1
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Chu X, Suo Z, Wang J. Confinement and Crowding Effects on Folding of a Multidomain Y-Family DNA Polymerase. J Chem Theory Comput 2020; 16:1319-1332. [PMID: 31972079 PMCID: PMC7258223 DOI: 10.1021/acs.jctc.9b01146] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Proteins in vivo endure highly various interactions from the luxuriant surrounding macromolecular cosolutes. Confinement and macromolecular crowding are the two major effects that should be considered while comparing the results of protein dynamics from in vitro to in vivo. However, efforts have been largely focused on single domain protein folding up to now, and the quantifications of the in vivo effects in terms of confinements and crowders on modulating the structure and dynamics as well as the physical understanding of the underlying mechanisms on multidomain protein folding are still challenging. Here we developed a topology-based model to investigate folding of a multidomain Y-family DNA polymerase (DPO4) within spherical confined space and in the presence of repulsive and attractive crowders. We uncovered that the entropic component of the thermodynamic driving force led by confinements and repulsive crowders increases the stability of folded states relative to the folding intermediates and unfolded states, while the enthalpic component of the thermodynamic driving force led by attractive crowders gives rise to the opposite effects with less stability. We found that the shapes of DPO4 conformations influenced by the confinements and the crowders are quite different even when only the entropic component of the thermodynamic driving force is considered. We uncovered that under all in vivo conditions, the folding cooperativity of DPO4 decreases compared to that in bulk. We showed that the loss of folding cooperativity can promote the sequential domain-wise folding, which was widely found in cotranslational multidomain protein folding, and effectively prohibit the backtracking led by topological frustrations during multidomain protein folding processes.
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Affiliation(s)
- Xiakun Chu
- Department of Chemistry, State University of New York at Stony Brook, Stony Brook, New York 11794, United States
| | - Zucai Suo
- Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, Florida 32306, United States
| | - Jin Wang
- Department of Chemistry, State University of New York at Stony Brook, Stony Brook, New York 11794, United States
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2
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Shaham G, Tuller T. Genome scale analysis of Escherichia coli with a comprehensive prokaryotic sequence-based biophysical model of translation initiation and elongation. DNA Res 2018; 25:195-205. [PMID: 29161365 PMCID: PMC6012489 DOI: 10.1093/dnares/dsx049] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 11/04/2017] [Indexed: 11/17/2022] Open
Abstract
Translation initiation in prokaryotes is affected by the mRNA folding and interaction of the ribosome binding site with the ribosomal RNA. The elongation rate is affected, among other factors, by the local biophysical properties of the coding regions, the decoding rates of different codons, and the interactions among ribosomes. Currently, there is no comprehensive biophysical model of translation that enables the prediction of mRNA translation dynamics based only on the transcript sequence and while considering all of these fundamental aspects of translation. In this study, we provide, for the first time, a computational simulative biophysical model of both translation initiation and elongation with all aspects mentioned above. We demonstrate our model performance and advantages focusing on Escherichia coli genes. We further show that the model enables prediction of translation rate, protein levels, and ribosome densities. In addition, our model enables quantifying the effect of silent mutations on translation rate in different parts of the transcript, the relative effect of mutations on translation initiation and elongation, and the effect of mutations on ribosome traffic jams. Thus, unlike previous models, the proposed one provides comprehensive information, facilitating future research in disciplines such as molecular evolution, synthetic biology, and functional genomics. A toolkit to estimate translation dynamics of transcripts is available at: https://www.cs.tau.ac.il/∼tamirtul/transim.
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Affiliation(s)
- Gilad Shaham
- Department of Biomedical Engineering, The Engineering Faculty, Tel Aviv University, Israel
| | - Tamir Tuller
- Department of Biomedical Engineering, The Engineering Faculty, Tel Aviv University, Israel
- The Sagol School of Neuroscience, Tel-Aviv University, Tel-Aviv, Israel
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3
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Yang JR. Does mRNA structure contain genetic information for regulating co-translational protein folding? Zool Res 2018; 38:36-43. [PMID: 28271668 PMCID: PMC5368379 DOI: 10.13918/j.issn.2095-8137.2017.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Currently many facets of genetic information are illdefined. In particular, how protein folding is genetically regulated has been a long-standing issue for genetics and protein biology. And a generic mechanistic model with supports of genomic data is still lacking. Recent technological advances have enabled much needed genome-wide experiments. While putting the effect of codon optimality on debate, these studies have supplied mounting evidence suggesting a role of mRNA structure in the regulation of protein folding by modulating translational elongation rate. In conjunctions with previous theories, this mechanistic model of protein folding guided by mRNA structure shall expand our understandings of genetic information and offer new insights into various biomedical puzzles.
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Affiliation(s)
- Jian-Rong Yang
- Department of Biology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China.
