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Pardo-Avila F, Kudva R, Levitt M, von Heijne G. Single-residue effects on the behavior of a nascent polypeptide chain inside the ribosome exit tunnel. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.20.608737. [PMID: 39229094 PMCID: PMC11370347 DOI: 10.1101/2024.08.20.608737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 09/05/2024]
Abstract
Nascent polypeptide chains (NCs) are extruded from the ribosome through an exit tunnel (ET) traversing the large ribosomal subunit. The ET's irregular and chemically complex wall allows for various NC-ET interactions. Translational arrest peptides (APs) bind in the ET to induce translational arrest, a property that can be exploited to study NC-ET interactions by Force Profile Analysis (FPA). We employed FPA and molecular dynamics (MD) simulations to investigate how individual residues placed in a glycine-serine repeat segment within an AP-stalled NC interact with the ET to exert a pulling force on the AP and release stalling. Our results indicate that large and hydrophobic residues generate a pulling force on the NC when placed ≳10 residues away from the peptidyl transfer center (PTC). Moreover, an asparagine placed 12 residues from the PTC makes a specific stabilizing interaction with the tip of ribosomal protein uL22 that reduces the pulling force on the NC, while a lysine or leucine residue in the same position increases the pulling force. Finally, the MD simulations suggest how the Mannheimia succiniproducens SecM AP interacts with the ET to promote translational stalling.
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Affiliation(s)
- Fátima Pardo-Avila
- Department of Structural Biology, Stanford University, Palo Alto, CA, USA
| | - Renuka Kudva
- Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden
- Science for Life Laboratory Stockholm University, Box 1031, SE-171 21 Solna, Sweden
| | - Michael Levitt
- Department of Structural Biology, Stanford University, Palo Alto, CA, USA
| | - Gunnar von Heijne
- Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden
- Science for Life Laboratory Stockholm University, Box 1031, SE-171 21 Solna, Sweden
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2
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A male germ-cell-specific ribosome controls male fertility. Nature 2022; 612:725-731. [PMID: 36517592 DOI: 10.1038/s41586-022-05508-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 11/01/2022] [Indexed: 12/23/2022]
Abstract
Ribosomes are highly sophisticated translation machines that have been demonstrated to be heterogeneous in the regulation of protein synthesis1,2. Male germ cell development involves complex translational regulation during sperm formation3. However, it remains unclear whether translation during sperm formation is performed by a specific ribosome. Here we report a ribosome with a specialized nascent polypeptide exit tunnel, RibosomeST, that is assembled with the male germ-cell-specific protein RPL39L, the paralogue of core ribosome (RibosomeCore) protein RPL39. Deletion of RibosomeST in mice causes defective sperm formation, resulting in substantially reduced fertility. Our comparison of single-particle cryo-electron microscopy structures of ribosomes from mouse kidneys and testes indicates that RibosomeST features a ribosomal polypeptide exit tunnel of distinct size and charge states compared with RibosomeCore. RibosomeST predominantly cotranslationally regulates the folding of a subset of male germ-cell-specific proteins that are essential for the formation of sperm. Moreover, we found that specialized functions of RibosomeST were not replaceable by RibosomeCore. Taken together, identification of this sperm-specific ribosome should greatly expand our understanding of ribosome function and tissue-specific regulation of protein expression pattern in mammals.
