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Krantz BA. Anthrax Toxin: Model System for Studying Protein Translocation. J Mol Biol 2024; 436:168521. [PMID: 38458604 DOI: 10.1016/j.jmb.2024.168521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 02/08/2024] [Accepted: 03/04/2024] [Indexed: 03/10/2024]
Abstract
Dedicated translocase channels are nanomachines that often, but not always, unfold and translocate proteins through narrow pores across the membrane. Generally, these molecular machines utilize external sources of free energy to drive these reactions, since folded proteins are thermodynamically stable, and once unfolded they contain immense diffusive configurational entropy. To catalyze unfolding and translocate the unfolded state at appreciable timescales, translocase channels often utilize analogous peptide-clamp active sites. Here we describe how anthrax toxin has been used as a biophysical model system to study protein translocation. The tripartite bacterial toxin is composed of an oligomeric translocase channel, protective antigen (PA), and two enzymes, edema factor (EF) and lethal factor (LF), which are translocated by PA into mammalian host cells. Unfolding and translocation are powered by the endosomal proton gradient and are catalyzed by three peptide-clamp sites in the PA channel: the α clamp, the ϕ clamp, and the charge clamp. These clamp sites interact nonspecifically with the chemically complex translocating chain, serve to minimize unfolded state configurational entropy, and work cooperatively to promote translocation. Two models of proton gradient driven translocation have been proposed: (i) an extended-chain Brownian ratchet mechanism and (ii) a proton-driven helix-compression mechanism. These models are not mutually exclusive; instead the extended-chain Brownian ratchet likely operates on β-sheet sequences and the helix-compression mechanism likely operates on α-helical sequences. Finally, we compare and contrast anthrax toxin with other related and unrelated translocase channels.
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Affiliation(s)
- Bryan A Krantz
- Department of Microbial Pathogenesis, School of Dentistry, University of Maryland, Baltimore, 650 W. Baltimore Street, Baltimore, MD 21201, USA.
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2
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Mukherjee S, Mepperi J, Sahu P, Barman DK, Kotamarthi HC. Single-Molecule Optical Tweezers As a Tool for Delineating the Mechanisms of Protein-Processing Mechanoenzymes. ACS OMEGA 2023; 8:87-97. [PMID: 36643560 PMCID: PMC9835622 DOI: 10.1021/acsomega.2c06044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 12/06/2022] [Indexed: 06/17/2023]
Abstract
Mechanoenzymes convert chemical energy from the hydrolysis of nucleotide triphosphates to mechanical energy for carrying out cellular functions ranging from DNA unwinding to protein degradation. Protein-processing mechanoenzymes either remodel the protein structures or translocate them across cellular compartments in an energy-dependent manner. Optical-tweezer-based single-molecule force spectroscopy assays have divulged information on details of chemo-mechanical coupling, directed motion, as well as mechanical forces these enzymes are capable of generating. In this review, we introduce the working principles of optical tweezers as a single-molecule force spectroscopy tool and assays developed to decipher the properties such as unfolding kinetics, translocation velocities, and step sizes by protein remodeling mechanoenzymes. We focus on molecular motors involved in protein degradation and disaggregation, i.e., ClpXP, ClpAP, and ClpB, and insights provided by single-molecule assays on kinetics and stepping dynamics during protein unfolding and translocation. Cellular activities such as protein synthesis, folding, and translocation across membranes are also energy dependent, and the recent single-molecule studies decoding the role of mechanical forces on these processes have been discussed.
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3
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Regulation of Translation, Translocation, and Degradation of Proteins at the Membrane of the Endoplasmic Reticulum. Int J Mol Sci 2022; 23:ijms23105576. [PMID: 35628387 PMCID: PMC9147092 DOI: 10.3390/ijms23105576] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 05/10/2022] [Accepted: 05/13/2022] [Indexed: 11/21/2022] Open
Abstract
The endoplasmic reticulum (ER) of mammalian cells is the central organelle for the maturation and folding of transmembrane proteins and for proteins destined to be secreted into the extracellular space. The proper folding of target proteins is achieved and supervised by a complex endogenous chaperone machinery. BiP, a member of the Hsp70 protein family, is the central chaperone in the ER. The chaperoning activity of BiP is assisted by ER-resident DnaJ (ERdj) proteins due to their ability to stimulate the low, intrinsic ATPase activity of BiP. Besides their co-chaperoning activity, ERdj proteins also regulate and tightly control the translation, translocation, and degradation of proteins. Disturbances in the luminal homeostasis result in the accumulation of unfolded proteins, thereby eliciting a stress response, the so-called unfolded protein response (UPR). Accumulated proteins are either deleterious due to the functional loss of the respective protein and/or due to their deposition as intra- or extracellular protein aggregates. A variety of metabolic diseases are known to date, which are associated with the dysfunction of components of the chaperone machinery. In this review, we will delineate the impact of ERdj proteins in controlling protein synthesis and translocation under physiological and under stress conditions. A second aspect of this review is dedicated to the role of ERdj proteins in the ER-associated degradation pathway, by which unfolded or misfolded proteins are discharged from the ER. We will refer to some of the most prominent diseases known to be based on the dysfunction of ERdj proteins.
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Haji Abdolvahab R, Niknam Hamidabad M. Pore shapes effects on polymer translocation. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2020; 43:76. [PMID: 33306147 DOI: 10.1140/epje/i2020-12001-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 11/12/2020] [Indexed: 06/12/2023]
Abstract
We translocated polymers through pores of different shapes and interaction patterns in three dimensions by Langevin molecular dynamics. There were four simple cylindrical pores of the same length but with different diameters. The results showed that even though decreasing the pore diameter would always decrease the translocation velocity, it was strongly dependent on the shape of the increased pore diameter. Although increasing the pore diameter made the translocation faster in simple cylindrical pores, it was complicated in different pore shapes, e.g. increasing the diameter in the middle decreased the translocation velocity. Investigating polymer shapes through the translocation process and comparing the shapes by the cumulative waiting time for different pore structures reveals the non-equilibrium properties of translocation. Moreover, polymer shape parameters such as gyration radius, polymer center of mass, and average aspect ratio help us to distinguish different pore shapes and/or different polymers.
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Komarudin AG, Driessen AJM. SecA-Mediated Protein Translocation through the SecYEG Channel. Microbiol Spectr 2019; 7:10.1128/microbiolspec.psib-0028-2019. [PMID: 31373268 PMCID: PMC10957188 DOI: 10.1128/microbiolspec.psib-0028-2019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Indexed: 01/02/2023] Open
Abstract
In bacteria, the Sec translocase mediates the translocation of proteins into and across the cytoplasmic membrane. It consists of a protein conducting channel SecYEG, the ATP-dependent motor SecA, and the accessory SecDF complex. Here we discuss the function and structure of the Sec translocase.
