwell, Harwell, Oxford, Didcot, UK
| | - Simone Weyand
- Membrane Protein Laboratory, Diamond Light Source Harwell Science and Innovation Campus, Chilton, Didcot, UK Division of Molecular Biosciences, Membrane Protein Crystallography Group Imperial College, London, UK Rutherford Appleton Laboratory, Research Complex at Harwell, Harwell, Oxford, Didcot, UK
| | - David Drew
- Division of Molecular Biosciences, Membrane Protein Crystallography Group Imperial College, London, UK
| | - Joseph Lanigan
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK
| | - David J Sharples
- School of Biomedical Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK
| | - Mark S P Sansom
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - So Iwata
- Membrane Protein Laboratory, Diamond Light Source Harwell Science and Innovation Campus, Chilton, Didcot, UK Division of Molecular Biosciences, Membrane Protein Crystallography Group Imperial College, London, UK Rutherford Appleton Laboratory, Research Complex at Harwell, Harwell, Oxford, Didcot, UK
| | - Colin W G Fishwick
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK
| | - A Peter Johnson
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK
| | - Alexander D Cameron
- Membrane Protein Laboratory, Diamond Light Source Harwell Science and Innovation Campus, Chilton, Didcot, UK Division of Molecular Biosciences, Membrane Protein Crystallography Group Imperial College, London, UK School of Life Sciences, University of Warwick, Coventry, UK
| | - Peter J F Henderson
- School of Biomedical Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK
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37
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Das A, Gur M, Cheng MH, Jo S, Bahar I, Roux B. Exploring the conformational transitions of biomolecular systems using a simple two-state anisotropic network model. PLoS Comput Biol 2014; 10:e1003521. [PMID: 24699246 PMCID: PMC3974643 DOI: 10.1371/journal.pcbi.1003521] [Citation(s) in RCA: 96] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Accepted: 02/01/2014] [Indexed: 11/19/2022] Open
Abstract
Biomolecular conformational transitions are essential to biological functions. Most experimental methods report on the long-lived functional states of biomolecules, but information about the transition pathways between these stable states is generally scarce. Such transitions involve short-lived conformational states that are difficult to detect experimentally. For this reason, computational methods are needed to produce plausible hypothetical transition pathways that can then be probed experimentally. Here we propose a simple and computationally efficient method, called ANMPathway, for constructing a physically reasonable pathway between two endpoints of a conformational transition. We adopt a coarse-grained representation of the protein and construct a two-state potential by combining two elastic network models (ENMs) representative of the experimental structures resolved for the endpoints. The two-state potential has a cusp hypersurface in the configuration space where the energies from both the ENMs are equal. We first search for the minimum energy structure on the cusp hypersurface and then treat it as the transition state. The continuous pathway is subsequently constructed by following the steepest descent energy minimization trajectories starting from the transition state on each side of the cusp hypersurface. Application to several systems of broad biological interest such as adenylate kinase, ATP-driven calcium pump SERCA, leucine transporter and glutamate transporter shows that ANMPathway yields results in good agreement with those from other similar methods and with data obtained from all-atom molecular dynamics simulations, in support of the utility of this simple and efficient approach. Notably the method provides experimentally testable predictions, including the formation of non-native contacts during the transition which we were able to detect in two of the systems we studied. An open-access web server has been created to deliver ANMPathway results. Many biomolecules are like tiny molecular machines that need to change their shapes and visit many states to perform their biological functions. For a complete molecular understanding of a biological process, one needs to have information on the relevant stable states of the system in question, as well as the pathways by which the system travels from one state to another. We report here an efficient computational method that uses the knowledge of experimental structures of a pair of stable states in order to construct an energetically favoravle pathway between them. We adopt a simple representation of the molecular system by replacing the atoms with beads connected by springs and constructing an energy function with two minima around the end-states. We searched for the structure with highest energy that the system is most likely to visit during the transition and created two paths starting from this structure and proceeding toward the end-states. The combined result of these two paths is the minimum energy pathway between the two stable states. We apply this method to study important structural changes in one enzyme and three large proteins that transport small molecules and ions across the cell membrane.