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4
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Qi F, Motz M, Jung K, Lassak J, Frishman D. Evolutionary analysis of polyproline motifs in Escherichia coli reveals their regulatory role in translation. PLoS Comput Biol 2018; 14:e1005987. [PMID: 29389943 PMCID: PMC5811046 DOI: 10.1371/journal.pcbi.1005987] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Revised: 02/13/2018] [Accepted: 01/17/2018] [Indexed: 12/14/2022] Open
Abstract
Translation of consecutive prolines causes ribosome stalling, which is alleviated but cannot be fully compensated by the elongation factor P. However, the presence of polyproline motifs in about one third of the E. coli proteins underlines their potential functional importance, which remains largely unexplored. We conducted an evolutionary analysis of polyproline motifs in the proteomes of 43 E. coli strains and found evidence of evolutionary selection against translational stalling, which is especially pronounced in proteins with high translational efficiency. Against the overall trend of polyproline motif loss in evolution, we observed their enrichment in the vicinity of translational start sites, in the inter-domain regions of multi-domain proteins, and downstream of transmembrane helices. Our analysis demonstrates that the time gain caused by ribosome pausing at polyproline motifs might be advantageous in protein regions bracketing domains and transmembrane helices. Polyproline motifs might therefore be crucial for co-translational folding and membrane insertion. Polyproline motifs induce ribosome stalling during translation, but the functional significance of this effect remains unclear. Our evolutionary analysis of polyproline motifs reveals that they are disfavored in E. coli proteomes as a consequence of the reduced translation efficiency, supporting the conjecture that translation efficiency-based evolutionary pressure shapes protein sequences. Enrichment of polyproline motifs in the protein regions bracketing structural domains and transmembrane helices indicates their regulatory role in co-translational protein folding and transmembrane helix insertion. Polyproline motifs could thus serve as protein-level cis-acting elements, which directly regulate the rate of translation elongation.
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Affiliation(s)
- Fei Qi
- Department of Bioinformatics, Wissenschaftzentrum Weihenstephan, Technische Universität München, Freising, Germany
| | - Magdalena Motz
- Center for Integrated Protein Science Munich, Ludwig-Maximilians-Universität München, Munich, Germany.,Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Martinsried, Germany
| | - Kirsten Jung
- Center for Integrated Protein Science Munich, Ludwig-Maximilians-Universität München, Munich, Germany.,Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Martinsried, Germany
| | - Jürgen Lassak
- Center for Integrated Protein Science Munich, Ludwig-Maximilians-Universität München, Munich, Germany.,Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Martinsried, Germany
| | - Dmitrij Frishman
- Department of Bioinformatics, Wissenschaftzentrum Weihenstephan, Technische Universität München, Freising, Germany.,St Petersburg State Polytechnic University, St Petersburg, Russia
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5
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Abstract
Hypoxic-ischemic encephalopathy (HIE) is a disease that occurs when the brain is subjected to hypoxia, resulting in neuronal death and neurological deficits, with a poor prognosis. The mechanisms underlying hypoxic-ischemic brain injury include excitatory amino acid release, cellular proteolysis, reactive oxygen species generation, nitric oxide synthesis, and inflammation. The molecular and cellular changes in HIE include protein misfolding, aggregation, and destruction of organelles. The apoptotic pathways activated by ischemia and hypoxia include the mitochondrial pathway, the extrinsic Fas receptor pathway, and the endoplasmic reticulum stress-induced pathway. Numerous treatments for hypoxic-ischemic brain injury caused by HIE have been developed over the last half century. Hypothermia, xenon gas treatment, the use of melatonin and erythropoietin, and hypoxic-ischemic preconditioning have proven effective in HIE patients. Molecular chaperones are proteins ubiquitously present in both prokaryotes and eukaryotes. A large number of molecular chaperones are induced after brain ischemia and hypoxia, among which the heat shock proteins are the most important. Heat shock proteins not only maintain protein homeostasis; they also exert anti-apoptotic effects. Heat shock proteins maintain protein homeostasis by helping to transport proteins to their target destinations, assisting in the proper folding of newly synthesized polypeptides, regulating the degradation of misfolded proteins, inhibiting the aggregation of proteins, and by controlling the refolding of misfolded proteins. In addition, heat shock proteins exert anti-apoptotic effects by interacting with various signaling pathways to block the activation of downstream effectors in numerous apoptotic pathways, including the intrinsic pathway, the endoplasmic reticulum-stress mediated pathway and the extrinsic Fas receptor pathway. Molecular chaperones play a key role in neuroprotection in HIE. In this review, we provide an overview of the mechanisms of HIE and discuss the various treatment strategies. Given their critical role in the disease, molecular chaperones are promising therapeutic targets for HIE.