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3
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Cotranslational Translocation and Folding of a Periplasmic Protein Domain in Escherichia coli. J Mol Biol 2021; 433:167047. [PMID: 33989648 DOI: 10.1016/j.jmb.2021.167047] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Revised: 04/13/2021] [Accepted: 05/04/2021] [Indexed: 01/26/2023]
Abstract
In Gram-negative bacteria, periplasmic domains in inner membrane proteins are cotranslationally translocated across the inner membrane through the SecYEG translocon. To what degree such domains also start to fold cotranslationally is generally difficult to determine using currently available methods. Here, we apply Force Profile Analysis (FPA) - a method where a translational arrest peptide is used to detect folding-induced forces acting on the nascent polypeptide - to follow the cotranslational translocation and folding of the large periplasmic domain of the E. coli inner membrane protease LepB in vivo. Membrane insertion of LepB's two N-terminal transmembrane helices is initiated when their respective N-terminal ends reach 45-50 residues away from the peptidyl transferase center (PTC) in the ribosome. The main folding transition in the periplasmic domain involves all but the ~15 most C-terminal residues of the protein and happens when the C-terminal end of the folded part is ~70 residues away from the PTC; a smaller putative folding intermediate is also detected. This implies that wildtype LepB folds post-translationally in vivo, and shows that FPA can be used to study both co- and post-translational protein folding in the periplasm.
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4
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Zimmer MH, Niesen MJM, Miller TF. Force transduction creates long-ranged coupling in ribosomes stalled by arrest peptides. Biophys J 2021; 120:2425-2435. [PMID: 33932440 DOI: 10.1016/j.bpj.2021.03.041] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 03/09/2021] [Accepted: 03/19/2021] [Indexed: 11/16/2022] Open
Abstract
Force-sensitive arrest peptides regulate protein biosynthesis by stalling the ribosome as they are translated. Synthesis can be resumed when the nascent arrest peptide experiences a pulling force of sufficient magnitude to break the stall. Efficient stalling is dependent on the specific identity of a large number of amino acids, including amino acids that are tens of angstroms away from the peptidyl transferase center (PTC). The mechanism of force-induced restart and the role of these essential amino acids far from the PTC is currently unknown. We use hundreds of independent molecular dynamics trajectories spanning over 120 μs in combination with kinetic analysis to characterize multiple barriers along the force-induced restart pathway for the arrest peptide SecM. We find that the essential amino acids far from the PTC play a major role in controlling the transduction of applied force. In successive states along the stall-breaking pathway, the applied force propagates up the nascent chain until it reaches the C-terminus of SecM and the PTC, inducing conformational changes that allow for restart of translation. A similar mechanism of force propagation through multiple states is observed in the VemP stall-breaking pathway, but secondary structure in VemP allows for heterogeneity in the order of transitions through intermediate states. Results from both arrest peptides explain how residues that are tens of angstroms away from the catalytic center of the ribosome impact stalling efficiency by mediating the response to an applied force and shielding the amino acids responsible for maintaining the stalled state of the PTC.
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Affiliation(s)
- Matthew H Zimmer
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California
| | - Michiel J M Niesen
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California
| | - Thomas F Miller
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California.
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5
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Nicolaus F, Metola A, Mermans D, Liljenström A, Krč A, Abdullahi SM, Zimmer M, Miller Iii TF, von Heijne G. Residue-by-residue analysis of cotranslational membrane protein integration in vivo. eLife 2021; 10:64302. [PMID: 33554862 PMCID: PMC7886326 DOI: 10.7554/elife.64302] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 02/05/2021] [Indexed: 12/16/2022] Open
Abstract
We follow the cotranslational biosynthesis of three multispanning Escherichia coli inner membrane proteins in vivo using high-resolution force profile analysis. The force profiles show that the nascent chain is subjected to rapidly varying pulling forces during translation and reveal unexpected complexities in the membrane integration process. We find that an N-terminal cytoplasmic domain can fold in the ribosome exit tunnel before membrane integration starts, that charged residues and membrane-interacting segments such as re-entrant loops and surface helices flanking a transmembrane helix (TMH) can advance or delay membrane integration, and that point mutations in an upstream TMH can affect the pulling forces generated by downstream TMHs in a highly position-dependent manner, suggestive of residue-specific interactions between TMHs during the integration process. Our results support the 'sliding' model of translocon-mediated membrane protein integration, in which hydrophobic segments are continually exposed to the lipid bilayer during their passage through the SecYEG translocon.