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Affiliation(s)
- Avisek Das
- Department of Biochemistry and Molecular Biology, Gordon Center for Integrative Science, University of Chicago, Chicago, Illinois, United States of America
| | - Mert Gur
- Department of Computational & Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Mary Hongying Cheng
- Department of Computational & Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Sunhwan Jo
- Department of Biochemistry and Molecular Biology, Gordon Center for Integrative Science, University of Chicago, Chicago, Illinois, United States of America
| | - Ivet Bahar
- Department of Computational & Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Benoît Roux
- Department of Biochemistry and Molecular Biology, Gordon Center for Integrative Science, University of Chicago, Chicago, Illinois, United States of America
- * E-mail:
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38
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Cheng MH, Bahar I. Coupled global and local changes direct substrate translocation by neurotransmitter-sodium symporter ortholog LeuT. Biophys J 2014; 105:630-9. [PMID: 23931311 DOI: 10.1016/j.bpj.2013.06.032] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Revised: 06/12/2013] [Accepted: 06/14/2013] [Indexed: 01/01/2023] Open
Abstract
Significant advances have been made in recent years in characterizing neurotransmitter:sodium symporter (NSS) family structure and function. Yet, many time-resolved events and intermediates that control the various stages of transport cycle remain to be elucidated. Whether NSSs harbor one or two sites for binding their substrates (neurotransmitters or amino acids), and what the role of the secondary site S2 is, if any, are still unresolved. Using molecular modeling and simulations for LeuT, a bacterial NSS, we present a comprehensive account of substrate-binding and -stabilization events, and subsequently triggered interactions leading to substrate (alanine) release. LeuT instantaneous conformation as it reconfigures from substrate-receiving (outward-facing) to -releasing (inward-facing) state appears to be a determinant of its affinity to bind substrate at site S2. In the outward-facing state, S1 robustly binds alanine and regulates subsequent redistribution of interactions to trigger extracellular gate closure; whereas S2 is only a transient binding site. The substrate-binding affinity at S2 increases in an intermediate close to inward-facing state. LeuT harbors the two substrate-binding sites, and small displacements of second substrate near S2 are observed to induce concerted small translocations in the substrate bound to primary site S1, although complete release requires collective structural rearrangements that fully expose the intracellular vestibule to the cytoplasm.
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Affiliation(s)
- Mary Hongying Cheng
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pennsylvania, USA
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39
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Adelman JL, Sheng Y, Choe S, Abramson J, Wright EM, Rosenberg JM, Grabe M. Structural determinants of water permeation through the sodium-galactose transporter vSGLT. Biophys J 2014; 106:1280-9. [PMID: 24655503 PMCID: PMC3984995 DOI: 10.1016/j.bpj.2014.01.006] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Revised: 12/19/2013] [Accepted: 01/02/2014] [Indexed: 01/26/2023] Open
Abstract
Sodium-glucose transporters (SGLTs) facilitate the movement of water across the cell membrane, playing a central role in cellular homeostasis. Here, we present a detailed analysis of the mechanism of water permeation through the inward-facing state of vSGLT based on nearly 10 μs of molecular dynamics simulations. These simulations reveal the transient formation of a continuous water channel through the transporter that permits water to permeate the protein. Trajectories in which spontaneous release of galactose is observed, as well as those in which galactose remains in the binding site, show that the permeation rate, although modulated by substrate occupancy, is not tightly coupled to substrate release. Using a, to our knowledge, novel channel-detection algorithm, we identify the key residues that control water flow through the transporter and show that solvent gating is regulated by side-chain motions in a small number of residues on the extracellular face. A sequence alignment reveals the presence of two insertion sites in mammalian SGLTs that flank these outer-gate residues. We hypothesize that the absence of these sites in vSGLT may account for the high water permeability values for vSGLT determined via simulation compared to the lower experimental estimates for mammalian SGLT1.
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Affiliation(s)
- Joshua L Adelman
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Ying Sheng
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Seungho Choe
- School of Basic Science, College of Convergence, Daegu Gyeongbuk Institute of Science & Technology, Daegu, Korea
| | - Jeff Abramson
- Department of Physiology, University of California, Los Angeles, California
| | - Ernest M Wright
- Department of Physiology, University of California, Los Angeles, California
| | - John M Rosenberg
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania.
| | - Michael Grabe
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania; Cardiovascular Research Institute, Department of Pharmaceutical Chemistry, University of California, San Francisco, California.