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Affiliation(s)
- Cong Hua
- Department of Neurosurgery, The First Hospital of Jilin University, Changchun, Jilin Province, China
| | - Wei-Na Ju
- Department of Neurology, The First Hospital of Jilin University, Changchun, Jilin Province, China
| | - Hang Jin
- Department of Neurology, The First Hospital of Jilin University, Changchun, Jilin Province, China
| | - Xin Sun
- Department of Neurology, The First Hospital of Jilin University, Changchun, Jilin Province, China
| | - Gang Zhao
- Department of Neurosurgery, The First Hospital of Jilin University, Changchun, Jilin Province, China
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6
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Faure G, Ogurtsov AY, Shabalina SA, Koonin EV. Role of mRNA structure in the control of protein folding. Nucleic Acids Res 2016; 44:10898-10911. [PMID: 27466388 PMCID: PMC5159526 DOI: 10.1093/nar/gkw671] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Revised: 07/12/2016] [Accepted: 07/14/2016] [Indexed: 11/13/2022] Open
Abstract
Specific structures in mRNA modulate translation rate and thus can affect protein folding. Using the protein structures from two eukaryotes and three prokaryotes, we explore the connections between the protein compactness, inferred from solvent accessibility, and mRNA structure, inferred from mRNA folding energy (ΔG). In both prokaryotes and eukaryotes, the ΔG value of the most stable 30 nucleotide segment of the mRNA (ΔGmin) strongly, positively correlates with protein solvent accessibility. Thus, mRNAs containing exceptionally stable secondary structure elements typically encode compact proteins. The correlations between ΔG and protein compactness are much more pronounced in predicted ordered parts of proteins compared to the predicted disordered parts, indicative of an important role of mRNA secondary structure elements in the control of protein folding. Additionally, ΔG correlates with the mRNA length and the evolutionary rate of synonymous positions. The correlations are partially independent and were used to construct multiple regression models which explain about half of the variance of protein solvent accessibility. These findings suggest a model in which the mRNA structure, particularly exceptionally stable RNA structural elements, act as gauges of protein co-translational folding by reducing ribosome speed when the nascent peptide needs time to form and optimize the core structure.
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Affiliation(s)
- Guilhem Faure
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Aleksey Y Ogurtsov
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Svetlana A Shabalina
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
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7
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D'Onofrio DJ, Abel DL. Redundancy of the genetic code enables translational pausing. Front Genet 2014; 5:140. [PMID: 24904640 PMCID: PMC4033003 DOI: 10.3389/fgene.2014.00140] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2014] [Accepted: 04/28/2014] [Indexed: 11/13/2022] Open
Abstract
The codon redundancy (“degeneracy”) found in protein-coding regions of mRNA also prescribes Translational Pausing (TP). When coupled with the appropriate interpreters, multiple meanings and functions are programmed into the same sequence of configurable switch-settings. This additional layer of Ontological Prescriptive Information (PIo) purposely slows or speeds up the translation-decoding process within the ribosome. Variable translation rates help prescribe functional folding of the nascent protein. Redundancy of the codon to amino acid mapping, therefore, is anything but superfluous or degenerate. Redundancy programming allows for simultaneous dual prescriptions of TP and amino acid assignments without cross-talk. This allows both functions to be coincident and realizable. We will demonstrate that the TP schema is a bona fide rule-based code, conforming to logical code-like properties. Second, we will demonstrate that this TP code is programmed into the supposedly degenerate redundancy of the codon table. We will show that algorithmic processes play a dominant role in the realization of this multi-dimensional code.
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Affiliation(s)
- David J D'Onofrio
- Control Systems Modeling and Simulation, General Dynamics Sterling Heights, MI, USA ; Department of Humanities and Science, Math Department, College of Humanities and Science, University of Phoenix Detroit, MI, USA
| | - David L Abel
- Department of ProtoBioCybernetics/ProtoBioSemiotics, The Gene Emergence Project of The Origin of Life Science Foundation, Inc. Greenbelt, MD, USA
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8
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Bhardwaj A. Investigating the role of site specific synonymous variation in disease association studies. Mitochondrion 2014; 16:83-8. [PMID: 24434286 DOI: 10.1016/j.mito.2013.12.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Revised: 12/15/2013] [Accepted: 12/24/2013] [Indexed: 02/05/2023]
Abstract
Synonymous codon changes may not always be neutral indicating their significance in disease association studies, which is almost always overlooked. Synonymous substitutions may affect protein-folding rates leading to protein misfolding and aggregation. Genome wide analysis of 2301 mitochondrial genomes is performed to evaluate the significance of synonymous codons in disease association studies. The analysis revealed usage of rare codons at several sites in mitochondrial genes with rare codon usage higher for hydrophobic amino acids. The analysis suggests that variation data in association studies should be analyzed using site-specific codon usage values to infer the potential phenotypic impact of synonymous changes.
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Affiliation(s)
- Anshu Bhardwaj
- Open Source Drug Discovery Unit, Council of Scientific and Industrial Research (CSIR), Delhi 110001, India.
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9
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Luo T, Park Y, Sun X, Liu C, Hu B. Protein misfolding, aggregation, and autophagy after brain ischemia. Transl Stroke Res 2013; 4:581-8. [PMID: 24323413 DOI: 10.1007/s12975-013-0299-5] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Revised: 10/17/2013] [Accepted: 10/20/2013] [Indexed: 01/02/2023]
Abstract
Ischemic brain injury is a common disorder linked to a variety of diseases. Significant progress has been made in our understanding of the underlying mechanisms. Previous studies show that protein misfolding, aggregation, and multiple organelle damage are major pathological events in postischemic neurons. The autophagy pathway is the chief route for bulk degradation of protein aggregates and damaged organelles. The latest studies suggest that impairment of autophagy contributes to abnormal protein aggregation and organelle damages after brain ischemia. This article reviews recent studies of protein misfolding, aggregation, and impairment of autophagy after brain ischemia.