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Affiliation(s)
- Amalina Ghaisani Komarudin
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, and the Zernike Institute of Advanced Materials, University of Groningen, Nijenborgh 7, 9747AG Groningen, The Netherlands
| | - Arnold J M Driessen
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, and the Zernike Institute of Advanced Materials, University of Groningen, Nijenborgh 7, 9747AG Groningen, The Netherlands
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6
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Abstract
Single-molecule studies provide unprecedented details about processes that are difficult to grasp by bulk biochemical assays that yield ensemble-averaged results. One of these processes is the translocation and insertion of proteins across and into the bacterial cytoplasmic membrane. This process is facilitated by the universally conserved secretion (Sec) system, a multi-subunit membrane protein complex that consists of dissociable cytoplasmic targeting components, a molecular motor, a protein-conducting membrane pore, and accessory membrane proteins. Here, we review recent insights into the mechanisms of protein translocation and membrane protein insertion from single-molecule studies.
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Affiliation(s)
- Anne-Bart Seinen
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute; and the Zernike Institute for Advanced Materials, University of Groningen, 9747 AG Groningen, Netherlands
- Current affiliation: Biophysics Group, AMOLF, 1098 XG Amsterdam, Netherlands
| | - Arnold J.M. Driessen
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute; and the Zernike Institute for Advanced Materials, University of Groningen, 9747 AG Groningen, Netherlands
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7
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Leininger SE, Trovato F, Nissley DA, O'Brien EP. Domain topology, stability, and translation speed determine mechanical force generation on the ribosome. Proc Natl Acad Sci U S A 2019; 116:5523-5532. [PMID: 30824598 PMCID: PMC6431206 DOI: 10.1073/pnas.1813003116] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The concomitant folding of a nascent protein domain with its synthesis can generate mechanical forces that act on the ribosome and alter translation speed. Such changes in speed can affect the structure and function of the newly synthesized protein as well as cellular phenotype. The domain properties that govern force generation have yet to be identified and understood, and the influence of translation speed is unknown because all reported measurements have been carried out on arrested ribosomes. Here, using coarse-grained molecular simulations and statistical mechanical modeling of protein synthesis, we demonstrate that force generation is determined by a domain's stability and topology, as well as translation speed. The statistical mechanical models we create predict how force profiles depend on these properties. These results indicate that force measurements on arrested ribosomes will not always accurately reflect what happens in a cell, especially for slow-folding domains, and suggest the possibility that certain domain properties may be enriched or depleted across the structural proteome of organisms through evolutionary selection pressures to modulate protein synthesis speed and posttranslational protein behavior.
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Affiliation(s)
- Sarah E Leininger
- Department of Chemistry, Pennsylvania State University, University Park, PA 16802
| | - Fabio Trovato
- Department of Chemistry, Pennsylvania State University, University Park, PA 16802
| | - Daniel A Nissley
- Department of Chemistry, Pennsylvania State University, University Park, PA 16802
| | - Edward P O'Brien
- Department of Chemistry, Pennsylvania State University, University Park, PA 16802;
- Bioinformatics and Genomics Graduate Program, The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802
- Institute for CyberScience, Pennsylvania State University, University Park, PA 16802
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8
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Ganesan I, Theg SM. Structural considerations of folded protein import through the chloroplast TOC/TIC translocons. FEBS Lett 2019; 593:565-572. [PMID: 30775779 DOI: 10.1002/1873-3468.13342] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 02/13/2019] [Accepted: 02/15/2019] [Indexed: 11/11/2022]
Abstract
Protein import into chloroplasts is carried out by the protein translocons at the outer and inner envelope membranes (TOC and TIC). Detailed structures for these translocons are lacking, with only a low-resolution TOC complex structure available. Recently, we showed that the TOC/TIC translocons can import folded proteins, a rather unique feat for a coupled double membrane system. We also determined the maximum functional TOC/TIC pore size to be 30-35 Å. Here, we discuss how such large pores could form and compare the structural dynamics of the pore-forming Toc75 subunit to its bacterial/mitochondrial Omp85 family homologs. We put forward structural models that can be empirically tested and also briefly review the pore dynamics of other protein translocons with known structures.
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Affiliation(s)
- Iniyan Ganesan
- Department of Plant Biology, University of California Davis, CA, USA
| | - Steven M Theg
- Department of Plant Biology, University of California Davis, CA, USA
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Fritch B, Kosolapov A, Hudson P, Nissley DA, Woodcock HL, Deutsch C, O'Brien EP. Origins of the Mechanochemical Coupling of Peptide Bond Formation to Protein Synthesis. J Am Chem Soc 2018; 140:5077-5087. [PMID: 29577725 DOI: 10.1021/jacs.7b11044] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Mechanical forces acting on the ribosome can alter the speed of protein synthesis, indicating that mechanochemistry can contribute to translation control of gene expression. The naturally occurring sources of these mechanical forces, the mechanism by which they are transmitted 10 nm to the ribosome's catalytic core, and how they influence peptide bond formation rates are largely unknown. Here, we identify a new source of mechanical force acting on the ribosome by using in situ experimental measurements of changes in nascent-chain extension in the exit tunnel in conjunction with all-atom and coarse-grained computer simulations. We demonstrate that when the number of residues composing a nascent chain increases, its unstructured segments outside the ribosome exit tunnel generate piconewtons of force that are fully transmitted to the ribosome's P-site. The route of force transmission is shown to be through the nascent polypetide's backbone, not through the wall of the ribosome's exit tunnel. Utilizing quantum mechanical calculations we find that a consequence of such a pulling force is to decrease the transition state free energy barrier to peptide bond formation, indicating that the elongation of a nascent chain can accelerate translation. Since nascent protein segments can start out as largely unfolded structural ensembles, these results suggest a pulling force is present during protein synthesis that can modulate translation speed. The mechanism of force transmission we have identified and its consequences for peptide bond formation should be relevant regardless of the source of the pulling force.
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Affiliation(s)
- Benjamin Fritch
- Department of Chemistry , Pennsylvania State University , University Park , Pennsylvania 16802 , United States
| | - Andrey Kosolapov
- Department of Physiology , University of Pennsylvania , Philadelphia , Pennsylvania 19104 , United States
| | - Phillip Hudson
- Department of Chemistry , University of South Florida , Tampa , Florida 33620 , United States.,Laboratory of Computational Biology , National Institutes of Health , Bethesda , Maryland 20892 , United States
| | - Daniel A Nissley
- Department of Chemistry , Pennsylvania State University , University Park , Pennsylvania 16802 , United States
| | - H Lee Woodcock
- Department of Chemistry , University of South Florida , Tampa , Florida 33620 , United States
| | - Carol Deutsch
- Department of Physiology , University of Pennsylvania , Philadelphia , Pennsylvania 19104 , United States
| | - Edward P O'Brien
- Department of Chemistry , Pennsylvania State University , University Park , Pennsylvania 16802 , United States.,Bioinformatics and Genomics Graduate Program, The Huck Institutes of the Life Sciences , Pennsylvania State University , University Park , Pennsylvania 16802 , United States
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Abdolvahab RH. Chaperone-driven polymer translocation through nanopore: Spatial distribution and binding energy. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2017; 40:41. [PMID: 28389823 DOI: 10.1140/epje/i2017-11528-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Accepted: 03/10/2017] [Indexed: 06/07/2023]
Abstract
Chaperones are binding proteins working as a driving force in biopolymer translocation. They bind to the biopolymer near the pore and prevent its backsliding. Chaperones may have different spatial distributions. Recently, we showed the importance of their spatial distribution in translocation and its effects on the sequence dependency of the translocation time. Here we focus on homopolymers and exponential distribution. Because of the exponential distribution of chaperones, the energy dependency of the translocation time will change. Here we find a minimum in translocation time versus binding effective energy (EBE) curve. The same trend can be seen in the scaling exponent of time versus polymer length, [Formula: see text] ([Formula: see text]), when plotted against EBE. Interestingly in some special cases, e.g. chaperones of size [Formula: see text] and with an exponential distribution rate of [Formula: see text], the minimum even reaches to an amount of less than 1 ([Formula: see text]). We explain the possibility of this rare result. Moreover, based on a theoretical discussion we show that, by taking into account the velocity dependency of the translocation on polymer length, one can truly predict the value of this minimum.
