1
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Tirincsi A, Sicking M, Hadzibeganovic D, Haßdenteufel S, Lang S. The Molecular Biodiversity of Protein Targeting and Protein Transport Related to the Endoplasmic Reticulum. Int J Mol Sci 2021; 23:143. [PMID: 35008565 PMCID: PMC8745461 DOI: 10.3390/ijms23010143] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 12/19/2021] [Accepted: 12/20/2021] [Indexed: 12/15/2022] Open
Abstract
Looking at the variety of the thousands of different polypeptides that have been focused on in the research on the endoplasmic reticulum from the last five decades taught us one humble lesson: no one size fits all. Cells use an impressive array of components to enable the safe transport of protein cargo from the cytosolic ribosomes to the endoplasmic reticulum. Safety during the transit is warranted by the interplay of cytosolic chaperones, membrane receptors, and protein translocases that together form functional networks and serve as protein targeting and translocation routes. While two targeting routes to the endoplasmic reticulum, SRP (signal recognition particle) and GET (guided entry of tail-anchored proteins), prefer targeting determinants at the N- and C-terminus of the cargo polypeptide, respectively, the recently discovered SND (SRP-independent) route seems to preferentially cater for cargos with non-generic targeting signals that are less hydrophobic or more distant from the termini. With an emphasis on targeting routes and protein translocases, we will discuss those functional networks that drive efficient protein topogenesis and shed light on their redundant and dynamic nature in health and disease.
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Affiliation(s)
- Andrea Tirincsi
- Department of Medical Biochemistry and Molecular Biology, Saarland University, 66421 Homburg, Germany; (A.T.); (M.S.); (D.H.)
| | - Mark Sicking
- Department of Medical Biochemistry and Molecular Biology, Saarland University, 66421 Homburg, Germany; (A.T.); (M.S.); (D.H.)
| | - Drazena Hadzibeganovic
- Department of Medical Biochemistry and Molecular Biology, Saarland University, 66421 Homburg, Germany; (A.T.); (M.S.); (D.H.)
| | - Sarah Haßdenteufel
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Sven Lang
- Department of Medical Biochemistry and Molecular Biology, Saarland University, 66421 Homburg, Germany; (A.T.); (M.S.); (D.H.)
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2
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Bhadra P, Helms V. Molecular Modeling of Signal Peptide Recognition by Eukaryotic Sec Complexes. Int J Mol Sci 2021; 22:10705. [PMID: 34639046 PMCID: PMC8509349 DOI: 10.3390/ijms221910705] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 09/17/2021] [Accepted: 09/27/2021] [Indexed: 12/23/2022] Open
Abstract
Here, we review recent molecular modelling and simulation studies of the Sec translocon, the primary component/channel of protein translocation into the endoplasmic reticulum (ER) and bacterial periplasm, respectively. Our focus is placed on the eukaryotic Sec61, but we also mention modelling studies on prokaryotic SecY since both systems operate in related ways. Cryo-EM structures are now available for different conformational states of the Sec61 complex, ranging from the idle or closed state over an inhibited state with the inhibitor mycolactone bound near the lateral gate, up to a translocating state with bound substrate peptide in the translocation pore. For all these states, computational studies have addressed the conformational dynamics of the translocon with respect to the pore ring, the plug region, and the lateral gate. Also, molecular simulations are addressing mechanistic issues of insertion into the ER membrane vs. translocation into the ER, how signal-peptides are recognised at all in the translocation pore, and how accessory proteins affect the Sec61 conformation in the co- and post-translational pathways.
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Affiliation(s)
| | - Volkhard Helms
- Center for Bioinformatics, Saarland Informatics Campus, Saarland University, Postfach 15 11 50, 66041 Saarbruecken, Germany;
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3
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Characterization of the Features of Water Inside the SecY Translocon. J Membr Biol 2021; 254:133-139. [PMID: 33811496 DOI: 10.1007/s00232-021-00178-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Accepted: 03/23/2021] [Indexed: 10/21/2022]
Abstract
Despite extended experimental and computational studies, the mechanism regulating membrane protein folding and stability in cell membranes is not fully understood. In this review, I will provide a personal and partial account of the scientific efforts undertaken by Dr. Stephen White to shed light on this topic. After briefly describing the role of water and the hydrophobic effect on cellular processes, I will discuss the physical chemistry of water confined inside the SecY translocon pore. I conclude with a review of recent literature that attempts to answer fundamental questions on the pathway and energetics of translocon-guided membrane protein insertion.