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Affiliation(s)
- Felix Nicolaus
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Ane Metola
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Daphne Mermans
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Amanda Liljenström
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Ajda Krč
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.,Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ljubljana, Slovenia
| | | | - Matthew Zimmer
- California Institute of Technology, Division of Chemistry and Chemical Engineering, Pasadena, United States
| | - Thomas F Miller Iii
- California Institute of Technology, Division of Chemistry and Chemical Engineering, Pasadena, United States
| | - Gunnar von Heijne
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.,Science for Life Laboratory Stockholm University, Solna, Sweden
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6
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Sahakyan H, Nazaryan K, Mushegian A, Sorokina I. Energy-dependent protein folding: modeling how a protein folding machine may work. F1000Res 2021; 10:3. [PMID: 33633838 PMCID: PMC7898354 DOI: 10.12688/f1000research.28175.1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 12/18/2020] [Indexed: 12/17/2022] Open
Abstract
Background: Proteins fold robustly and reproducibly in vivo, but many cannot fold in vitro in isolation from cellular components. Despite the remarkable progress that has been achieved by the artificial intelligence approaches in predicting the protein native conformations, the pathways that lead to such conformations, either in vitro or in vivo, remain largely unknown. The slow progress in recapitulating protein folding pathways in silico may be an indication of the fundamental deficiencies in our understanding of folding as it occurs in nature. Here we consider the possibility that protein folding in living cells may not be driven solely by the decrease in Gibbs free energy and propose that protein folding in vivo should be modeled as an active energy-dependent process. The mechanism of action of such a protein folding machine might include direct manipulation of the peptide backbone. Methods: To show the feasibility of a protein folding machine, we conducted molecular dynamics simulations that were augmented by the application of mechanical force to rotate the C-terminal amino acid while simultaneously limiting the N-terminal amino acid movements. Results: Remarkably, the addition of this simple manipulation of peptide backbones to the standard molecular dynamics simulation indeed facilitated the formation of native structures in five diverse alpha-helical peptides. Steric clashes that arise in the peptides due to the forced directional rotation resulted in the behavior of the peptide backbone no longer resembling a freely jointed chain. Conclusions: These simulations show the feasibility of a protein folding machine operating under the conditions when the movements of the polypeptide backbone are restricted by applying external forces and constraints. Further investigation is needed to see whether such an effect may play a role during co-translational protein folding in vivo and how it can be utilized to facilitate folding of proteins in artificial environments.
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Affiliation(s)
- Harutyun Sahakyan
- Institute of Molecular Biology, Academy of Sciences of Republic of Armenia, Yerevan, Armenia
| | - Karen Nazaryan
- Institute of Molecular Biology, Academy of Sciences of Republic of Armenia, Yerevan, Armenia
| | - Arcady Mushegian
- Division of Molecular and Cellular Biosciences, National Science Foundation, Alexandria, USA
- Clare Hall College, University of Cambridge, Cambridge, UK
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7
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Elfageih R, Karyolaimos A, Kemp G, de Gier J, von Heijne G, Kudva R. Cotranslational folding of alkaline phosphatase in the periplasm of Escherichia coli. Protein Sci 2020; 29:2028-2037. [PMID: 32790204 PMCID: PMC7513700 DOI: 10.1002/pro.3927] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 08/08/2020] [Accepted: 08/11/2020] [Indexed: 01/10/2023]
Abstract
Cotranslational protein folding studies using Force Profile Analysis, a method where the SecM translational arrest peptide is used to detect folding-induced forces acting on the nascent polypeptide, have so far been limited mainly to small domains of cytosolic proteins that fold in close proximity to the translating ribosome. In this study, we investigate the cotranslational folding of the periplasmic, disulfide bond-containing Escherichia coli protein alkaline phosphatase (PhoA) in a wild-type strain background and a strain background devoid of the periplasmic thiol: disulfide interchange protein DsbA. We find that folding-induced forces can be transmitted via the nascent chain from the periplasm to the polypeptide transferase center in the ribosome, a distance of ~160 Å, and that PhoA appears to fold cotranslationally via at least two disulfide-stabilized folding intermediates. Thus, Force Profile Analysis can be used to study cotranslational folding of proteins in an extra-cytosolic compartment, like the periplasm.