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Collinson I, Corey RA, Allen WJ. Channel crossing: how are proteins shipped across the bacterial plasma membrane? Philos Trans R Soc Lond B Biol Sci 2016; 370:rstb.2015.0025. [PMID: 26370937 PMCID: PMC4632601 DOI: 10.1098/rstb.2015.0025] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The structure of the first protein-conducting channel was determined more than a decade ago. Today, we are still puzzled by the outstanding problem of protein translocation—the dynamic mechanism underlying the consignment of proteins across and into membranes. This review is an attempt to summarize and understand the energy transducing capabilities of protein-translocating machines, with emphasis on bacterial systems: how polypeptides make headway against the lipid bilayer and how the process is coupled to the free energy associated with ATP hydrolysis and the transmembrane protein motive force. In order to explore how cargo is driven across the membrane, the known structures of the protein-translocation machines are set out against the background of the historic literature, and in the light of experiments conducted in their wake. The paper will focus on the bacterial general secretory (Sec) pathway (SecY-complex), and its eukaryotic counterpart (Sec61-complex), which ferry proteins across the membrane in an unfolded state, as well as the unrelated Tat system that assembles bespoke channels for the export of folded proteins.
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Affiliation(s)
- Ian Collinson
- School of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, UK
| | - Robin A Corey
- School of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, UK
| | - William J Allen
- School of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, UK
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12
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Kumar S, Kumar R, Janke W. Periodically driven DNA: Theory and simulation. Phys Rev E 2016; 93:010402. [PMID: 26871010 DOI: 10.1103/physreve.93.010402] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Indexed: 11/07/2022]
Abstract
We propose a generic model of driven DNA under the influence of an oscillatory force of amplitude F and frequency ν and show the existence of a dynamical transition for a chain of finite length. We find that the area of the hysteresis loop, A_{loop}, scales with the same exponents as observed in a recent study based on a much more detailed model. However, towards the true thermodynamic limit, the high-frequency scaling regime extends to lower frequencies for larger chain length L and the system has only one scaling (A_{loop}≈ν^{-1}F^{2}). Expansion of an analytical expression for A_{loop} obtained for the model system in the low-force regime revealed that there is a new scaling exponent associated with force (A_{loop}≈ν^{-1}F^{2.5}), which has been validated by high-precision numerical calculation. By a combination of analytical and numerical arguments, we also deduce that for large but finite L, the exponents are robust and independent of temperature and friction coefficient.
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Affiliation(s)
- Sanjay Kumar
- Department of Physics, Banaras Hindu University, Varanasi 221 005, India
| | - Ravinder Kumar
- Institut für Theoretische Physik, Universität Leipzig, Postfach 100 920, D-04009 Leipzig, Germany
| | - Wolfhard Janke
- Institut für Theoretische Physik, Universität Leipzig, Postfach 100 920, D-04009 Leipzig, Germany
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Keller RCA. The role and significance of potential lipid-binding regions in the mitochondrial protein import motor: an in-depth in silico study. 3 Biotech 2015; 5:1041-1051. [PMID: 28324412 PMCID: PMC4624131 DOI: 10.1007/s13205-015-0310-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2015] [Accepted: 05/12/2015] [Indexed: 12/05/2022] Open
Abstract
Over the last two decades, an impressive progress has been made in the identification of novel factors in the translocation machineries of the mitochondrial protein import and their possible roles. The role of lipids and possible protein–lipids interactions remains a relatively unexplored territory. Investigating the role of potential lipid-binding regions in the sub-units of the mitochondrial motor might help to shed some more light in our understanding of protein–lipid interactions mechanistically. Bioinformatics results seem to indicate multiple potential lipid-binding regions in each of the sub-units. The subsequent characterization of some of those regions in silico provides insight into the mechanistic functioning of this intriguing and essential part of the protein translocation machinery. Details about the way the regions interact with phospholipids were found by the use of Monte Carlo simulations. For example, Pam18 contains one possible transmembrane region and two tilted surface bound conformations upon interaction with phospholipids. The results demonstrate that the presented bioinformatics approach might be useful in an attempt to expand the knowledge of the possible role of protein–lipid interactions in the mitochondrial protein translocation process.
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Affiliation(s)
- Rob C A Keller
- Section Chemistry, Charlemagne College, Wilhelminastraat 13-15, 6524 AJ, Nijmegen, The Netherlands.
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Denks K, Vogt A, Sachelaru I, Petriman NA, Kudva R, Koch HG. The Sec translocon mediated protein transport in prokaryotes and eukaryotes. Mol Membr Biol 2014; 31:58-84. [DOI: 10.3109/09687688.2014.907455] [Citation(s) in RCA: 123] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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15
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Hingorani KS, Gierasch LM. Comparing protein folding in vitro and in vivo: foldability meets the fitness challenge. Curr Opin Struct Biol 2014; 24:81-90. [PMID: 24434632 DOI: 10.1016/j.sbi.2013.11.007] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Revised: 10/21/2013] [Accepted: 11/21/2013] [Indexed: 01/09/2023]
Abstract
In this review, we compare and contrast current knowledge about in vitro and in vivo protein folding. Major advances in understanding fundamental principles underlying protein folding in optimized in vitro conditions have yielded detailed physicochemical principles of folding landscapes for small, single domain proteins. In addition, there has been increased research focusing on the key features of protein folding in the cell that differentiate it from in vitro folding, such as co-translational folding, chaperone-facilitated folding, and folding in crowded conditions with many weak interactions. Yet these two research areas have not been bridged effectively in research carried out to date. This review points to gaps between the two that are ripe for future research. Moreover, we emphasize the biological selection pressures that impact protein folding in vivo and how fitness drives the evolution of protein sequences in ways that may place foldability in tension with other requirements on a given protein. We suggest that viewing the physicochemical process of protein folding through the lens of evolution will unveil new insights and pose novel challenges about in-cell folding landscapes.
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Affiliation(s)
- Karan S Hingorani
- Program in Molecular and Cellular Biology, University of Massachusetts, Amherst, Amherst, MA 01003, United States; Department of Biochemistry & Molecular Biology, University of Massachusetts, Amherst, Amherst, MA 01003, United States
| | - Lila M Gierasch
- Program in Molecular and Cellular Biology, University of Massachusetts, Amherst, Amherst, MA 01003, United States; Department of Biochemistry & Molecular Biology, University of Massachusetts, Amherst, Amherst, MA 01003, United States; Department of Chemistry, University of Massachusetts, Amherst, Amherst, MA 01003, United States.