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Affiliation(s)
- Tianfei Luo
- Shock, Trauma and Anesthesiology Research Center, Department of Anesthesiology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
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10
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Hoffmann A, Neupane K, Woodside MT. Single-molecule assays for investigating protein misfolding and aggregation. Phys Chem Chem Phys 2013; 15:7934-48. [PMID: 23612887 DOI: 10.1039/c3cp44564j] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Protein misfolding and aggregation are relevant to many fields. Recently, their investigation has experienced a revival as a central topic in the research of numerous human diseases, including Parkinson's and Alzheimer's. Much has been learned from ensemble biochemical approaches, but the inherently heterogeneous nature of the underlying processes has obscured many important details. Single-molecule techniques offer unique capabilities to study heterogeneous systems, while providing high temporal and structural resolution to characterize them. In this Perspective, we give an overview of the single-molecule assays that have been applied to protein misfolding and aggregation, which are mainly based on fluorescence and force spectroscopy. We describe some of the technical challenges involved in studying aggregation at the single-molecule level and discuss what has been learned about aggregation mechanisms from the different approaches.
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Affiliation(s)
- Armin Hoffmann
- Department of Physics, University of Alberta, Edmonton, AB, Canada
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11
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Bhattacharya A, Best RB, Mittal J. Smoothing of the GB1 hairpin folding landscape by interfacial confinement. Biophys J 2013; 103:596-600. [PMID: 22947876 DOI: 10.1016/j.bpj.2012.07.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2012] [Revised: 06/26/2012] [Accepted: 07/02/2012] [Indexed: 11/30/2022] Open
Abstract
We study the effects of confinement between planar walls on the folding thermodynamics of a β-hairpin, using large-scale replica-exchange molecular-dynamics simulations with an all-atom model and explicit solvent. We find that the folding free-energy landscape of this peptide observed in bulk is significantly modified when the peptide is confined between the walls. Most notably, the propensity of the peptide to form a misfolded state observed in the bulk solution becomes negligible under confinement. The absence of the misfolded state under confinement can be explained by an increased tendency of hydrophobic aromatic side chains to stay near the walls, because the misfolded state is characterized by a nonnative arrangement of aromatic side chains. These results from a simple confinement model may provide clues about the role of chaperonin confinement in smoothing folding landscapes by avoiding trapped intermediates.
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Affiliation(s)
| | - Robert B Best
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Jeetain Mittal
- Department of Chemical Engineering, Lehigh University, Bethlehem, Pennsylvania.
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12
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Kumar R. Role of androgen receptor polyQ chain elongation in Kennedy's disease and use of natural osmolytes as potential therapeutic targets. IUBMB Life 2012; 64:879-84. [PMID: 23024039 DOI: 10.1002/iub.1088] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2012] [Accepted: 08/10/2012] [Indexed: 02/05/2023]
Abstract
Instability of CAG triplet repeat encoding polyglutamine (polyQ) stretches in the gene for target protein has been implicated as a putative mechanism in several inherited neurodegenerative diseases. Expansion of polyQ chain length in the androgen receptor (AR) causes spinal and bulbar muscular atrophy (SBMA) or Kennedy's disease. Although the mechanisms underlying gain-of-neurotoxic function are not completely understood, suggested pathological mechanisms of SBMA involve the formation of AR nuclear and cytoplasmic aggregates, a characteristic feature of patients with SBMA. The fact that certain AR coactivators are sequestered into the nuclear inclusions in SBMA possibly through protein-protein interactions supports the notion that AR transcriptional dysregulation may be a potential pathological mechanism leading to SBMA. AR conformational states associated with aberrant polyQ tract also modulate the interaction of AR with several coactivators. In many cases, such diseases can be treated through protein replacement therapy; however, because recombinant proteins do not cross the blood-brain barrier, the effectiveness of such therapies is limited in case of neurodegenerative diseases that warrant alternative therapeutic approaches. Among different approaches, inhibiting protein aggregation with small molecules that can stimulate protein folding and reverse aggregation are the most promising ones. Thus, naturally occurring osmolytes or "chemical chaperones" that can easily cross the blood-brain barrier and stabilize the functional form of a mutated protein by shifting the folding equilibrium away from degradation and/or aggregation is a useful therapeutic approach. In this review, we discuss the role of polyQ chain length extension in the pathophysiology of SBMA and the use of osmolytes as potential therapeutic tool.
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Affiliation(s)
- Raj Kumar
- Department of Basic Sciences, The Commonwealth Medical College, Scranton, PA 18509, USA.