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4
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Paul S, Ainavarapu SRK, Venkatramani R. Variance of Atomic Coordinates as a Dynamical Metric to Distinguish Proteins and Protein-Protein Interactions in Molecular Dynamics Simulations. J Phys Chem B 2020; 124:4247-4262. [PMID: 32281802 DOI: 10.1021/acs.jpcb.0c01191] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Protein dynamics is a manifestation of the complex trajectories of these biomolecules on a multidimensional rugged potential energy surface (PES) driven by thermal energy. At present, computational methods such as atomistic molecular dynamics (MD) simulations can describe thermal protein conformational changes in fully solvated environments over millisecond timescales. Despite these advances, a quantitative assessment of protein dynamics remains a complicated topic, intricately linked to issues such as sampling convergence and the identification of appropriate reaction coordinates/structural features to describe protein conformational states and motions. Here, we present the cumulative variance of atomic coordinate fluctuations (CVCF) along trajectories as an intuitive PES sensitive metric to assess both the extent of sampling and protein dynamics captured in MD simulations. We first examine the sampling problem in model one- (1D) and two-dimensional (2D) PES to demonstrate that the CVCF when traced as a function of the sampling variable (time in MD simulations) can identify local and global equilibria. Further, even far from global equilibrium, a situation representative of standard MD trajectories of proteins, the CVCF can distinguish different PES and therefore resolve the resultant protein dynamics. We demonstrate the utility of our CVCF analysis by applying it to distinguish the dynamics of structurally homologous proteins from the ubiquitin family (ubiquitin, SUMO1, SUMO2) and ubiquitin protein-protein interactions. Our CVCF analysis reveals that differential side-chain dynamics from the structured part of the protein (the conserved β-grasp fold) present distinct protein PES to distinguish ubiquitin from SUMO isoforms. Upon binding to two functionally distinct protein partners (UBCH5A and UEV), intrinsic ubiquitin dynamics changes to reflect the binding context even though the two proteins have similar binding modes, which lead to negligible (sub-angstrom scale) structural changes.
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Affiliation(s)
- Sanjoy Paul
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Dr. Homi Bhabha Road, Colaba, Mumbai 400005, Maharashtra, India
| | - Sri Rama Koti Ainavarapu
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Dr. Homi Bhabha Road, Colaba, Mumbai 400005, Maharashtra, India
| | - Ravindra Venkatramani
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Dr. Homi Bhabha Road, Colaba, Mumbai 400005, Maharashtra, India
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5
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Niesen MJM, Zimmer MH, Miller TF. Dynamics of Co-translational Membrane Protein Integration and Translocation via the Sec Translocon. J Am Chem Soc 2020; 142:5449-5460. [PMID: 32130863 PMCID: PMC7338273 DOI: 10.1021/jacs.9b07820] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
An important aspect of cellular function is the correct targeting and delivery of newly synthesized proteins. Central to this task is the machinery of the Sec translocon, a transmembrane channel that is involved in both the translocation of nascent proteins across cell membranes and the integration of proteins into the membrane. Considerable experimental and computational effort has focused on the Sec translocon and its role in nascent protein biosynthesis, including the correct folding and expression of integral membrane proteins. However, the use of molecular simulation methods to explore Sec-facilitated protein biosynthesis is hindered by the large system sizes and long (i.e., minute) time scales involved. In this work, we describe the development and application of a coarse-grained simulation approach that addresses these challenges and allows for direct comparison with both in vivo and in vitro experiments. The method reproduces a wide range of experimental observations, providing new insights into the underlying molecular mechanisms, predictions for new experiments, and a strategy for the rational enhancement of membrane protein expression levels.
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Affiliation(s)
- Michiel J M Niesen
- Department of Chemistry & Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Matthew H Zimmer
- Department of Chemistry & Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Thomas F Miller
- Department of Chemistry & Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
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6
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Energy landscape underlying spontaneous insertion and folding of an alpha-helical transmembrane protein into a bilayer. Nat Commun 2018; 9:4949. [PMID: 30470737 PMCID: PMC6251876 DOI: 10.1038/s41467-018-07320-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 10/18/2018] [Indexed: 11/08/2022] Open
Abstract
Membrane protein folding mechanisms and rates are notoriously hard to determine. A recent force spectroscopy study of the folding of an α-helical membrane protein, GlpG, showed that the folded state has a very high kinetic stability and a relatively low thermodynamic stability. Here, we simulate the spontaneous insertion and folding of GlpG into a bilayer. An energy landscape analysis of the simulations suggests that GlpG folds via sequential insertion of helical hairpins. The rate-limiting step involves simultaneous insertion and folding of the final helical hairpin. The striking features of GlpG's experimentally measured landscape can therefore be explained by a partially inserted metastable state, which leads us to a reinterpretation of the rates measured by force spectroscopy. Our results are consistent with the helical hairpin hypothesis but call into question the two-stage model of membrane protein folding as a general description of folding mechanisms in the presence of bilayers.