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16
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The mitochondrial disulfide relay system: roles in oxidative protein folding and beyond. Int J Cell Biol 2013; 2013:742923. [PMID: 24348563 PMCID: PMC3848088 DOI: 10.1155/2013/742923] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Accepted: 10/01/2013] [Indexed: 12/31/2022] Open
Abstract
Disulfide bond formation drives protein import of most proteins of the mitochondrial intermembrane space (IMS). The main components of this disulfide relay machinery are the oxidoreductase Mia40 and the sulfhydryl oxidase Erv1/ALR. Their precise functions have been elucidated in molecular detail for the yeast and human enzymes in vitro and in intact cells. However, we still lack knowledge on how Mia40 and Erv1/ALR impact cellular and organism physiology and whether they have functions beyond their role in disulfide bond formation. Here we summarize the principles of oxidation-dependent protein import mediated by the mitochondrial disulfide relay. We proceed by discussing recently described functions of Mia40 in the hypoxia response and of ALR in influencing mitochondrial morphology and its importance for tissue development and embryogenesis. We also include a discussion of the still mysterious function of Erv1/ALR in liver regeneration.
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Zhang Y, Iqbal S, O'Leary MFN, Menzies KJ, Saleem A, Ding S, Hood DA. Altered mitochondrial morphology and defective protein import reveal novel roles for Bax and/or Bak in skeletal muscle. Am J Physiol Cell Physiol 2013; 305:C502-11. [DOI: 10.1152/ajpcell.00058.2013] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The function Bax and/or Bak in constituting a gateway for mitochondrial apoptosis in response to apoptotic stimuli has been unequivocally demonstrated. However, recent work has suggested that Bax/Bak may have unrecognized nonapoptotic functions related to mitochondrial function in nonstressful environments. Wild-type (WT) and Bax/Bak double knockout (DKO) mice were used to determine alternative roles for Bax and Bak in mitochondrial morphology and protein import in skeletal muscle. The absence of Bax and/or Bak altered mitochondrial dynamics by regulating protein components of the organelle fission and fusion machinery. Moreover, DKO mice exhibited defective mitochondrial protein import, both into the matrix and outer membrane compartments, which was consistent with our observations of impaired membrane potential and attenuated expression of protein import machinery (PIM) components in intermyofibrillar mitochondria. Furthermore, the cytosolic chaperones heat-shock protein 90 (Hsp90) and binding immunoglobulin protein (BiP) were markedly increased with the deletion of Bax/Bak, indicating that the cytosolic environment related to protein folding may be changed in DKO mice. Interestingly, endurance training fully restored the deficiency of protein import in DKO mice, likely via the upregulation of PIM components and through improved cytosolic chaperone protein expression. Thus our results emphasize novel roles for Bax and/or Bak in mitochondrial function and provide evidence, for the first time, of a curative function of exercise training in ameliorating a condition of defective mitochondrial protein import.
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Affiliation(s)
- Yuan Zhang
- School of Kinesiology and Health Science, York University, Toronto, Ontario, Canada
- Muscle Health Research Centre, York University, Toronto, Ontario, Canada
- Key Laboratory of Adolescent Health Assessment and Exercise Intervention, Ministry of Education of China, Shanghai, China; and
- College of Physical Education and Health, East China Normal University, Shanghai, China
| | - Sobia Iqbal
- School of Kinesiology and Health Science, York University, Toronto, Ontario, Canada
- Muscle Health Research Centre, York University, Toronto, Ontario, Canada
| | - Michael F. N. O'Leary
- School of Kinesiology and Health Science, York University, Toronto, Ontario, Canada
- Muscle Health Research Centre, York University, Toronto, Ontario, Canada
| | - Keir J. Menzies
- Muscle Health Research Centre, York University, Toronto, Ontario, Canada
| | - Ayesha Saleem
- School of Kinesiology and Health Science, York University, Toronto, Ontario, Canada
- Muscle Health Research Centre, York University, Toronto, Ontario, Canada
| | - Shuzhe Ding
- Key Laboratory of Adolescent Health Assessment and Exercise Intervention, Ministry of Education of China, Shanghai, China; and
- College of Physical Education and Health, East China Normal University, Shanghai, China
| | - David A. Hood
- School of Kinesiology and Health Science, York University, Toronto, Ontario, Canada
- Muscle Health Research Centre, York University, Toronto, Ontario, Canada
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Kudva R, Denks K, Kuhn P, Vogt A, Müller M, Koch HG. Protein translocation across the inner membrane of Gram-negative bacteria: the Sec and Tat dependent protein transport pathways. Res Microbiol 2013; 164:505-34. [DOI: 10.1016/j.resmic.2013.03.016] [Citation(s) in RCA: 122] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Accepted: 03/11/2013] [Indexed: 11/28/2022]
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19
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Mishra RK, Mishra G, Giri D, Kumar S. Scaling of hysteresis loop of interacting polymers under a periodic force. J Chem Phys 2013; 138:244905. [DOI: 10.1063/1.4809985] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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20
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Abstract
Proteins need to be unfolded when translocated through the pores in mitochondrial and other cellular membranes. Knotted proteins, however, might get stuck during this process since the diameter of the pore is smaller than the size of maximally tightened knot. In the present article, I briefly review the experimental and numerical studies of tight knots in proteins, with a particular emphasis on the estimates of the size of these knots. Next, I discuss the process of protein translocation through the mitochondrial pores and report the results of molecular dynamics simulations of knotted protein translocation, which show how the knot can indeed block the pore.
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21
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Feld GK, Brown MJ, Krantz BA. Ratcheting up protein translocation with anthrax toxin. Protein Sci 2012; 21:606-24. [PMID: 22374876 DOI: 10.1002/pro.2052] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2012] [Revised: 02/21/2012] [Accepted: 02/22/2012] [Indexed: 01/09/2023]
Abstract
Energy-consuming nanomachines catalyze the directed movement of biopolymers in the cell. They are found both dissolved in the aqueous cytosol as well as embedded in lipid bilayers. Inquiries into the molecular mechanism of nanomachine-catalyzed biopolymer transport have revealed that these machines are equipped with molecular parts, including adjustable clamps, levers, and adaptors, which interact favorably with substrate polypeptides. Biological nanomachines that catalyze protein transport, known as translocases, often require that their substrate proteins unfold before translocation. An unstructured protein chain is likely entropically challenging to bind, push, or pull in a directional manner, especially in a way that produces an unfolding force. A number of ingenious solutions to this problem are now evident in the anthrax toxin system, a model used to study protein translocation. Here we highlight molecular ratchets and current research on anthrax toxin translocation. A picture is emerging of proton-gradient-driven anthrax toxin translocation, and its associated ratchet mechanism likely applies broadly to other systems. We suggest a cyclical thermodynamic order-to-disorder mechanism (akin to a heat-engine cycle) is central to underlying protein translocation: peptide substrates nonspecifically bind to molecular clamps, which possess adjustable affinities; polypeptide substrates compress into helical structures; these clamps undergo proton-gated switching; and the substrate subsequently expands regaining its unfolded state conformational entropy upon translocation.