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13
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Bogacheva EN, Bogachev AN, Dmitriev IB, Dolgov AA, Chulichkov AL, Shishkov AV, Baratova LA. Modeling of protein spatial structure using tritium planigraphy. Biophysics (Nagoya-shi) 2012. [DOI: 10.1134/s0006350911060030] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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14
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Liu CH, Zhang F, Krisrian T, Polster B, Fiskum GM, Hu B. Protein Aggregation and Multiple Organelle Damage After Brain Ischemia. Transl Stroke Res 2012. [DOI: 10.1007/978-1-4419-9530-8_5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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15
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Carugo O. Participation of protein sequence termini in crystal contacts. Protein Sci 2011; 20:2121-4. [PMID: 21739502 DOI: 10.1002/pro.690] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2011] [Revised: 06/27/2011] [Accepted: 06/30/2011] [Indexed: 11/08/2022]
Abstract
The analysis of the crystal packing interactions, in a nonredundant set of high resolution and monomeric globular protein crystal structures, shows that the residues located at the N- and C-termini of the sequence tend to participate in packing interaction more often than expected and that often they interact with each other. Since the sequence termini are, in general, conformationally very flexible and since they host electrical charges of opposite sign, it can be hypothesized that they play a crucial role in the early formation of the nonphysiological contacts that bring to protein crystallization. It is thus not surprising that modest lengthening/shortening of the sequence termini have often a dramatic effect on protein crystallogenesis.
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16
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Clark PL, Ugrinov KG. Measuring cotranslational folding of nascent polypeptide chains on ribosomes. Methods Enzymol 2009; 466:567-90. [PMID: 21609877 DOI: 10.1016/s0076-6879(09)66024-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Protein folding has been studied extensively in vitro, but much less is known about how folding proceeds in vivo. A particular distinction of folding in vivo is that folding begins while the nascent polypeptide chain is still undergoing synthesis by the ribosome. Studies of cotranslational protein folding are inherently much more complex than classical in vitro protein folding studies, and historically there have been few methods available to produce the quantities of pure material required for biophysical studies of the nascent chain, or assays to specifically interrogate its conformation. However, the past few years have produced dramatic methodological advances, which now place cotranslational folding studies within reach of more biochemists, enabling a detailed comparison of the earliest stages of protein folding on the ribosome to the wealth of information available for the refolding of full-length polypeptide chains in vitro.
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Affiliation(s)
- Patricia L Clark
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
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17
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Hsu STD, Blaser G, Jackson SE. The folding, stability and conformational dynamics of beta-barrel fluorescent proteins. Chem Soc Rev 2009; 38:2951-65. [PMID: 19771338 DOI: 10.1039/b908170b] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This critical review describes our current knowledge on the folding, stability and conformational dynamics of fluorescent proteins (FPs). The biophysical studies that have led to the elucidation of many of the key features of the complex energy landscape for folding for GFP and its variants are discussed. These illustrate some important issues surrounding how the large beta-barrel structure forms, and will be of interest to the protein folding community. In addition, the review highlights the importance of some of these results for the use of FPs in in vivo applications. The results should facilitate and aid in experimental designs of in vivo applications, as well as the interpretation of in vivo experimental data. The review is therefore of interest to all those working with FPs in vivo (103 references).
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Affiliation(s)
- Shang-Te Danny Hsu
- Chemistry Department, University of Cambridge, Lensfield Road, Cambridge, UK CB2 1EW
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18
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Abstract
Peroxisomes play an important role in lipid metabolic pathways and are implicated in many human disorders. Their biogenesis has been studied over the last two decades using many uni and multi-cellular model systems and many aspects of the mechanisms and proteins involved in peroxisome biogenesis are conserved from yeast to humans. In this manuscript we review the recent progress made in our understanding of the mechanisms by which matrix and membrane proteins are sorted to and assembled into peroxisomes.
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Affiliation(s)
- Changle Ma
- Section of Molecular Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093-0322, USA
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19
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Structure, Dynamics and Folding of an Immunoglobulin Domain of the Gelation Factor (ABP-120) from Dictyostelium discoideum. J Mol Biol 2009; 388:865-79. [DOI: 10.1016/j.jmb.2009.02.063] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2008] [Revised: 02/15/2009] [Accepted: 02/21/2009] [Indexed: 11/19/2022]
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20
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Abstract
Irreversible translation arrest occurs in reperfused neurons that will die by delayed neuronal death. It is now recognized that suppression of protein synthesis is a general response of eukaryotic cells to exogenous stressors. Indeed, stress-induced translation arrest can be viewed as a component of cell stress responses, and consists of initiation, maintenance, and termination phases that work in concert with stress-induced transcriptional mechanisms. Within this framework, we review translation arrest in reperfused neurons. This framework provides a basis to recognize that phosphorylation of the alpha subunit of eukaryotic initiation factor 2 is the initiator of translation arrest, and a key marker indicating activation of neuronal stress responses. However, eIF2 alpha phosphorylation is reversible. Other phases of stress-induced translation arrest appear to contribute to irreversible translation arrest specifically in ischemic vulnerable neuron populations. We detail two lines of evidence supporting this view. First, ischemia, as a stress stimulus, induces irreversible co-translational protein misfolding and aggregation after 4 to 6 h of reperfusion, trapping protein synthesis machinery into functionally inactive protein aggregates. Second, ischemia and reperfusion leads to modifications of stress granules (SGs) that sequester functionally inactive 48S preinitiation complexes to maintain translation arrest. At later reperfusion durations, these mechanisms may converge such that SGs become sequestered in protein aggregates. These mechanisms result in elimination of functionally active ribosomes and preclude recovery of protein synthesis in selectively vulnerable neurons. Thus, recognizing translation arrest as a component of endogenous cellular stress response pathways will aid in making sense of the complexities of postischemic translation arrest.