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7
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Niesen MJM, Müller-Lucks A, Hedman R, von Heijne G, Miller TF. Forces on Nascent Polypeptides during Membrane Insertion and Translocation via the Sec Translocon. Biophys J 2018; 115:1885-1894. [PMID: 30366631 DOI: 10.1016/j.bpj.2018.10.002] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 09/15/2018] [Accepted: 10/02/2018] [Indexed: 12/21/2022] Open
Abstract
During ribosomal translation, nascent polypeptide chains (NCs) undergo a variety of physical processes that determine their fate in the cell. This study utilizes a combination of arrest peptide experiments and coarse-grained molecular dynamics to measure and elucidate the molecular origins of forces that are exerted on NCs during cotranslational membrane insertion and translocation via the Sec translocon. The approach enables deconvolution of force contributions from NC-translocon and NC-ribosome interactions, membrane partitioning, and electrostatic coupling to the membrane potential. In particular, we show that forces due to NC-lipid interactions provide a readout of conformational changes in the Sec translocon, demonstrating that lateral gate opening only occurs when a sufficiently hydrophobic segment of NC residues reaches the translocon. The combination of experiment and theory introduced here provides a detailed picture of the molecular interactions and conformational changes during ribosomal translation that govern protein biogenesis.
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Affiliation(s)
- Michiel J M Niesen
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California
| | - Annika Müller-Lucks
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Rickard Hedman
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Gunnar von Heijne
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Thomas F Miller
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California.
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8
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Gumbart JC, Ulmschneider MB, Hazel A, White SH, Ulmschneider JP. Computed Free Energies of Peptide Insertion into Bilayers are Independent of Computational Method. J Membr Biol 2018; 251:345-356. [PMID: 29520628 PMCID: PMC6030508 DOI: 10.1007/s00232-018-0026-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 02/27/2018] [Indexed: 01/15/2023]
Abstract
We show that the free energy of inserting hydrophobic peptides into lipid bilayer membranes from surface-aligned to transmembrane inserted states can be reliably calculated using atomistic models. We use two entirely different computational methods: high temperature spontaneous peptide insertion calculations as well as umbrella sampling potential-of-mean-force (PMF) calculations, both yielding the same energetic profiles. The insertion free energies were calculated using two different protein and lipid force fields (OPLS protein/united-atom lipids and CHARMM36 protein/all-atom lipids) and found to be independent of the simulation parameters. In addition, the free energy of insertion is found to be independent of temperature for both force fields. However, we find major difference in the partitioning kinetics between OPLS and CHARMM36, likely due to the difference in roughness of the underlying free energy surfaces. Our results demonstrate not only a reliable method to calculate insertion free energies for peptides, but also represent a rare case where equilibrium simulations and PMF calculations can be directly compared.
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Affiliation(s)
| | | | | | - Stephen H White
- Department of Physiology & Biophysics, University of California at Irvine, Irvine, CA, USA
| | - Jakob P Ulmschneider
- Department of Physics and the Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai, 200240, China.
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9
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Niesen MJM, Marshall SS, Miller TF, Clemons WM. Improving membrane protein expression by optimizing integration efficiency. J Biol Chem 2017; 292:19537-19545. [PMID: 28918393 DOI: 10.1074/jbc.m117.813469] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Revised: 09/12/2017] [Indexed: 12/22/2022] Open
Abstract
The heterologous overexpression of integral membrane proteins in Escherichia coli often yields insufficient quantities of purifiable protein for applications of interest. The current study leverages a recently demonstrated link between co-translational membrane integration efficiency and protein expression levels to predict protein sequence modifications that improve expression. Membrane integration efficiencies, obtained using a coarse-grained simulation approach, robustly predicted effects on expression of the integral membrane protein TatC for a set of 140 sequence modifications, including loop-swap chimeras and single-residue mutations distributed throughout the protein sequence. Mutations that improve simulated integration efficiency were 4-fold enriched with respect to improved experimentally observed expression levels. Furthermore, the effects of double mutations on both simulated integration efficiency and experimentally observed expression levels were cumulative and largely independent, suggesting that multiple mutations can be introduced to yield higher levels of purifiable protein. This work provides a foundation for a general method for the rational overexpression of integral membrane proteins based on computationally simulated membrane integration efficiencies.