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Affiliation(s)
- Rageia Elfageih
- Department of Biochemistry and BiophysicsStockholm UniversityStockholmSweden
| | | | - Grant Kemp
- Department of Biochemistry and BiophysicsStockholm UniversityStockholmSweden
| | - Jan‐Willem de Gier
- Department of Biochemistry and BiophysicsStockholm UniversityStockholmSweden
| | - Gunnar von Heijne
- Department of Biochemistry and BiophysicsStockholm UniversityStockholmSweden
- Science for Life Laboratory Stockholm UniversitySolnaSweden
| | - Renuka Kudva
- Department of Biochemistry and BiophysicsStockholm UniversityStockholmSweden
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8
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Cotranslational folding cooperativity of contiguous domains of α-spectrin. Proc Natl Acad Sci U S A 2020; 117:14119-14126. [PMID: 32513720 DOI: 10.1073/pnas.1909683117] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Proteins synthesized in the cell can begin to fold during translation before the entire polypeptide has been produced, which may be particularly relevant to the folding of multidomain proteins. Here, we study the cotranslational folding of adjacent domains from the cytoskeletal protein α-spectrin using force profile analysis (FPA). Specifically, we investigate how the cotranslational folding behavior of the R15 and R16 domains are affected by their neighboring R14 and R16, and R15 and R17 domains, respectively. Our results show that the domains impact each other's folding in distinct ways that may be important for the efficient assembly of α-spectrin, and may reduce its dependence on chaperones. Furthermore, we directly relate the experimentally observed yield of full-length protein in the FPA assay to the force exerted by the folding protein in piconewtons. By combining pulse-chase experiments to measure the rate at which the arrested protein is converted into full-length protein with a Bell model of force-induced rupture, we estimate that the R16 domain exerts a maximal force on the nascent chain of ∼15 pN during cotranslational folding.
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9
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Nascent SecM chain interacts with outer ribosomal surface to stabilize translation arrest. Biochem J 2020; 477:557-566. [PMID: 31913464 PMCID: PMC6993859 DOI: 10.1042/bcj20190723] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 01/06/2020] [Accepted: 01/08/2020] [Indexed: 11/28/2022]
Abstract
SecM, a bacterial secretion monitor protein, posttranscriptionally regulates downstream gene expression via translation elongation arrest. SecM contains a characteristic amino acid sequence called the arrest sequence at its C-terminus, and this sequence acts within the ribosomal exit tunnel to stop translation. It has been widely assumed that the arrest sequence within the ribosome tunnel is sufficient for translation arrest. We have previously shown that the nascent SecM chain outside the ribosomal exit tunnel stabilizes translation arrest, but the molecular mechanism is unknown. In this study, we found that residues 57–98 of the nascent SecM chain are responsible for stabilizing translation arrest. We performed alanine/serine-scanning mutagenesis of residues 57–98 to identify D79, Y80, W81, H84, R87, I90, R91, and F95 as the key residues responsible for stabilization. The residues were predicted to be located on and near an α-helix-forming segment. A striking feature of the α-helix is the presence of an arginine patch, which interacts with the negatively charged ribosomal surface. A photocross-linking experiment showed that Y80 is adjacent to the ribosomal protein L23, which is located next to the ribosomal exit tunnel when translation is arrested. Thus, the folded nascent SecM chain that emerges from the ribosome exit tunnel interacts with the outer surface of the ribosome to stabilize translation arrest.