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Affiliation(s)
- Geoffrey K Feld
- Department of Chemistry, University of California, Berkeley, California 94720, USA
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22
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Abdolvahab RH, Metzler R, Ejtehadi MR. First passage time distribution of chaperone driven polymer translocation through a nanopore: Homopolymer and heteropolymer cases. J Chem Phys 2011; 135:245102. [DOI: 10.1063/1.3669427] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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23
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SecA, a remarkable nanomachine. Cell Mol Life Sci 2011; 68:2053-66. [PMID: 21479870 PMCID: PMC3101351 DOI: 10.1007/s00018-011-0681-y] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2011] [Revised: 03/22/2011] [Accepted: 03/28/2011] [Indexed: 01/03/2023]
Abstract
Biological cells harbor a variety of molecular machines that carry out mechanical work at the nanoscale. One of these nanomachines is the bacterial motor protein SecA which translocates secretory proteins through the protein-conducting membrane channel SecYEG. SecA converts chemically stored energy in the form of ATP into a mechanical force to drive polypeptide transport through SecYEG and across the cytoplasmic membrane. In order to accommodate a translocating polypeptide chain and to release transmembrane segments of membrane proteins into the lipid bilayer, SecYEG needs to open its central channel and the lateral gate. Recent crystal structures provide a detailed insight into the rearrangements required for channel opening. Here, we review our current understanding of the mode of operation of the SecA motor protein in concert with the dynamic SecYEG channel. We conclude with a new model for SecA-mediated protein translocation that unifies previous conflicting data.
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Midzak A, Rone M, Aghazadeh Y, Culty M, Papadopoulos V. Mitochondrial protein import and the genesis of steroidogenic mitochondria. Mol Cell Endocrinol 2011; 336:70-9. [PMID: 21147195 PMCID: PMC3057322 DOI: 10.1016/j.mce.2010.12.007] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/19/2010] [Revised: 12/03/2010] [Accepted: 12/05/2010] [Indexed: 11/23/2022]
Abstract
The principal site of regulation of steroid hormone biosynthesis is the transfer of cholesterol from the outer to inner mitochondrial membrane. Hormonal stimulation of steroidogenic cells promotes this mitochondrial lipid import through a multi-protein complex, termed the transduceosome, spanning the two membranes. The transduceosome complex is assembled from multiple proteins, such as the steroidogenic acute regulatory (STAR) protein and translocator protein (TSPO), and requires their targeting to the mitochondria for transduceosome function. The vast majority of mitochondrial proteins, including those participating in cholesterol import, are encoded in the nucleus. Their subsequent mitochondrial incorporation is performed through a series of protein import machineries located in the outer and inner mitochondrial membranes. Here we review our current knowledge of the mitochondrial cholesterol import machinery of the transduceosome. This is complemented with descriptions of mitochondrial protein import machineries and mechanisms by which these machineries assemble the transduceosome in steroidogenic mitochondria.
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Affiliation(s)
- Andrew Midzak
- Research Institute of the McGill University Health Centre, McGill University, Montreal, Quebec, H3G 1A4, Canada
- Department of Medicine, McGill University, Montreal, Quebec, H3G 1A4, Canada
| | - Malena Rone
- Research Institute of the McGill University Health Centre, McGill University, Montreal, Quebec, H3G 1A4, Canada
- Department of Medicine, McGill University, Montreal, Quebec, H3G 1A4, Canada
| | - Yassaman Aghazadeh
- Research Institute of the McGill University Health Centre, McGill University, Montreal, Quebec, H3G 1A4, Canada
- Department of Medicine, McGill University, Montreal, Quebec, H3G 1A4, Canada
| | - Martine Culty
- Research Institute of the McGill University Health Centre, McGill University, Montreal, Quebec, H3G 1A4, Canada
- Department of Medicine, McGill University, Montreal, Quebec, H3G 1A4, Canada
- Department of Pharmacology & Therapeutics, McGill University, Montreal, Quebec, H3G 1A4, Canada
| | - Vassilios Papadopoulos
- Research Institute of the McGill University Health Centre, McGill University, Montreal, Quebec, H3G 1A4, Canada
- Department of Medicine, McGill University, Montreal, Quebec, H3G 1A4, Canada
- Department of Pharmacology & Therapeutics, McGill University, Montreal, Quebec, H3G 1A4, Canada
- Department of Biochemistry, McGill University, Montreal, Quebec, H3G 1A4, Canada
- Correspondence at The Research Institute of the McGill University Health Center, Montreal General Hospital, 1650 Cedar Avenue, C10-148, Montreal, Quebec H3G 1A4, Canada. Tel: 514-934-1934 ext. 44580; Fax: 514-934-8261;
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25
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Palladino P, Saviano G, Tancredi T, Benedetti E, Rossi F, Ragone R. Structural determinants of protein translocation in bacteria: conformational flexibility of SecA IRA1 loop region. J Pept Sci 2011; 17:263-9. [DOI: 10.1002/psc.1324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2010] [Revised: 10/04/2010] [Accepted: 10/08/2010] [Indexed: 11/09/2022]
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26
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Singh K, Hood DA. Effect of denervation-induced muscle disuse on mitochondrial protein import. Am J Physiol Cell Physiol 2011; 300:C138-45. [DOI: 10.1152/ajpcell.00181.2010] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
This study determined whether muscle disuse affects mitochondrial protein import and whether changes in protein import are related to mitochondrial content and function. Protein import was measured using a model of unilateral peroneal nerve denervation in rats for 3 ( n = 10), 7 ( n = 12), or 14 ( n = 14) days. We compared the import of preproteins into the matrix of subsarcolemmal (SS) and intermyofibrillar (IMF) mitochondria isolated from the denervated and the contralateral control tibialis anterior muscles. Denervation led to 50% and 29% reductions in protein import after 14 days of disuse in SS and IMF mitochondria, respectively. This was accompanied by significant decreases in mitochondrial state 3 respiration, muscle mass, and whole muscle cytochrome c oxidase activity. To investigate the mechanisms involved, we assessed disuse-related changes in 1) protein import machinery components and 2) mitochondrial function, reflected by respiration and reactive oxygen species (ROS) production. Denervation significantly reduced the expression of translocases localized in the inner membrane (Tim23), outer membrane (Tom20), and mitochondrial heat shock protein 70 (mtHsp70), especially in the SS subfraction. Denervation also resulted in elevated ROS generation, and exogenous ROS was found to markedly reduce protein import. Thus our data indicate that protein import kinetics are closely related to alterations in mitochondrial respiratory capacity ( r = 0.95) and are negatively impacted by ROS. Deleterious changes in the protein import system likely facilitate the reduction in mitochondrial content and the increase in organelle dysfunction (i.e., increased ROS production and decreased respiration) during chronic disuse, which likely contribute to the activation of degradative pathways leading to muscle atrophy.