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Affiliation(s)
- Michiel J M Niesen
- From the Department of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125
| | - Stephen S Marshall
- From the Department of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125
| | - Thomas F Miller
- From the Department of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125
| | - William M Clemons
- From the Department of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125
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10
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Niesen MJM, Wang CY, Van Lehn RC, Miller TF. Structurally detailed coarse-grained model for Sec-facilitated co-translational protein translocation and membrane integration. PLoS Comput Biol 2017; 13:e1005427. [PMID: 28328943 PMCID: PMC5381951 DOI: 10.1371/journal.pcbi.1005427] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Revised: 04/05/2017] [Accepted: 02/28/2017] [Indexed: 01/05/2023] Open
Abstract
We present a coarse-grained simulation model that is capable of simulating the minute-timescale dynamics of protein translocation and membrane integration via the Sec translocon, while retaining sufficient chemical and structural detail to capture many of the sequence-specific interactions that drive these processes. The model includes accurate geometric representations of the ribosome and Sec translocon, obtained directly from experimental structures, and interactions parameterized from nearly 200 μs of residue-based coarse-grained molecular dynamics simulations. A protocol for mapping amino-acid sequences to coarse-grained beads enables the direct simulation of trajectories for the co-translational insertion of arbitrary polypeptide sequences into the Sec translocon. The model reproduces experimentally observed features of membrane protein integration, including the efficiency with which polypeptide domains integrate into the membrane, the variation in integration efficiency upon single amino-acid mutations, and the orientation of transmembrane domains. The central advantage of the model is that it connects sequence-level protein features to biological observables and timescales, enabling direct simulation for the mechanistic analysis of co-translational integration and for the engineering of membrane proteins with enhanced membrane integration efficiency.
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Affiliation(s)
- Michiel J. M. Niesen
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, United States of America
| | - Connie Y. Wang
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, United States of America
| | - Reid C. Van Lehn
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, United States of America
| | - Thomas F. Miller
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, United States of America
- * E-mail:
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11
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Marshall SS, Niesen MJM, Müller A, Tiemann K, Saladi SM, Galimidi RP, Zhang B, Clemons WM, Miller TF. A Link between Integral Membrane Protein Expression and Simulated Integration Efficiency. Cell Rep 2016; 16:2169-2177. [PMID: 27524616 DOI: 10.1016/j.celrep.2016.07.042] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Revised: 06/09/2016] [Accepted: 07/16/2016] [Indexed: 01/16/2023] Open
Abstract
Integral membrane proteins (IMPs) control the flow of information and nutrients across cell membranes, yet IMP mechanistic studies are hindered by difficulties in expression. We investigate this issue by addressing the connection between IMP sequence and observed expression levels. For homologs of the IMP TatC, observed expression levels vary widely and are affected by small changes in protein sequence. The effect of sequence changes on experimentally observed expression levels strongly correlates with the simulated integration efficiency obtained from coarse-grained modeling, which is directly confirmed using an in vivo assay. Furthermore, mutations that improve the simulated integration efficiency likewise increase the experimentally observed expression levels. Demonstration of these trends in both Escherichia coli and Mycobacterium smegmatis suggests that the results are general to other expression systems. This work suggests that IMP integration is a determinant for successful expression, raising the possibility of controlling IMP expression via rational design.
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Affiliation(s)
- Stephen S Marshall
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Michiel J M Niesen
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Axel Müller
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Katrin Tiemann
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Shyam M Saladi
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Rachel P Galimidi
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Bin Zhang
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - William M Clemons
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
| | - Thomas F Miller
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
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12
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Zhang B, Zheng W, Papoian GA, Wolynes PG. Exploring the Free Energy Landscape of Nucleosomes. J Am Chem Soc 2016; 138:8126-33. [DOI: 10.1021/jacs.6b02893] [Citation(s) in RCA: 93] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
| | | | - Garegin A. Papoian
- Department
of Chemistry and Biochemistry and Institute for Physical Science and
Technology, University of Maryland, College Park, Maryland 20742, United States
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13
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Gumbart JC, Chipot C. Decrypting protein insertion through the translocon with free-energy calculations. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:1663-71. [PMID: 26896694 DOI: 10.1016/j.bbamem.2016.02.017] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Revised: 02/11/2016] [Accepted: 02/12/2016] [Indexed: 12/23/2022]
Abstract
Protein insertion into a membrane is a complex process involving numerous players. The most prominent of these players is the Sec translocon complex, a conserved protein-conducting channel present in the cytoplasmic membrane of bacteria and the membrane of the endoplasmic reticulum in eukaryotes. The last decade has seen tremendous leaps forward in our understanding of how insertion is managed by the translocon and its partners, coming from atomic-detailed structures, innovative experiments, and well-designed simulations. In this review, we discuss how experiments and simulations, hand-in-hand, teased out the secrets of the translocon-facilitated membrane insertion process. In particular, we focus on the role of free-energy calculations in elucidating membrane insertion. Amazingly, despite all its apparent complexity, protein insertion into membranes is primarily driven by simple thermodynamic and kinetic principles. This article is part of a Special Issue entitled: Membrane proteins edited by J.C. Gumbart and Sergei Noskov.