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Affiliation(s)
- Donald J DeGracia
- Department of Physiology and the Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan 48201, USA.
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21
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Abstract
Focal brain ischemia leads to a slow type of neuronal death in the penumbra that starts several hours after ischemia and continues to mature for days. During this maturation period, blood flow, cellular ATP and ionic homeostasis are gradually recovered in the penumbral region. In striking contrast, protein synthesis is irreversibly inhibited. This study used a rat focal brain ischemia model to investigate whether or not irreversible translational inhibition is due to abnormal aggregation of translational complex components, i.e. the ribosomes and their associated nascent polypeptides, protein synthesis initiation factors and co-translational chaperones. Under electron microscopy, most rosette-shaped polyribosomes were relatively evenly distributed in the cytoplasm of sham-operated control neurons, but clumped into large abnormal aggregates in penumbral neurons subjected to 2 h of focal ischemia followed by 4 h of reperfusion. The abnormal ribosomal protein aggregation lasted until the onset of delayed neuronal death at 24-48 h of reperfusion after ischemia. Biochemical study further suggested that translational complex components, including small ribosomal subunit protein 6 (S6), large subunit protein 28 (L28), eukaryotic initiation factors 2alpha, 4E and 3eta, and co-translational chaperone heat-shock cognate protein 70 (HSC70) and co-chaperone Hdj1, were all irreversibly clumped into large abnormal protein aggregates after ischemia. Translational complex components were also highly ubiquitinated. This study clearly demonstrates that focal ischemia leads to irreversible aggregation of protein synthesis machinery that contributes to neuronal death after focal brain ischemia.
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Affiliation(s)
- F Zhang
- Neurochemistry Laboratory of Brain Injury and Ischemia, Department of Neurology, University of Miami School of Medicine, Miami, Florida, USA
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22
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Contreras Martínez LM, Martínez-Veracoechea FJ, Pohkarel P, Stroock AD, Escobedo FA, DeLisa MP. Protein translocation through a tunnel induces changes in folding kinetics: a lattice model study. Biotechnol Bioeng 2006; 94:105-17. [PMID: 16528757 DOI: 10.1002/bit.20832] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Compaction of a nascent polypeptide chain inside the ribosomal exit tunnel, before it leaves the ribosome, has been proposed to accelerate the folding of newly synthesized proteins following their release from the ribosome. Thus, we used Kinetic Monte Carlo simulations of a minimalist on-lattice model to explore the effect that polypeptide translocation through a variety of channels has on protein folding kinetics. Our results demonstrate that tunnel confinement promotes faster folding of a well-designed protein relative to its folding in free space by displacing the unfolded state towards more compact structures that are closer to the transition state. Since the tunnel only forbids rarely visited, extended configurations, it has little effect on a "poorly designed" protein whose unfolded state is largely composed of low-energy, compact, misfolded configurations. The beneficial effect of the tunnel depends on its width; for example, a too-narrow tunnel enforces unfolded states with limited or no access to the transition state, while a too-wide tunnel has no effect on the unfolded state entropy. We speculate that such effects are likely to play an important role in the folding of some proteins or protein domains in the cellular environment and might dictate whether a protein folds co-translationally or post-translationally.
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23
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Wang N, Hebert DN. Tyrosinase maturation through the mammalian secretory pathway: bringing color to life. ACTA ACUST UNITED AC 2006; 19:3-18. [PMID: 16420243 DOI: 10.1111/j.1600-0749.2005.00288.x] [Citation(s) in RCA: 164] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Tyrosinase has been extensively utilized as a model substrate to study the maturation of glycoproteins in the mammalian secretory pathway. The visual nature of its enzymatic activity (melanin production) has facilitated the identification and characterization of the proteins that assist it becoming a functional enzyme, localized to its proper cellular location. Here, we review the steps involved in the maturation of tyrosinase from when it is first synthesized by cytosolic ribosomes until the mature protein reaches its post-Golgi residence in the melanosomes. These steps include protein processing, covalent modifications, chaperone binding, oligomerization, and trafficking. The disruption of any of these steps can lead to a wide range of pigmentation disorders.
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Affiliation(s)
- Ning Wang
- Program in Molecular and Cellular Biology, Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, MA, USA
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24
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Ying BW, Taguchi H, Kondo M, Ueda T. Co-translational involvement of the chaperonin GroEL in the folding of newly translated polypeptides. J Biol Chem 2005; 280:12035-40. [PMID: 15664980 DOI: 10.1074/jbc.m500364200] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
A large fraction of the newly translated polypeptides emerging from the ribosome require certain proteins, the so-called molecular chaperones, to assist in their folding. In Escherichia coli, three major chaperone systems are considered to contribute to the folding of newly synthesized cytosolic polypeptides. Trigger factor (TF), a ribosome-tethered chaperone, and DnaK are known to exhibit overlapping co-translational roles, whereas the cage-shaped GroEL, with the aid of the co-chaperonin, GroES, and ATP, is believed to be implicated in folding only after the polypeptides are released from the ribosome. However, the recent finding that GroEL-GroES overproduction permits the growth of E. coli cells lacking both TF and DnaK raised questions regarding the separate roles of these chaperones. Here, we report the puromycin-sensitive association of GroEL-GroES with translating ribosomes in vivo. Further experiments in vitro, using a reconstituted cell-free translation system, clearly demonstrate that GroEL associates with the translation complex and accomplishes proper folding by encapsulating the newly translated polypeptides in the central cavity formed by GroES. Therefore, we propose that GroEL is a versatile chaperone, which participates in the folding pathway co-translationally and also achieves correct folding post-translationally.