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40
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Witz S, Panwar P, Schober M, Deppe J, Pasha FA, Lemieux MJ, Möhlmann T. Structure-function relationship of a plant NCS1 member--homology modeling and mutagenesis identified residues critical for substrate specificity of PLUTO, a nucleobase transporter from Arabidopsis. PLoS One 2014; 9:e91343. [PMID: 24621654 PMCID: PMC3951388 DOI: 10.1371/journal.pone.0091343] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Accepted: 02/08/2014] [Indexed: 11/18/2022] Open
Abstract
Plastidic uracil salvage is essential for plant growth and development. So far, PLUTO, the plastidic nucleobase transporter from Arabidopsis thaliana is the only known uracil importer at the inner plastidic membrane which represents the permeability barrier of this organelle. We present the first homology model of PLUTO, the sole plant NCS1 member from Arabidopsis based on the crystal structure of the benzyl hydantoin transporter MHP1 from Microbacterium liquefaciens and validated by molecular dynamics simulations. Polar side chains of residues Glu-227 and backbones of Val-145, Gly-147 and Thr-425 are proposed to form the binding site for the three PLUTO substrates uracil, adenine and guanine. Mutational analysis and competition studies identified Glu-227 as an important residue for uracil and to a lesser extent for guanine transport. A differential response in substrate transport was apparent with PLUTO double mutants E227Q G147Q and E227Q T425A, both of which most strongly affected adenine transport, and in V145A G147Q, which markedly affected guanine transport. These differences could be explained by docking studies, showing that uracil and guanine exhibit a similar binding mode whereas adenine binds deep into the catalytic pocket of PLUTO. Furthermore, competition studies confirmed these results. The present study defines the molecular determinants for PLUTO substrate binding and demonstrates key differences in structure-function relations between PLUTO and other NCS1 family members.
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Affiliation(s)
- Sandra Witz
- Department of Plant Physiology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Pankaj Panwar
- Membrane Protein Disease Research Group, Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Markus Schober
- Department of Plant Physiology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Johannes Deppe
- Department of Plant Physiology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Farhan Ahmad Pasha
- Catalysis Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia
| | - M. Joanne Lemieux
- Membrane Protein Disease Research Group, Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Torsten Möhlmann
- Department of Plant Physiology, University of Kaiserslautern, Kaiserslautern, Germany
- * E-mail:
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41
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Suárez E, Lettieri S, Zwier MC, Stringer CA, Subramanian SR, Chong LT, Zuckerman DM. Simultaneous Computation of Dynamical and Equilibrium Information Using a Weighted Ensemble of Trajectories. J Chem Theory Comput 2014; 10:2658-2667. [PMID: 25246856 PMCID: PMC4168800 DOI: 10.1021/ct401065r] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2013] [Indexed: 12/05/2022]
Abstract
![]()
Equilibrium formally can be represented
as an ensemble of uncoupled
systems undergoing unbiased dynamics in which detailed balance is
maintained. Many nonequilibrium processes can be described by suitable
subsets of the equilibrium ensemble. Here, we employ the “weighted
ensemble” (WE) simulation protocol [Huber and Kim, Biophys. J.1996, 70, 97–110]
to generate equilibrium trajectory ensembles and extract nonequilibrium
subsets for computing kinetic quantities. States do not need to be
chosen in advance. The procedure formally allows estimation of kinetic
rates between arbitrary states chosen after the simulation, along
with their equilibrium populations. We also describe a related history-dependent
matrix procedure for estimating equilibrium and nonequilibrium observables
when phase space has been divided into arbitrary non-Markovian regions,
whether in WE or ordinary simulation. In this proof-of-principle study,
these methods are successfully applied and validated on two molecular
systems: explicitly solvated methane association and the implicitly
solvated Ala4 peptide. We comment on challenges remaining in WE calculations.