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Affiliation(s)
- James C Gumbart
- School of Physics, Georgia Institute of Technology, Atlanta, GA 30332, USA.
| | - Christophe Chipot
- Laboratoire International Associé Centre National de la Recherche Scientifique and University of Illinois at Urbana-Champaign, UMR n° 7565, Université de Lorraine, B.P. 70239, 54506 Vandœuvre-lès-Nancy, France; Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
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14
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Van Lehn RC, Zhang B, Miller TF. Regulation of multispanning membrane protein topology via post-translational annealing. eLife 2015; 4. [PMID: 26408961 PMCID: PMC4635508 DOI: 10.7554/elife.08697] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Accepted: 09/25/2015] [Indexed: 12/19/2022] Open
Abstract
The canonical mechanism for multispanning membrane protein topogenesis suggests that protein topology is established during cotranslational membrane integration. However, this mechanism is inconsistent with the behavior of EmrE, a dual-topology protein for which the mutation of positively charged loop residues, even close to the C-terminus, leads to dramatic shifts in its topology. We use coarse-grained simulations to investigate the Sec-facilitated membrane integration of EmrE and its mutants on realistic biological timescales. This work reveals a mechanism for regulating membrane-protein topogenesis, in which initially misintegrated configurations of the proteins undergo post-translational annealing to reach fully integrated multispanning topologies. The energetic barriers associated with this post-translational annealing process enforce kinetic pathways that dictate the topology of the fully integrated proteins. The proposed mechanism agrees well with the experimentally observed features of EmrE topogenesis and provides a range of experimentally testable predictions regarding the effect of translocon mutations on membrane protein topogenesis. DOI:http://dx.doi.org/10.7554/eLife.08697.001 Proteins are long chains of smaller molecules called amino acids, and are built inside cells by a molecular machine called the ribosome. Many important proteins must be inserted into the membrane that surrounds each cell in order to carry out their role. As these proteins are being built by the ribosome, they thread their way into a membrane-spanning channel (called the translocon) from the inner side of the membrane. Short segments of these integral membrane proteins (called transmembrane domains) then become embedded in the membrane, while other parts of the protein remain on either side of the membrane. For a membrane protein to work properly, the end of each of its transmembrane domains must be on the correct side of the membrane (i.e., the protein must obtain the correct ‘topology’). The conventional model for this process suggests that topology is fixed when the first transmembrane domain of a protein is initially integrated into the membrane, while the ribosome is still building the protein. This model can explain most integral membrane proteins, which only have a single topology. However, it cannot explain the family of membrane proteins that have an almost equal chance of adopting one of two different topologies (so-called ‘dual-topology proteins’). Van Lehn et al. have now used computer modeling to simulate how a bacterial protein called EmrE (which is a dual-topology protein) integrates into the membrane via the translocon. The results reveal that a few transmembrane domains in EmrE do not fully integrate into the membrane while the ribosome is building the protein. Instead, these transmembrane domains slowly integrate after the ribosome has finished its job. These findings contradict the conventional model and suggest that some membrane proteins only become fully integrated after the protein-building process is complete. The next step in this work is to experimentally test predictions from the computer simulations. DOI:http://dx.doi.org/10.7554/eLife.08697.002
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Affiliation(s)
- Reid C Van Lehn
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, United States
| | - Bin Zhang
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, United States
| | - Thomas F Miller
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, United States
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15
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Abstract
The heterotrimeric SecY translocon complex is required for the cotranslational assembly of membrane proteins in bacteria and archaea. The insertion of transmembrane (TM) segments during nascent-chain passage through the translocon is generally viewed as a simple partitioning process between the water-filled translocon and membrane lipid bilayer, suggesting that partitioning is driven by the hydrophobic effect. Indeed, the apparent free energy of partitioning of unnatural aliphatic amino acids on TM segments is proportional to accessible surface area, which is a hallmark of the hydrophobic effect [Öjemalm K, et al. (2011) Proc Natl Acad Sci USA 108(31):E359-E364]. However, the apparent partitioning solvation parameter is less than one-half the value expected for simple bulk partitioning, suggesting that the water in the translocon departs from bulk behavior. To examine the state of water in a SecY translocon complex embedded in a lipid bilayer, we carried out all-atom molecular-dynamics simulations of the Pyrococcus furiosus SecYE, which was determined to be in a "primed" open state [Egea PF, Stroud RM (2010) Proc Natl Acad Sci USA 107(40):17182-17187]. Remarkably, SecYE remained in this state throughout our 450-ns simulation. Water molecules within SecY exhibited anomalous diffusion, had highly retarded rotational dynamics, and aligned their dipoles along the SecY transmembrane axis. The translocon is therefore not a simple water-filled pore, which raises the question of how anomalous water behavior affects the mechanism of translocon function and, more generally, the partitioning of hydrophobic molecules. Because large water-filled cavities are found in many membrane proteins, our findings may have broader implications.