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Affiliation(s)
- Bei-Wen Ying
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, FSB401, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan
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25
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26
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Wujek P, Kida E, Walus M, Wisniewski KE, Golabek AA. N-glycosylation is crucial for folding, trafficking, and stability of human tripeptidyl-peptidase I. J Biol Chem 2003; 279:12827-39. [PMID: 14702339 DOI: 10.1074/jbc.m313173200] [Citation(s) in RCA: 85] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Tripeptidyl-peptidase I (TPP I) is a lysosomal serine-carboxyl peptidase that sequentially removes tripeptides from polypeptides. Naturally occurring mutations in TPP I are associated with the classic late infantile neuronal ceroid lipofuscinosis. Human TPP I has five potential N-glycosylation sites at Asn residues 210, 222, 286, 313, and 443. To analyze the role of N-glycosylation in the function of the enzyme, we obliterated each N- glycosylation consensus sequence by substituting Gln for Asn, either individually or in combinations, and expressed mutated cDNAs in Chinese hamster ovary and human embryonic kidney 293 cells. Here, we demonstrate that human TPP I in vivo utilizes all five N-glycosylation sites. Elimination of one of these sites, at Asn-286, dramatically affected the folding of the enzyme. However, in contrast to other misfolded proteins that are retained in the endoplasmic reticulum, only a fraction of misfolded TPP I mutant expressed in Chinese hamster ovary cells, but not in human embryonic kidney 293 cells, was arrested in the ER, whereas its major portion was secreted. Secreted proenzyme formed non-native, interchain disulfide bridges and displayed only residual TPP I activity upon acidification. A small portion of TPP I missing Asn-286-linked glycan reached the lysosome and was processed to an active species; however, it showed low thermal and pH stability. N-Glycans at Asn-210, Asn-222, Asn-313, and Asn-443 contributed slightly to the specific activity of the enzyme and its resistance to alkaline pH-induced inactivation. Phospholabeling experiments revealed that N-glycans at Asn-210 and Asn-286 of TPP I preferentially accept a phosphomannose marker. Thus, a dual role of oligosaccharide at Asn-286 in folding and lysosomal targeting could contribute to the unusual, but cell type-dependent, fate of misfolded TPP I conformer and represent the molecular basis of the disease process in subjects with naturally occurring missense mutation at Asn-286.
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Affiliation(s)
- Peter Wujek
- Department of Developmental Neurobiology, New York State Institute for Basic Research in Developmental Disabilities, 1050 Forest Hill Road, Staten Island, NY 10314, USA
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27
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Nölting B, Schälike W, Hampel P, Grundig F, Gantert S, Sips N, Bandlow W, Qi PX. Structural determinants of the rate of protein folding. J Theor Biol 2003; 223:299-307. [PMID: 12850450 DOI: 10.1016/s0022-5193(03)00091-2] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
To understand the mechanism of protein folding and to assist rational design of fast-folding, non-aggregating and stable artificial enzymes, it is essential to determine the structural parameters which govern the rate constants of folding, kf. It has been found that -logkf is a linear function of the so-called chain topology parameter (CTP) within the range of 10(-1)s(-1)< or = kf < or =10(8)s(-1). The correlation between -logkf and CTP is much improved than using previously published contact order (CO) method. It has been further suggested that short sequence separations may be preferred for the establishment of stable interactions for the design of novel artificial enzymes and the modification of slow-folding proteins with aggregating intermediates.
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Affiliation(s)
- Bengt Nölting
- Prussian Private Institute of Technology at Berlin, Am Schlosspark 30, Berlin D-13187, Germany.
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28
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Schnell DJ, Hebert DN. Protein translocons: multifunctional mediators of protein translocation across membranes. Cell 2003; 112:491-505. [PMID: 12600313 DOI: 10.1016/s0092-8674(03)00110-7] [Citation(s) in RCA: 195] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Protein translocation systems consist of complex molecular machines whose activities are not limited to unidirectional protein targeting. Protein translocons and their associated receptor systems can be viewed as dynamic modular units whose interactions, and therefore functions, are regulated in response to specific signals. This flexibility allows translocons to interact with multiple signal receptor systems to manage the targeting of topologically distinct classes of proteins, to mediate targeting to different suborganellar compartments, and to respond to stress and developmental cues. Furthermore, the activities of translocons are tightly coordinated with downstream events, thereby providing a direct link between targeting and protein maturation.