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Affiliation(s)
- Kaustabh Singh
- Muscle Health Research Center,
- School of Kinesiology and Health Science, and
| | - David A. Hood
- Muscle Health Research Center,
- School of Kinesiology and Health Science, and
- Department of Biology, York University, Toronto, Ontario, Canada
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27
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The prediction of novel multiple lipid-binding regions in protein translocation motor proteins: a possible general feature. Cell Mol Biol Lett 2010; 16:40-54. [PMID: 20957445 PMCID: PMC6275888 DOI: 10.2478/s11658-010-0036-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2010] [Accepted: 10/12/2010] [Indexed: 11/20/2022] Open
Abstract
Protein translocation is an important cellular process. SecA is an essential protein component in the Sec system, as it contains the molecular motor that facilitates protein translocation. In this study, a bioinformatics approach was applied in the search for possible lipid-binding helix regions in protein translocation motor proteins. Novel lipid-binding regions in Escherichia coli SecA were identified. Remarkably, multiple lipid-binding sites were also identified in other motor proteins such as BiP, which is involved in ER protein translocation. The prokaryotic signal recognition particle receptor FtsY, though not a motor protein, is in many ways related to SecA, and was therefore included in this study. The results demonstrate a possible general feature for motor proteins involved in protein translocation.
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28
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Bohnsack MT, Schleiff E. The evolution of protein targeting and translocation systems. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2010; 1803:1115-30. [DOI: 10.1016/j.bbamcr.2010.06.005] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2010] [Revised: 05/26/2010] [Accepted: 06/11/2010] [Indexed: 11/28/2022]
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29
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du Plessis DJF, Nouwen N, Driessen AJM. The Sec translocase. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2010; 1808:851-65. [PMID: 20801097 DOI: 10.1016/j.bbamem.2010.08.016] [Citation(s) in RCA: 195] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2010] [Revised: 08/19/2010] [Accepted: 08/20/2010] [Indexed: 11/18/2022]
Abstract
The vast majority of proteins trafficking across or into the bacterial cytoplasmic membrane occur via the translocon. The translocon consists of the SecYEG complex that forms an evolutionarily conserved heterotrimeric protein-conducting membrane channel that functions in conjunction with a variety of ancillary proteins. For posttranslational protein translocation, the translocon interacts with the cytosolic motor protein SecA that drives the ATP-dependent stepwise translocation of unfolded polypeptides across the membrane. For the cotranslational integration of membrane proteins, the translocon interacts with ribosome-nascent chain complexes and membrane insertion is coupled to polypeptide chain elongation at the ribosome. These processes are assisted by the YidC and SecDF(yajC) complex that transiently interacts with the translocon. This review summarizes our current understanding of the structure-function relationship of the translocon and its interactions with ancillary components during protein translocation and membrane protein insertion. This article is part of a Special Issue entitled Protein translocation across or insertion into membranes.
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Affiliation(s)
- David J F du Plessis
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute and the Zernike Institute for Advanced Materials, University of Groningen, 9751NN Haren, The Netherlands
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30
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Muddana HS, Sengupta S, Mallouk TE, Sen A, Butler PJ. Substrate catalysis enhances single-enzyme diffusion. J Am Chem Soc 2010; 132:2110-1. [PMID: 20108965 PMCID: PMC2832858 DOI: 10.1021/ja908773a] [Citation(s) in RCA: 148] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We show that diffusion of single urease enzyme molecules increases in the presence of urea in a concentration-dependent manner and calculate the force responsible for this increase. Urease diffusion measured using fluorescence correlation spectroscopy increased by 16-28% over buffer controls at urea concentrations ranging from 0.001 to 1 M. This increase was significantly attenuated when urease was inhibited with pyrocatechol, demonstrating that the increase in diffusion was the result of enzyme catalysis of urea. Local molecular pH changes as measured using the pH-dependent fluorescence lifetime of SNARF-1 conjugated to urease were not sufficient to explain the increase in diffusion. Thus, a force generated by self-electrophoresis remains the most plausible explanation. This force, evaluated using Brownian dynamics simulations, was 12 pN per reaction turnover. These measurements demonstrate force generation by a single enzyme molecule and lay the foundation for a further understanding of biological force generation and the development of enzyme-driven nanomotors.
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Affiliation(s)
- Hari S Muddana
- Departments of Bioengineering, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
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31
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van der Laan M, Hutu DP, Rehling P. On the mechanism of preprotein import by the mitochondrial presequence translocase. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2010; 1803:732-9. [PMID: 20100523 DOI: 10.1016/j.bbamcr.2010.01.013] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2009] [Revised: 01/05/2010] [Accepted: 01/11/2010] [Indexed: 12/22/2022]
Abstract
Mitochondria are organelles of endosymbiontic origin that contain more than one thousand different proteins. The vast majority of these proteins is synthesized in the cytosol and imported into one of four mitochondrial subcompartments: outer membrane, intermembrane space, inner membrane and matrix. Several import pathways exist and are committed to different classes of precursor proteins. The presequence translocase of the inner mitochondrial membrane (TIM23 complex) mediates import of precursor proteins with cleavable amino-terminal presequences. Presequences direct precursors across the inner membrane. The combination of this presequence with adjacent regions determines if a precursor is fully translocated into the matrix or laterally sorted into the inner mitochondrial membrane. The membrane-embedded TIM23(SORT) complex mediates the membrane potential-dependent membrane insertion of precursor proteins with a stop-transfer sequence downstream of the mitochondrial targeting signal. In contrast, translocation of precursor proteins into the matrix requires the recruitment of the presequence translocase-associated motor (PAM) to the TIM23 complex. This ATP-driven import motor consists of mitochondrial Hsp70 and several membrane-associated co-chaperones. These two structurally and functionally distinct forms of the TIM23 complex (TIM23(SORT) and TIM23(MOTOR)) are in a dynamic equilibrium with each other. In this review, we discuss recent advances in our understanding of the mechanisms of matrix translocation and membrane insertion by the TIM23 machinery.
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Affiliation(s)
- Martin van der Laan
- Institut für Biochemie und Molekularbiologie, Universität Freiburg, D-79104 Freiburg, Germany
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32
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Yarmola EG, Bubb MR. How depolymerization can promote polymerization: the case of actin and profilin. Bioessays 2010; 31:1150-60. [PMID: 19795407 DOI: 10.1002/bies.200900049] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Rapid polymerization and depolymerization of actin filaments in response to extracellular stimuli is required for normal cell motility and development. Profilin is one of the most important actin-binding proteins; it regulates actin polymerization and interacts with many cytoskeletal proteins that link actin to extracellular membrane. The molecular mechanism of profilin has been extensively considered and debated in the literature for over two decades. Here we discuss several accepted hypotheses regarding the mechanism of profilin function as well as new recently emerged possibilities. Thermal noise is routine in molecular world and unsurprisingly, nature has found a way to utilize it. An increasing amount of theoretical and experimental research suggests that fluctuation-based processes play important roles in many cell events. Here we show how a fluctuation-based process of exchange diffusion is involved in the regulation of actin polymerization.
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Affiliation(s)
- Elena G Yarmola
- Department of Medicine, University of Florida, Gainesville, FL 32610, USA.