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16
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Peptide Folding in Translocon-Like Pores. J Membr Biol 2015; 248:407-17. [DOI: 10.1007/s00232-015-9808-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Accepted: 05/05/2015] [Indexed: 10/23/2022]
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17
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Nissley DA, O'Brien EP. Timing is everything: unifying codon translation rates and nascent proteome behavior. J Am Chem Soc 2014; 136:17892-8. [PMID: 25486504 DOI: 10.1021/ja510082j] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Experiments have demonstrated that changing the rate at which the ribosome translates a codon position in an mRNA molecule's open reading frame can alter the behavior of the newly synthesized protein. That is, codon translation rates can govern nascent proteome behavior. We emphasize that this phenomenon is a manifestation of the nonequilibrium nature of cotranslational processes, and as such, there exist theoretical tools that offer a potential means to quantitatively predict the influence of codon translation rates on the broad spectrum of nascent protein behaviors including cotranslational folding, aggregation, and translocation. We provide a review of the experimental evidence for the impact that codon translation rates can have, followed by a discussion of theoretical methods that can describe this phenomenon. The development and application of these tools are likely to provide fundamental insights into protein maturation and homeostasis, codon usage bias in organisms, the origins of translation related diseases, and new rational design methods for biotechnology and biopharmaceutical applications.
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Affiliation(s)
- Daniel A Nissley
- Department of Chemistry, Pennsylvania State University , University Park, Pennsylvania 16802, United States
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18
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Wang CY, Miller TF. Allosteric response and substrate sensitivity in peptide binding of the signal recognition particle. J Biol Chem 2014; 289:30868-30879. [PMID: 25237192 DOI: 10.1074/jbc.m114.584912] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
We characterize the conformational dynamics and substrate selectivity of the signal recognition particle (SRP) using a thermodynamic free energy cycle approach and microsecond timescale molecular dynamics simulations. The SRP is a central component of the co-translational protein targeting machinery that binds to the N-terminal signal peptide (SP) of nascent proteins. We determined the shift in relative conformational stability of the SRP upon substrate binding to quantify allosteric coupling between SRP domains. In particular, for dipeptidyl aminopeptidase, an SP that is recognized by the SRP for co-translational targeting, it is found that substrate binding induces substantial changes in the SRP toward configurations associated with targeting of the nascent protein, and it is found that the changes are modestly enhanced by a mutation that increases the hydrophobicity of the SP. However, for alkaline phosphatase, an SP that is recognized for post-translational targeting, substrate binding induces the reverse change in the SRP conformational distribution away from targeting configurations. Microsecond timescale trajectories reveal the intrinsic flexibility of the SRP conformational landscape and provide insight into recent single molecule studies by illustrating that 10-nm lengthscale changes between FRET pairs occur via the rigid-body movement of SRP domains connected by the flexible linker region. In combination, these results provide direct evidence for the hypothesis that substrate-controlled conformational switching in the SRP provides a mechanism for discriminating between different SPs and for connecting substrate binding to downstream steps in the protein targeting pathway.
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Affiliation(s)
- Connie Y Wang
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91106
| | - Thomas F Miller
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91106.
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Mackinnon AL, Paavilainen VO, Sharma A, Hegde RS, Taunton J. An allosteric Sec61 inhibitor traps nascent transmembrane helices at the lateral gate. eLife 2014; 3:e01483. [PMID: 24497544 PMCID: PMC3913039 DOI: 10.7554/elife.01483] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Membrane protein biogenesis requires the coordinated movement of hydrophobic transmembrane domains (TMD) from the cytosolic vestibule of the Sec61 channel into the lipid bilayer. Molecular insight into TMD integration has been hampered by the difficulty of characterizing intermediates during this intrinsically dynamic process. In this study, we show that cotransin, a substrate-selective Sec61 inhibitor, traps nascent TMDs in the cytosolic vestibule, permitting detailed interrogation of an early pre-integration intermediate. Site-specific crosslinking revealed the pre-integrated TMD docked to Sec61 near the cytosolic tip of the lateral gate. Escape from cotransin-arrest depends not only on cotransin concentration, but also on the biophysical properties of the TMD. Genetic selection of cotransin-resistant cancer cells uncovered multiple mutations clustered near the lumenal plug of Sec61α, thus revealing cotransin’s likely site of action. Our results suggest that TMD/lateral gate interactions facilitate TMD transfer into the membrane, a process that is allosterically modulated by cotransin binding to the plug. DOI:http://dx.doi.org/10.7554/eLife.01483.001 Cells are surrounded by a plasma membrane that acts like a barrier around the cell—keeping the cell’s boundaries distinct from surrounding cells and helping to regulate the contents of the cell. This plasma membrane is made up mostly of two layers of fatty molecules, and is also studded with proteins. Some of these membrane proteins act as channels that allow nutrients and other chemicals to enter and leave the cell, while others allow the cell to communicate with other cells and the outside environment. Like all proteins, membrane proteins are chains of amino acids that are linked together by a molecular machine called a ribosome. The ribosomes that make membrane proteins are located