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10
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Abstract
As the influence of translation rates on protein folding and function has come to light, the mechanisms by which translation speed is modulated have become an important issue. One mechanism entails the generation of force by the nascent protein. Cotranslational processes, such as nascent protein folding, the emergence of unfolded nascent chain segments from the ribosome's exit tunnel, and insertion of the nascent chain into or translocation of the nascent chain through membranes, can generate forces that are transmitted back to the peptidyl transferase center and affect translation rates. In this Perspective, we examine the processes that generate these forces, the mechanisms of transmission along the ribosomal exit tunnel to the peptidyl transferase center, and the effects of force on the ribosome's catalytic cycle. We also discuss the physical models that have been developed to predict and explain force generation for individual processes and speculate about other processes that may generate forces that have yet to be tested.
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Affiliation(s)
- Sarah Leininger
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Karthik Narayan
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802, 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
- Institute for CyberScience, Pennsylvania State University, University Park, Pennsylvania 16802, United States
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11
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The role of circular dichroism spectroscopy in the era of integrative structural biology. Curr Opin Struct Biol 2019; 58:191-196. [DOI: 10.1016/j.sbi.2019.04.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Revised: 03/28/2019] [Accepted: 04/01/2019] [Indexed: 12/25/2022]
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12
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Ito K, Mori H, Chiba S. Monitoring substrate enables real-time regulation of a protein localization pathway. FEMS Microbiol Lett 2019; 365:4983124. [PMID: 29790986 DOI: 10.1093/femsle/fny109] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 04/23/2018] [Indexed: 12/20/2022] Open
Abstract
Protein localization machinery supports cell survival and physiology, suggesting the potential importance of its expression regulation. Here, we summarize a remarkable scheme of regulation, which allows real-time feedback regulation of the machinery expression. A class of regulatory nascent polypeptides, called monitoring substrates, undergoes force-sensitive translation arrest. The resulting ribosome stalling on the mRNA then affects mRNA folding to expose the ribosome-binding site of the downstream target gene and upregulate its translation. The target gene encodes a component of the localization machinery, whose physical action against the monitoring substrate leads to arrest cancellation. Thus, this scheme of feedback loop allows the cell to adjust the amount of the machinery to correlate inversely with the effectiveness of the process at a given moment. The system appears to have emerged late in evolution, in which a narrow range of organisms selected a distinct monitoring substrate-machinery combination. Currently, regulatory systems of SecM-SecA, VemP-SecDF2 and MifM-YidC2 are known to occur in different bacterial species.
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Affiliation(s)
- Koreaki Ito
- Faculty of Life Sciences and Institute for Protein Dynamics, Kyoto Sangyo University, Kita-Ku, Kyoto 603-8555, Japan
| | - Hiroyuki Mori
- Japan and Institute for Frontier Life and Medical Sciences, Kyoto University, Sakyo-Ku, Kyoto, 606-8507, Japan
| | - Shinobu Chiba
- Faculty of Life Sciences and Institute for Protein Dynamics, Kyoto Sangyo University, Kita-Ku, Kyoto 603-8555, Japan
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13
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Kemp G, Kudva R, de la Rosa A, von Heijne G. Force-Profile Analysis of the Cotranslational Folding of HemK and Filamin Domains: Comparison of Biochemical and Biophysical Folding Assays. J Mol Biol 2019; 431:1308-1314. [DOI: 10.1016/j.jmb.2019.01.043] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 01/27/2019] [Accepted: 01/29/2019] [Indexed: 12/31/2022]
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14
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Bañó-Polo M, Baeza-Delgado C, Tamborero S, Hazel A, Grau B, Nilsson I, Whitley P, Gumbart JC, von Heijne G, Mingarro I. Transmembrane but not soluble helices fold inside the ribosome tunnel. Nat Commun 2018; 9:5246. [PMID: 30531789 PMCID: PMC6286305 DOI: 10.1038/s41467-018-07554-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 11/09/2018] [Indexed: 12/15/2022] Open
Abstract
Integral membrane proteins are assembled into the ER membrane via a continuous ribosome-translocon channel. The hydrophobicity and thickness of the core of the membrane bilayer leads to the expectation that transmembrane (TM) segments minimize the cost of harbouring polar polypeptide backbones by adopting a regular pattern of hydrogen bonds to form α-helices before integration. Co-translational folding of nascent chains into an α-helical conformation in the ribosomal tunnel has been demonstrated previously, but the features governing this folding are not well understood. In particular, little is known about what features influence the propensity to acquire α-helical structure in the ribosome. Using in vitro translation of truncated nascent chains trapped within the ribosome tunnel and molecular dynamics simulations, we show that folding in the ribosome is attained for TM helices but not for soluble helices, presumably facilitating SRP (signal recognition particle) recognition and/or a favourable conformation for membrane integration upon translocon entry.