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33
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Szymczak P, Janovjak H. Periodic forces trigger a complex mechanical response in ubiquitin. J Mol Biol 2009; 390:443-56. [PMID: 19426737 DOI: 10.1016/j.jmb.2009.04.071] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2009] [Revised: 04/27/2009] [Accepted: 04/28/2009] [Indexed: 01/12/2023]
Abstract
Mechanical forces govern physiological processes in all living organisms. Many cellular forces, for example, those generated in cyclic conformational changes of biological machines, have repetitive components. In apparent contrast, little is known about how dynamic protein structures respond to periodic mechanical information. Ubiquitin is a small protein found in all eukaryotes. We developed molecular dynamics simulations to unfold single and multimeric ubiquitins with periodic forces. By using a coarse-grained representation, we were able to model forces with periods about 2 orders of magnitude longer than the protein's relaxation time. We found that even a moderate periodic force weakened the protein and shifted its unfolding pathways in a frequency- and amplitude-dependent manner. A complex dynamic response with secondary structure refolding and an increasing importance of local interactions was revealed. Importantly, repetitive forces with broadly distributed frequencies elicited very similar molecular responses compared to fixed-frequency forces. When testing the influence of pulling geometry on ubiquitin's mechanical stability, it was found that the linkage involved in the mechanical degradation of cellular proteins renders the protein remarkably insensitive to periodic forces. We also devised a complementary kinetic energy landscape model that traces these observations and explains periodic-force, single-molecule measurements. In turn, this analytical model is capable of predicting dynamic protein responses. These results provide new insights into ubiquitin mechanics and a potential mechanical role during protein degradation, as well as first frameworks for dynamic protein stability and the modeling of repetitive mechanical processes.
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Affiliation(s)
- Piotr Szymczak
- Institute of Theoretical Physics, Warsaw University, Poland
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34
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Nouwen N, Berrelkamp G, Driessen AJM. Charged amino acids in a preprotein inhibit SecA-dependent protein translocation. J Mol Biol 2009; 386:1000-10. [PMID: 19244616 DOI: 10.1016/j.jmb.2009.01.031] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Sec translocase catalyzes membrane protein insertion and translocation. We have introduced stretches of charged amino acid residues into the preprotein proOmpA and have analyzed their effect on in vitro protein translocation into Escherichia coli inner membrane vesicles. Both negatively and positively charged amino acid residues inhibit translocation of proOmpA, yielding a partially translocated polypeptide chain that blocks the translocation site and no longer activates preprotein-stimulated SecA ATPase activity. Stretches of positively charged residues are much stronger translocation inhibitors and suppressors of the preprotein-stimulated SecA ATPase activity than negatively charged residues. These results indicate that both clusters of positively and negatively charged amino acids are poor substrates for the Sec translocase and that this is reflected by their inability to stimulate the ATPase activity of SecA.
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Affiliation(s)
- Nico Nouwen
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9751 NN Haren, The Netherlands
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35
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Altschuler GM, Willison KR. Development of free-energy-based models for chaperonin containing TCP-1 mediated folding of actin. J R Soc Interface 2009; 5:1391-408. [PMID: 18708324 DOI: 10.1098/rsif.2008.0185] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
A free-energy-based approach is used to describe the mechanism through which chaperonin-containing TCP-1 (CCT) folds the filament-forming cytoskeletal protein actin, which is one of its primary substrates. The experimental observations on the actin folding and unfolding pathways are collated and then re-examined from this perspective, allowing us to determine the position of the CCT intervention on the actin free-energy folding landscape. The essential role for CCT in actin folding is to provide a free-energy contribution from its ATP cycle, which drives actin to fold from a stable, trapped intermediate I3, to a less stable but now productive folding intermediate I2. We develop two hypothetical mechanisms for actin folding founded upon concepts established for the bacterial type I chaperonin GroEL and extend them to the much more complex CCT system of eukaryotes. A new model is presented in which CCT facilitates free-energy transfer through direct coupling of the nucleotide hydrolysis cycle to the phases of actin substrate maturation.
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Affiliation(s)
- Gabriel M Altschuler
- Cancer Research UK Centre for Cell and Molecular Biology, Chester Beatty Laboratories, Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK
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36
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Abstract
To explain the effect of profilin on actin critical concentration in a manner consistent with thermodynamic constraints and available experimental data, we built a thermodynamically rigorous model of actin steady-state dynamics in the presence of profilin. We analyzed previously published mechanisms theoretically and experimentally and, based on our analysis, suggest a new explanation for the effect of profilin. It is based on a general principle of indirect energy coupling. The fluctuation-based process of exchange diffusion indirectly couples the energy of ATP hydrolysis to actin polymerization. Profilin modulates this coupling, producing two basic effects. The first is based on the acceleration of exchange diffusion by profilin, which indicates, paradoxically, that a faster rate of actin depolymerization promotes net polymerization. The second is an affinity-based mechanism similar to the one suggested in 1993 by Pantaloni and Carlier although based on indirect rather than direct energy coupling. In the model by Pantaloni and Carlier, transformation of chemical energy of ATP hydrolysis into polymerization energy is regulated by direct association of each step in the hydrolysis reaction with a corresponding step in polymerization. Thus, hydrolysis becomes a time-limiting step in actin polymerization. In contrast, indirect coupling allows ATP hydrolysis to lag behind actin polymerization, consistent with experimental results.
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37
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Awe K, Lambert C, Prange R. Mammalian BiP controls posttranslational ER translocation of the hepatitis B virus large envelope protein. FEBS Lett 2008; 582:3179-84. [PMID: 18708056 DOI: 10.1016/j.febslet.2008.07.062] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2008] [Revised: 07/28/2008] [Accepted: 07/30/2008] [Indexed: 11/16/2022]
Abstract
The hepatitis B virus L protein forms a dual topology in the endoplasmic reticulum (ER) via a process involving cotranslational membrane integration and subsequent posttranslational translocation of its preS subdomain. Here, we show that preS posttranslocation depends on the action of the ER chaperone BiP. To modulate the in vivo BiP activity, we designed an approach based on overexpressing its positive and negative regulators, ER-localized DnaJ-domain containing protein 4 (ERdj4) and BiP-associated protein (BAP), respectively. The feasibility of this approach was confirmed by demonstrating that BAP, but not ERdj4, destabilizes the L/BiP complex. Overexpressing BAP or ERdj4 inhibits preS posttranslocation as does the reduction of ATP levels. These results hint to a new role of BiP in guiding posttranslational polypeptide import into the mammalian ER.
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Affiliation(s)
- Karin Awe
- Department of Medical Microbiology and Hygiene, Johannes Gutenberg-University Mainz, D-55101 Mainz, Germany
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38
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Saridaki T, Sanchez CP, Pfahler J, Lanzer M. A conditional export system provides new insights into protein export in Plasmodium falciparum-infected erythrocytes. Cell Microbiol 2008; 10:2483-95. [PMID: 18691247 DOI: 10.1111/j.1462-5822.2008.01223.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The human malarial parasite Plasmodium falciparum exports determinants of virulence and pathology to destinations within its host erythrocyte, including the cytoplasm, the plasma membrane and membrane profiles of parasite origin termed Maurer's clefts. While there is some information regarding the signals that allot proteins for export, the trafficking route itself has remained largely obscure, partly due to technical limitations in following protein trafficking with time. To overcome these shortcomings, we have established a conditional protein export system in P. falciparum, based on the previously described conditional aggregation domain (CAD domain) that self-aggregates in the endoplasmic reticulum in a manner that is reversible by the addition of a small molecule. By fusing the CAD domain to the first 80 amino acids of STEVOR and full-length PfSBP1, we were able to control export of a soluble and a transmembrane protein to the erythrocyte cytosol and the Maurer's clefts respectively. The conditional export system allowed us to study the temporal sequence of events of protein export and identify intermediate steps. We further explored the potential of the conditional export system in identifying factors that interact with exported proteins en route. Our data provide evidence for a physical interaction of exported proteins with the molecular chaperone PfBiP during early export steps.