on the outside of a membrane-enclosed compartment within the cell called the endoplasmic reticulum. To eventually become embedded within a membrane, a new protein must—at the same time as it is being built—enter a channel within the membrane of the endoplasmic reticulum. The newly synthesized protein chain enters this channel, called Sec61, via an entrance near the ribosome and then threads its way toward the inside of the endoplasmic reticulum. However, there is also a ‘side-gate’ in Sec61 that allows specific segments the new protein to escape the channel and become embedded within the membrane. From here, the membrane protein can be trafficked to other destinations within the cell, including the plasma membrane. However, how the newly forming protein chain passes through the side-gate of Sec61 is not well understood. Now MacKinnon, Paavilainen et al. have used a small molecule called cotransin—which is known to interfere with the passage of proteins through Sec61—to observe the interactions between the Sec61 channel and the new protein. Cotransin appears to trap the new protein chain within the Sec61 channel by essentially ‘locking’ the side-gate. MacKinnon, Paavilainen et al. observed that the trapped protein interacts with the inside of the channel at the end closest to the ribosome—which is the likely location of the side-gate. In contrast, cotransin likely binds at the other end of the channel, to a piece of Sec61 that serves to plug the exit into the endoplasmic reticulum; and this plug is directly connected to the side-gate. By preventing the plug from moving out of the way, cotransin can somehow stop the new protein from passing through the side-gate. However, MacKinnon, Paavilainen et al. did find that some membrane proteins with certain physical and chemical properties could get through the gate, despite the presence of cotransin. The next challenge is to resolve exactly how interactions between cotransin and the Sec61 plug can block the escape of new proteins into the membrane. DOI:http://dx.doi.org/10.7554/eLife.01483.002
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Affiliation(s)
- Andrew L Mackinnon
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, United States
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20
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Abstract
The Sec61 translocon forms a pore to translocate polypeptide sequences across the membrane and offers a lateral gate for membrane integration of hydrophobic (H) segments. A central constriction of six apolar residues has been shown to form a seal, but also to determine the hydrophobicity threshold for membrane integration: Mutation of these residues in yeast Sec61p to glycines, serines, aspartates, or lysines lowered the hydrophobicity required for integration; mutation to alanines increased it. Whereas four leucines distributed in an oligo-alanine H segment were sufficient for 50% integration, we now find four leucines in the N-terminal half of the H segment to produce significantly more integration than in the C-terminal half, suggesting functional asymmetry within the translocon. Scanning a cluster of three leucines through an oligo-alanine H segment showed high integration levels, except around the position matching that of the hydrophobic constriction in the pore where integration was strongly reduced. Both asymmetry and the position effect of H-segment integration disappeared upon mutation of the constriction residues to glycines or serines, demonstrating that hydrophobicity at this position within the translocon is responsible for the phenomenon. Asymmetry was largely retained, however, when constriction residues were replaced by alanines. These results reflect on the integration mechanism of transmembrane domains and show that membrane insertion of H segments strongly depends not only on their intrinsic hydrophobicity but also on the local conditions in the translocon interior. Thus, the contribution of hydrophobic residues in the H segment is not simply additive and displays cooperativeness depending on their relative position.
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21
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Vélez Pérez JA, Guzmán O, Navarro-García F. Steric contribution of macromolecular crowding to the time and activation energy for preprotein translocation across the endoplasmic reticulum membrane. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2013; 88:012725. [PMID: 23944508 DOI: 10.1103/physreve.88.012725] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Indexed: 06/02/2023]
Abstract
Protein translocation from the cytosol to the endoplasmic reticulum (ER) or vice versa, an essential process for cell function, includes the transport of preproteins destined to become secretory, luminal, or integral membrane proteins (translocation) or misfolded proteins returned to the cytoplasm to be degraded (retrotranslocation). An important aspect in this process that has not been fully studied is the molecular crowding at both sides of the ER membrane. By using models of polymers crossing a membrane through a pore, in an environment crowded by either static or dynamic spherical agents, we computed the following transport properties: the free energy, the activation energy, the force, and the transport times for translocation and retrotranslocation. Using experimental protein crowding data for the cytoplasm and ER sides, we showed that dynamic crowding, which resembles biological environments where proteins are translocated or retrotranslocated, increases markedly all the physical properties of translocation and retrotranslocation as compared with translocation in a diluted system. By contrast, transport properties in static crowded systems were similar to those in diluted conditions. In the dynamic regime, the effects of crowding were more notorious in the transport times, leading to a huge difference for large chains. We indicate that this difference is the result of the synergy between the free energy and the diffusivity of the translocating chain. That synergy leads to translocation rates similar to experimental measures in diluted systems, which indicates that the effects of crowding can be measured. Our data also indicate that effects of crowding cannot be neglected when studying translocation because protein dynamic crowding has a relevant steric contribution, which changes the properties of translocation.