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Affiliation(s)
- Manuel Bañó-Polo
- Estructura de Recerca Interdisciplinar en Biotecnologia i Biomedicina (ERI BioTecMed), Departament de Bioquímica i Biologia Molecular, Universitat de València, E-46100, Burjassot, Spain
| | - Carlos Baeza-Delgado
- Estructura de Recerca Interdisciplinar en Biotecnologia i Biomedicina (ERI BioTecMed), Departament de Bioquímica i Biologia Molecular, Universitat de València, E-46100, Burjassot, Spain
| | - Silvia Tamborero
- Estructura de Recerca Interdisciplinar en Biotecnologia i Biomedicina (ERI BioTecMed), Departament de Bioquímica i Biologia Molecular, Universitat de València, E-46100, Burjassot, Spain
| | - Anthony Hazel
- School of Physics, School of Chemistry and Biochemistry, Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, USA
| | - Brayan Grau
- Estructura de Recerca Interdisciplinar en Biotecnologia i Biomedicina (ERI BioTecMed), Departament de Bioquímica i Biologia Molecular, Universitat de València, E-46100, Burjassot, Spain
| | - IngMarie Nilsson
- Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, SE-10691, Stockholm, Sweden
| | - Paul Whitley
- Department of Biology and Biochemistry, Centre for Regenerative Medicine, University of Bath, Bath, BA2 7AY, UK
| | - James C Gumbart
- School of Physics, School of Chemistry and Biochemistry, Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, USA
| | - Gunnar von Heijne
- Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, SE-10691, Stockholm, Sweden
| | - Ismael Mingarro
- Estructura de Recerca Interdisciplinar en Biotecnologia i Biomedicina (ERI BioTecMed), Departament de Bioquímica i Biologia Molecular, Universitat de València, E-46100, Burjassot, Spain.
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15
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Kaiser CM, Liu K. Folding up and Moving on-Nascent Protein Folding on the Ribosome. J Mol Biol 2018; 430:4580-4591. [PMID: 29981746 PMCID: PMC6384192 DOI: 10.1016/j.jmb.2018.06.050] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 06/26/2018] [Accepted: 06/28/2018] [Indexed: 01/01/2023]
Abstract
All cellular proteins are synthesized by the ribosome, an intricate molecular machine that translates the information of protein coding genes into the amino acid alphabet. The linear polypeptides synthesized by the ribosome must generally fold into specific three-dimensional structures to become biologically active. Folding has long been recognized to begin before synthesis is complete. Recently, biochemical and biophysical studies have shed light onto how the ribosome shapes the folding pathways of nascent proteins. Here, we discuss recent progress that is beginning to define the role of the ribosome in the folding of newly synthesized polypeptides.