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Affiliation(s)
- Ernesto Suárez
- Department of Computational and Systems Biology, University of Pittsburgh , 4200 Fifth Ave, Pittsburgh, Pennsylvania 15260, United States
| | - Steven Lettieri
- Department of Computational and Systems Biology, University of Pittsburgh , 4200 Fifth Ave, Pittsburgh, Pennsylvania 15260, United States
| | - Matthew C Zwier
- Department of Chemistry, University of Pittsburgh , 4200 Fifth Ave, Pittsburgh, Pennsylvania 15260, United States
| | - Carsen A Stringer
- Gatsby Computational Neuroscience Unit, University College London , Gower St, London WC1E 6BT, United Kingdom
| | - Sundar Raman Subramanian
- Department of Computational and Systems Biology, University of Pittsburgh , 4200 Fifth Ave, Pittsburgh, Pennsylvania 15260, United States
| | - Lillian T Chong
- Department of Chemistry, University of Pittsburgh , 4200 Fifth Ave, Pittsburgh, Pennsylvania 15260, United States
| | - Daniel M Zuckerman
- Department of Computational and Systems Biology, University of Pittsburgh , 4200 Fifth Ave, Pittsburgh, Pennsylvania 15260, United States
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42
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Dickson A, Brooks CL. WExplore: hierarchical exploration of high-dimensional spaces using the weighted ensemble algorithm. J Phys Chem B 2014; 118:3532-42. [PMID: 24490961 DOI: 10.1021/jp411479c] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
As most relevant motions in biomolecular systems are inaccessible to conventional molecular dynamics simulations, algorithms that enhance sampling of rare events are indispensable. Increasing interest in intrinsically disordered systems and the desire to target ensembles of protein conformations (rather than single structures) in drug development motivate the need for enhanced sampling algorithms that are not limited to "two-basin" problems, and can efficiently determine structural ensembles. For systems that are not well-studied, this must often be done with little or no information about the dynamics of interest. Here we present a novel strategy to determine structural ensembles that uses dynamically defined sampling regions that are organized in a hierarchical framework. It is based on the weighted ensemble algorithm, where an ensemble of copies of the system ("replicas") is directed to new regions of configuration space through merging and cloning operations. The sampling hierarchy allows for a large number of regions to be defined, while using only a small number of replicas that can be balanced over multiple length scales. We demonstrate this algorithm on two model systems that are analytically solvable and examine the 10-residue peptide chignolin in explicit solvent. The latter system is analyzed using a configuration space network, and novel hydrogen bonds are found that facilitate folding.
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Affiliation(s)
- Alex Dickson
- Department of Chemistry, University of Michigan , Ann Arbor, Michigan, United States
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43
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Hills RD. Balancing bond, nonbond, and gō-like terms in coarse grain simulations of conformational dynamics. Methods Mol Biol 2014; 1084:123-140. [PMID: 24061919 DOI: 10.1007/978-1-62703-658-0_7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Characterization of the protein conformational landscape remains a challenging problem, whether it concerns elucidating folding mechanisms, predicting native structures or modeling functional transitions. Coarse-grained molecular dynamics simulation methods enable exhaustive sampling of the energetic landscape at resolutions of biological interest. The general utility of structure-based models is reviewed along with their differing levels of approximation. Simple Gō models incorporate attractive native interactions and repulsive nonnative contacts, resulting in an ideal smooth landscape. Non-Gō coarse-grained models reduce the parameter set as needed but do not include bias to any desired native structure. While non-Gō models have achieved limited success in protein coarse-graining, they can be combined with native structured-based potentials to create a balanced and powerful force field. Recent applications of such Gō-like models have yielded insight into complex folding mechanisms and conformational transitions in large macromolecules. The accuracy and usefulness of reduced representations are also revealed to be a function of the mathematical treatment of the intrinsic bonded topology.
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Affiliation(s)
- Ronald D Hills
- Department of Pharmaceutical Sciences, University of New England, Portland, ME, USA
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44
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Zhao C, Noskov SY. The molecular mechanism of ion-dependent gating in secondary transporters. PLoS Comput Biol 2013; 9:e1003296. [PMID: 24204233 PMCID: PMC3812048 DOI: 10.1371/journal.pcbi.1003296] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Accepted: 09/08/2013] [Indexed: 11/29/2022] Open
Abstract
LeuT-like fold Na-dependent secondary active transporters form a large family of integral membrane proteins that transport various substrates against their concentration gradient across lipid membranes, using the free energy stored in the downhill concentration gradient of sodium ions. These transporters play an active role in synaptic transmission, the delivery of key nutrients, and the maintenance of osmotic pressure inside the cell. It is generally believed that binding of an ion and/or a substrate drives the conformational dynamics of the transporter. However, the exact mechanism for converting ion binding into useful work has yet to be established. Using a multi-dimensional path sampling (string-method) followed by all-atom free energy simulations, we established the principal thermodynamic and kinetic components governing the ion-dependent conformational dynamics of a LeuT-like fold transporter, the sodium/benzyl-hydantoin symporter Mhp1, for an entire conformational cycle. We found that inward-facing and outward-facing states of Mhp1 display nearly the same free energies with an ion absent from the Na2 site conserved across the LeuT-like fold transporters. The barrier separating an apo-state from inward-facing or outward-facing states of the transporter is very low, suggesting stochastic gating in the absence of ion/substrate bound. In contrast, the binding of a Na2 ion shifts the free energy stabilizing the outward-facing state and promoting substrate binding. Our results indicate that ion binding to the Na2 site may also play a key role in the intracellular thin gate dynamics modulation by altering its interactions with the transmembrane helix 5 (TM5). The Potential of Mean Force (PMF) computations for a substrate entrance displays two energy minima that correspond to the locations of the main binding site S1 and proposed allosteric S2 binding site. However, it was found that substrate's binds to the site S1 ∼5 kcal/mol more favorable than that to the site S2 for all studied bound combinations of ions and a substrate.