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Affiliation(s)
- Theodora Saridaki
- Hygiene Institut, Abteilung Parasitologie, Universitätsklinikum Heidelberg, Im Neuenheimer Feld 324, 69120 Heidelberg, Germany
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39
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Affiliation(s)
- Arnold J.M. Driessen
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute and the Zernike Institute for Advanced Materials, University of Groningen, 9751 NN, Haren, The Netherlands; ,
| | - Nico Nouwen
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute and the Zernike Institute for Advanced Materials, University of Groningen, 9751 NN, Haren, The Netherlands; ,
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40
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Zweers JC, Barák I, Becher D, Driessen AJ, Hecker M, Kontinen VP, Saller MJ, Vavrová L, van Dijl JM. Towards the development of Bacillus subtilis as a cell factory for membrane proteins and protein complexes. Microb Cell Fact 2008; 7:10. [PMID: 18394159 PMCID: PMC2323362 DOI: 10.1186/1475-2859-7-10] [Citation(s) in RCA: 86] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2007] [Accepted: 04/04/2008] [Indexed: 01/16/2023] Open
Abstract
Background The Gram-positive bacterium Bacillus subtilis is an important producer of high quality industrial enzymes and a few eukaryotic proteins. Most of these proteins are secreted into the growth medium, but successful examples of cytoplasmic protein production are also known. Therefore, one may anticipate that the high protein production potential of B. subtilis can be exploited for protein complexes and membrane proteins to facilitate their functional and structural analysis. The high quality of proteins produced with B. subtilis results from the action of cellular quality control systems that efficiently remove misfolded or incompletely synthesized proteins. Paradoxically, cellular quality control systems also represent bottlenecks for the production of various heterologous proteins at significant concentrations. Conclusion While inactivation of quality control systems has the potential to improve protein production yields, this could be achieved at the expense of product quality. Mechanisms underlying degradation of secretory proteins are nowadays well understood and often controllable. It will therefore be a major challenge for future research to identify and modulate quality control systems of B. subtilis that limit the production of high quality protein complexes and membrane proteins, and to enhance those systems that facilitate assembly of these proteins.
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Affiliation(s)
- Jessica C Zweers
- Department of Medical Microbiology, University Medical Center Groningen and University of Groningen, Hanzeplein 1, P,O, Box 30001, 9700 RB Groningen, The Netherlands.
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Erlandson KJ, Or E, Osborne AR, Rapoport TA. Analysis of polypeptide movement in the SecY channel during SecA-mediated protein translocation. J Biol Chem 2008; 283:15709-15. [PMID: 18359943 PMCID: PMC2409214 DOI: 10.1074/jbc.m710356200] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
In bacteria most secretory proteins are transported across the plasma
membrane by the interplay of the ATPase SecA with the translocation channel
formed by the SecY complex; SecA uses cycles of ATP hydrolysis to
“push” consecutive segments of a polypeptide substrate through the
channel. Here we have addressed the mechanism of this process by following the
fate of stalled translocation intermediates. These were generated by using a
polypeptide substrate containing a bulky disulfide-bonded loop, thus
preventing the final residues from passing through the channel. Protease
protection experiments showed that the intermediates were stable in the
presence of ATP and could complete translocation once the block was removed.
The translocation intermediate was also stable when SecA associated with
ATPγS, a poorly hydrolyzable ATP analog, or ADP plus AlF4,
which mimics the transition state during ATP hydrolysis. In contrast, when
SecA was in its ADP-bound state, the translocating polypeptide moved back into
the cytosol, as indicated by the disappearance of the protected fragment.
Backsliding was not significantly altered by deletion of the plug domain, a
short helix in the center of the SecY channel, but it was slowed down when
changes were introduced into the pore ring, the constriction of the
hourglass-shaped channel. In all cases, backsliding was significantly slower
than forward translocation. Together, these data suggest that SecA binds the
polypeptide chain in its ATP state and releases it in the ADP state. The
channel itself does not bind the polypeptide chain but provides
“friction” that minimizes backsliding when ADP-bound SecA resets
to “grab” the next segment of the substrate.
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Affiliation(s)
- Karl J Erlandson
- Howard Hughes Medical Institute and Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
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De Rasmo D, Panelli D, Sardanelli AM, Papa S. cAMP-dependent protein kinase regulates the mitochondrial import of the nuclear encoded NDUFS4 subunit of complex I. Cell Signal 2008; 20:989-97. [PMID: 18291624 DOI: 10.1016/j.cellsig.2008.01.017] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2008] [Revised: 01/22/2008] [Accepted: 01/23/2008] [Indexed: 11/29/2022]
Abstract
The subunits of complex I encoded by the mammalian nuclear genes NDUFS4 (AQDQ protein) and NDUFB11 (ESSS protein) contain serine/threonine consensus phosphorylation sequences (CPS) in their presequence, the first also in the C-terminus. We have studied the impact of PKA mediated phosphorylation on the mitochondrial import of in vitro and in vivo synthesized NDUFS4 protein. The intramitochondrial accumulation of the mature form of in vitro synthesized NDUFS4 protein, but not that of ESSS protein, was promoted by PKA and depressed by alkaline phosphatase (AP). In HeLa cells, control or transfected with the NDUFS4 cDNA construct, the mitochondrial level of mature NDUFS4 protein was promoted by 8-Br-cAMP and depressed by H89. Ser173Ala mutagenesis in the C-terminus CPS abolished the appearance in mitochondria of the mature form of NDUFS4 protein. The promoting effect of PKA on the mitochondrial accumulation of mature NDUFS4 protein appears to be due to inhibition of its retrograde diffusion into the cytosol.
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Affiliation(s)
- Domenico De Rasmo
- Department of Medical Biochemistry, Biology and Physics (DIBIFIM), University of Bari, 70124 Bari, Italy
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Charpian S, Przyborski JM. Protein Transport Across the Parasitophorous Vacuole of Plasmodium falciparum: Into the Great Wide Open. Traffic 2007; 9:157-65. [DOI: 10.1111/j.1600-0854.2007.00648.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Sec- and Tat-mediated protein secretion across the bacterial cytoplasmic membrane--distinct translocases and mechanisms. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2007; 1778:1735-56. [PMID: 17935691 DOI: 10.1016/j.bbamem.2007.07.015] [Citation(s) in RCA: 343] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2007] [Revised: 07/23/2007] [Accepted: 07/24/2007] [Indexed: 11/20/2022]
Abstract
In bacteria, two major pathways exist to secrete proteins across the cytoplasmic membrane. The general Secretion route, termed Sec-pathway, catalyzes the transmembrane translocation of proteins in their unfolded conformation, whereupon they fold into their native structure at the trans-side of the membrane. The Twin-arginine translocation pathway, termed Tat-pathway, catalyses the translocation of secretory proteins in their folded state. Although the targeting signals that direct secretory proteins to these pathways show a high degree of similarity, the translocation mechanisms and translocases involved are vastly different.
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