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Affiliation(s)
- Christian M Kaiser
- Department of Biology, Johns Hopkins University, 3400 N Charles St., Baltimore, MD 21218, USA; Department of Biophysics, Johns Hopkins University, 3400 N Charles St., Baltimore, MD 21218, USA.
| | - Kaixian Liu
- Department of Biology, Johns Hopkins University, 3400 N Charles St., Baltimore, MD 21218, USA; CMDB Graduate Program, Johns Hopkins University, 3400 N Charles St., Baltimore, MD 21218, USA
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16
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Investigating the Effect of Chain Connectivity on the Folding of a Beta-Sheet Protein On and Off the Ribosome. J Mol Biol 2018; 430:5207-5216. [PMID: 30365950 PMCID: PMC6288478 DOI: 10.1016/j.jmb.2018.10.011] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 09/11/2018] [Accepted: 10/16/2018] [Indexed: 11/21/2022]
Abstract
Determining the relationship between protein folding pathways on and off the ribosome remains an important area of investigation in biology. Studies on isolated domains have shown that alteration of the separation of residues in a polypeptide chain, while maintaining their spatial contacts, may affect protein stability and folding pathway. Due to the vectorial emergence of the polypeptide chain from the ribosome, chain connectivity may have an important influence upon cotranslational folding. Using MATH, an all β-sandwich domain, we investigate whether the connectivity of residues and secondary structure elements is a key determinant of when cotranslational folding can occur on the ribosome. From Φ-value analysis, we show that the most structured region of the transition state for folding in MATH includes the N and C terminal strands, which are located adjacent to each other in the structure. However, arrest peptide force-profile assays show that wild-type MATH is able to fold cotranslationally, while some C-terminal residues remain sequestered in the ribosome, even when destabilized by 2–3 kcal mol−1. We show that, while this pattern of Φ-values is retained in two circular permutants in our studies of the isolated domains, one of these permutants can fold only when fully emerged from the ribosome. We propose that in the case of MATH, onset of cotranslational folding is determined by the ability to form a sufficiently stable folding nucleus involving both β-sheets, rather than by the location of the terminal strands in the ribosome tunnel. Adjacent N and C terminal strands are most structured region in the transition state. Two circular permutants retain the same folding pathway as wild-type MATH. On the ribosome, early emergence of terminal strands does not promote earlier folding. Formation of both β-sheets is energetically critical for folding on the ribosome. Folding pathway minimizes formation of partly structured states prone to mis-folding.
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Farías-Rico JA, Ruud Selin F, Myronidi I, Frühauf M, von Heijne G. Effects of protein size, thermodynamic stability, and net charge on cotranslational folding on the ribosome. Proc Natl Acad Sci U S A 2018; 115:E9280-E9287. [PMID: 30224455 PMCID: PMC6176590 DOI: 10.1073/pnas.1812756115] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
During the last five decades, studies of protein folding in dilute buffer solutions have produced a rich picture of this complex process. In the cell, however, proteins can start to fold while still attached to the ribosome (cotranslational folding) and it is not yet clear how the ribosome affects the folding of protein domains of different sizes, thermodynamic stabilities, and net charges. Here, by using arrest peptides as force sensors and on-ribosome pulse proteolysis, we provide a comprehensive picture of how the distance from the peptidyl transferase center in the ribosome at which proteins fold correlates with protein size. Moreover, an analysis of a large collection of mutants of the Escherichia coli ribosomal protein S6 shows that the force exerted on the nascent chain by protein folding varies linearly with the thermodynamic stability of the folded state, and that the ribosome environment disfavors folding of domains of high net-negative charge.
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Affiliation(s)
| | - Frida Ruud Selin
- Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Ioanna Myronidi
- Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Marie Frühauf
- Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Gunnar von Heijne
- Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden;
- Science for Life Laboratory, Stockholm University, SE-171 21 Solna, Sweden
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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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19
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Kubyshkin V, Acevedo-Rocha CG, Budisa N. On universal coding events in protein biogenesis. Biosystems 2018; 164:16-25. [DOI: 10.1016/j.biosystems.2017.10.004] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Revised: 10/02/2017] [Accepted: 10/03/2017] [Indexed: 12/14/2022]
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