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Affiliation(s)
- José Antonio Vélez Pérez
- Departamento de Física, Universidad Autónoma Metropolitana-Iztapalapa, 09340 México, DF, México.
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22
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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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Gumbart JC, Teo I, Roux B, Schulten K. Reconciling the roles of kinetic and thermodynamic factors in membrane-protein insertion. J Am Chem Soc 2013; 135:2291-7. [PMID: 23298280 PMCID: PMC3573731 DOI: 10.1021/ja310777k] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
![]()
For the vast majority of membrane proteins, insertion
into a membrane
is not direct, but rather is catalyzed by a protein-conducting channel,
the translocon. This channel provides a lateral exit into the bilayer
while simultaneously offering a pathway into the aqueous lumen. The
determinants of a nascent protein’s choice between these two
pathways are not comprehensively understood, although both energetic
and kinetic factors have been observed. To elucidate the specific
roles of some of these factors, we have carried out extensive all-atom
molecular dynamics simulations of different nascent transmembrane
segments embedded in a ribosome-bound bacterial translocon, SecY.
Simulations on the μs time scale reveal a spontaneous motion
of the substrate segment into the membrane or back into the channel,
depending on its hydrophobicity. Potential of mean force (PMF) calculations
confirm that the observed motion is the result of local free-energy
differences between channel and membrane. Based on these and other
PMFs, the time-dependent probability of membrane insertion is determined
and is shown to mimic a two-state partition scheme with an apparent
free energy that is compressed relative to the molecular-level PMFs.
It is concluded that insertion kinetics underlies the experimentally
observed thermodynamic partitioning process.
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Affiliation(s)
- James C Gumbart
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30363, USA
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24
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Abstract
The elucidation of the molecular nature of the translocon-assisted protein insertion is a challenging problem due to the complexity of this process. Furthermore, the limited availability of crucial structural information makes it hard to interpret the hints about the insertion mechanism provided by biochemical studies. At present, it is not practical to explore the insertion process by brute force simulation approaches due to the extremely lengthy process and very complex landscape. Thus, this work uses our previously developed coarse-grained model and explores the energetics of the membrane insertion and translocation paths. The trend in the calculated free-energy profiles is verified by evaluating the correlation between the calculated and observed effect of mutations as well as the effect of inverting the signal peptide that reflects the "positive-inside" rule. Furthermore, the effect of the tentative opening induced by the ribosome is found to reduce the kinetic barrier. Significantly, the trend of the forward and backward energy barriers provides a powerful way to analyze key energetics information. Thus, it is concluded that the insertion process is most likely a nonequilibrium process. Moreover, we provided a general formulation for the analysis of the elusive apparent membrane insertion energy, ΔG(app), and conclude that this important parameter is unlikely to correspond to the free-energy difference between the translocon and membrane. Our formulation seems to resolve the controversy about ΔG(app) for Arg.
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Zhang B, Miller TF. Long-timescale dynamics and regulation of Sec-facilitated protein translocation. Cell Rep 2012; 2:927-37. [PMID: 23084746 PMCID: PMC3483636 DOI: 10.1016/j.celrep.2012.08.039] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2012] [Revised: 07/21/2012] [Accepted: 08/31/2012] [Indexed: 01/11/2023] Open
Abstract
We present a coarse-grained modeling approach that spans the nanosecond- to minute-timescale dynamics of cotranslational protein translocation. The method enables direct simulation of both integral membrane protein topogenesis and transmembrane domain (TM) stop-transfer efficiency. Simulations reveal multiple kinetic pathways for protein integration, including a mechanism in which the nascent protein undergoes slow-timescale reorientation, or flipping, in the confined environment of the translocon channel. Competition among these pathways gives rise to the experimentally observed dependence of protein topology on ribosomal translation rate and protein length. We further demonstrate that sigmoidal dependence of stop-transfer efficiency on TM hydrophobicity arises from local equilibration of the TM across the translocon lateral gate, and it is predicted that slowing ribosomal translation yields decreased stop-transfer efficiency in long proteins. This work reveals the balance between equilibrium and nonequilibrium processes in protein targeting, and it provides insight into the molecular regulation of the Sec translocon.
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Affiliation(s)
- Bin Zhang
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
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