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Affiliation(s)
- Chunfeng Zhao
- Center for Molecular Simulations, Department of Biological Sciences, University of Calgary, Calgary, Canada
| | - Sergei Yu. Noskov
- Center for Molecular Simulations, Department of Biological Sciences, University of Calgary, Calgary, Canada
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45
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Abstract
It has been suggested that the native state of a protein acts as a kinetic hub that can facilitate transitions between nonnative states. Using recently developed tools to quantify mediation probabilities ("hub scores"), we quantify hub-like behavior in atomic resolution trajectories for the first time. We use a data set of trajectory ensembles for 12 fast-folding proteins previously published by D. E. Shaw Research (Lindorff-Larsen, K.; et al. How Fast-Folding Proteins Fold. Science2011, 334, 517) with an aggregate simulation time of over 8.2 ms. We visualize the free-energy landscape of each molecule using configuration space networks, and show that dynamic quantities can be qualitatively understood from visual inspection of the networks. Modularity optimization is used to provide a parameter-free means of tessellating the network into a group of communities. Using hub scores, we find that the percentage of trajectories that are mediated by the native state is 31% when averaged over all molecules, and reaches a maximum of 52% for the homeodomain and chignolin. Furthermore, for these mediated transitions, we use Markov models to determine whether the native state acts as a facilitator for the transition, or as a trap (i.e., an off-pathway detour). Although instances of facilitation are found in 4 of the 12 molecules, we conclude that the native state acts primarily as a trap, which is consistent with the idea of a funnel-like landscape.
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Affiliation(s)
- Alex Dickson
- Department of Chemistry, The University of Michigan, Ann Arbor, MI
| | - Charles L. Brooks
- Department of Chemistry, The University of Michigan, Ann Arbor, MI
- Biophysics Program, The University of Michigan, Ann Arbor, MI
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46
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Adelman JL, Grabe M. Simulating rare events using a weighted ensemble-based string method. J Chem Phys 2013; 138:044105. [PMID: 23387566 PMCID: PMC3568092 DOI: 10.1063/1.4773892] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2012] [Accepted: 12/17/2012] [Indexed: 11/14/2022] Open
Abstract
We introduce an extension to the weighted ensemble (WE) path sampling method to restrict sampling to a one-dimensional path through a high dimensional phase space. Our method, which is based on the finite-temperature string method, permits efficient sampling of both equilibrium and non-equilibrium systems. Sampling obtained from the WE method guides the adaptive refinement of a Voronoi tessellation of order parameter space, whose generating points, upon convergence, coincide with the principle reaction pathway. We demonstrate the application of this method to several simple, two-dimensional models of driven Brownian motion and to the conformational change of the nitrogen regulatory protein C receiver domain using an elastic network model. The simplicity of the two-dimensional models allows us to directly compare the efficiency of the WE method to conventional brute force simulations and other path sampling algorithms, while the example of protein conformational change demonstrates how the method can be used to efficiently study transitions in the space of many collective variables.
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Affiliation(s)
- Joshua L Adelman
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA.
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47
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Bisha I, Laio A, Magistrato A, Giorgetti A, Sgrignani J. A Candidate Ion-Retaining State in the Inward-Facing Conformation of Sodium/Galactose Symporter: Clues from Atomistic Simulations. J Chem Theory Comput 2013; 9:1240-6. [PMID: 26588767 DOI: 10.1021/ct3008233] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The recent Vibrio parahaemolyticus sodium/galactose (vSGLT) symporter crystal structure captures the protein in an inward-facing substrate-bound conformation, with the sodium ion placed, by structural alignment, in a site equivalent to the Na2 site of the leucine transporter (LeuT). A recent study, based on molecular dynamics simulations, showed that the sodium ion spontaneously leaves its initial position diffusing outside vSGLT, toward the intracellular space. This suggested that the crystal structure corresponds to an ion-releasing state of the transporter. Here, using metadynamics, we identified a more stable Na(+) binding site corresponding to a putative ion-retaining state of the transporter. In addition, our simulations, consistently with mutagenesis studies, highlight the importance of D189 that, without being one of the Na(+)-coordinating residues, regulates its binding/release.
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Affiliation(s)
- Ina Bisha
- SISSA , Via Bonomea 265, 34165 Trieste, Italy
| | | | - Alessandra Magistrato
- CNR-IOM-Democritos National Simulation Center c/o SISSA , via Bonomea 265, 34165 Trieste, Italy
| | - Alejandro Giorgetti
- University of Verona , Ca' Vignal 1, Strada Le Grazie 15, 37134 Verona, Italy
| | - Jacopo Sgrignani
- CNR-IOM-Democritos National Simulation Center c/o SISSA , via Bonomea 265, 34165 Trieste, Italy
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48
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Krypotou E, Kosti V, Amillis S, Myrianthopoulos V, Mikros E, Diallinas G. Modeling, substrate docking, and mutational analysis identify residues essential for the function and specificity of a eukaryotic purine-cytosine NCS1 transporter. J Biol Chem 2012; 287:36792-803. [PMID: 22969088 DOI: 10.1074/jbc.m112.400382] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The recent elucidation of crystal structures of a bacterial member of the NCS1 family, the Mhp1 benzyl-hydantoin permease from Microbacterium liquefaciens, allowed us to construct and validate a three-dimensional model of the Aspergillus nidulans purine-cytosine/H(+) FcyB symporter. The model consists of 12 transmembrane α-helical, segments (TMSs) and cytoplasmic N- and C-tails. A distinct core of 10 TMSs is made of two intertwined inverted repeats (TMS1-5 and TMS6-10) that are followed by two additional TMSs. TMS1, TMS3, TMS6, and TMS8 form an open cavity that is predicted to host the substrate binding site. Based on primary sequence alignment, three-dimensional topology, and substrate docking, we identified five residues as potentially essential for substrate binding in FcyB; Ser-85 (TMS1), Trp-159, Asn-163 (TMS3), Trp-259 (TMS6), and Asn-354 (TMS8). To validate the role of these and other putatively critical residues, we performed a systematic functional analysis of relevant mutants. We show that the proposed substrate binding residues, plus Asn-350, Asn-351, and Pro-353 are irreplaceable for FcyB function. Among these residues, Ser-85, Asn-163, Asn-350, Asn-351, and Asn-354 are critical for determining the substrate binding affinity and/or the specificity of FcyB. Our results suggest that Ser-85, Asn-163, and Asn-354 directly interact with substrates, Trp-159 and Trp-259 stabilize binding through π-π stacking interactions, and Pro-353 affects the local architecture of substrate binding site, whereas Asn-350 and Asn-351 probably affect substrate binding indirectly. Our work is the first systematic approach to address structure-function-specificity relationships in a eukaryotic member of NCS1 family by combining genetic and computational approaches.
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Affiliation(s)
- Emilia Krypotou
- Faculty of Biology, University of Athens, Panepistimiopolis, Athens 15784, Greece
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49
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A comparative study of structures and structural transitions of secondary transporters with the LeuT fold. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2012; 42:181-97. [PMID: 22552869 PMCID: PMC3578728 DOI: 10.1007/s00249-012-0802-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/06/2012] [Revised: 02/29/2012] [Accepted: 03/07/2012] [Indexed: 12/22/2022]
Abstract
Secondary active transporters from several protein families share a core of two five-helix inverted repeats that has become known as the LeuT fold. The known high-resolution protein structures with this fold were analyzed by structural superposition of the core transmembrane domains (TMDs). Three angle parameters derived from the mean TMD axes correlate with accessibility of the central binding site from the outside or inside. Structural transitions between distinct conformations were analyzed for four proteins in terms of changes in relative TMD arrangement and in internal conformation of TMDs. Collectively moving groups of TMDs were found to be correlated in the covariance matrix of elastic network models. The main features of the structural transitions can be reproduced with the 5 % slowest normal modes of anisotropic elastic network models. These results support the rocking bundle model for the major conformational change between the outward- and inward-facing states of the protein and point to an important role for the independently moving last TMDs of each repeat in occluding access to the central binding site. Occlusion is also supported by flexing of some individual TMDs in the collectively moving bundle and hash motifs.
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