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Affiliation(s)
- Danny J Schnell
- Program in Plant Biology, University of Massachusetts, Amherst, MA 01003, USA.
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29
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Daniels R, Kurowski B, Johnson AE, Hebert DN. N-linked glycans direct the cotranslational folding pathway of influenza hemagglutinin. Mol Cell 2003; 11:79-90. [PMID: 12535523 DOI: 10.1016/s1097-2765(02)00821-3] [Citation(s) in RCA: 214] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
For proteins that traverse the secretory pathway, folding commences cotranslationally upon translocation into the endoplasmic reticulum. In this study, we have comprehensively analyzed the earliest maturation steps of the model glycoprotein influenza hemagglutinin (HA). These steps include cleavage of the signal sequence, glycosylation, binding by the chaperones calnexin and calreticulin, and the oxidoreductase ERp57, and oxidation. Our results show that the molecular choreography of the nascent HA chain is largely directed by multiple glycans that are strategically placed to elicit the binding of lectin chaperones. These chaperones are recruited to specific nascent chain locations to regulate and facilitate glycoprotein folding, thereby suggesting that the positioning of N-linked glycans in critical regions has evolved to optimize the folding process in the cell.
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Affiliation(s)
- Robert Daniels
- Department of Biochemistry and Molecular Biology, Program in Molecular and Cellular Biology, University of Massachusetts, Amherst, MA 01003, USA
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30
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Molinari M, Helenius A. Analyzing cotranslational protein folding and disulfide formation by diagonal sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Methods Enzymol 2002; 348:35-42. [PMID: 11885290 DOI: 10.1016/s0076-6879(02)48623-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Affiliation(s)
- Maurizio Molinari
- Institute for Research in Biomedicine, CH-6500 Bellinzona, Switzerland
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31
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Abstract
Recent years have witnessed dramatic advances in our understanding of how newly translated proteins fold in the cell and the contribution of molecular chaperones to this process. Folding in the cell must be achieved in a highly crowded macromolecular environment, in which release of nonnative polypeptides into the cytosolic solution might lead to formation of potentially toxic aggregates. Here I review the cellular mechanisms that ensure efficient folding of newly translated proteins in vivo. De novo protein folding appears to occur in a protected environment created by a highly processive chaperone machinery that is directly coupled to translation. Genetic and biochemical analysis shows that several distinct chaperone systems, including Hsp70 and the cylindrical chaperonins, assist the folding of proteins upon translation in the cytosol of both prokaryotic and eukaryotic cells. The cellular chaperone machinery is specifically recruited to bind to ribosomes and protects nascent chains and folding intermediates from nonproductive interactions. In addition, initiation of folding during translation appears to be important for efficient folding of multidomain proteins.
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Affiliation(s)
- J Frydman
- Department of Biological Sciences, Stanford University, Stanford, California 94305-5020, USA.
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32
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Forster AC, Weissbach H, Blacklow SC. A simplified reconstitution of mRNA-directed peptide synthesis: activity of the epsilon enhancer and an unnatural amino acid. Anal Biochem 2001; 297:60-70. [PMID: 11567528 DOI: 10.1006/abio.2001.5329] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The study of the early events in translation would be greatly facilitated by reconstitution with easily purified components. Here, Escherichia coli oligopeptide synthesis has been reconstituted using five purified recombinant His-tagged E. coli initiation and elongation factors. Highly purified ribosomes are required to yield products with strong dependencies on the translation factors. Based on HPLC separation of radiolabeled translation products from an mRNA encoding a tetrapeptide, approximately 80% of peptide products are full length, and the remaining 20% are the dipeptide and tripeptide products resulting from pausing or premature termination. Oligopeptide synthesis is enhanced when a commonly used epsilon (enhancer of protein synthesis initiation) sequence is included in the mRNA. The system incorporates a selectable, large, unnatural amino acid and may ultimately form the basis of a pure translation display technology for the directed evolution of peptidomimetic ligands and drug candidates. The recombinant clones can be exploited to prepare initiation factors and initiation complexes for structural studies, to study initiation and elongation in ribosomal peptide synthesis, and to screen for eubacterial-specific drugs.
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Affiliation(s)
- A C Forster
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, 75 Francis Street, Boston, Massachusetts 02115, USA.
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33
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Qin ZJ, Tang YQ, Jing GZ, Li ZY, Huang GC, Perrett S, Guo ZQ, Zhou JM. Conformational adjustments of SNase R and its N-terminal fragments probed by monoclonal antibodies. BIOCHIMICA ET BIOPHYSICA ACTA 2001; 1548:203-12. [PMID: 11513965 DOI: 10.1016/s0167-4838(01)00231-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Two monoclonal antibodies specific for staphylococcal nuclease R (SNase R) (McAb2C9 and McAb1B8) were prepared and used to probe protein folding during peptide elongation, by measuring antibody binding to seven N-terminal fragments (SNR141, SNR135, SNR121, SNR110, SNR102, SNR79 and SNR52) of SNase R. Comparative studies of the conformations of the N-terminal fragments have shown that all seven fragments of SNase R have a certain amount of residual structure, indicating that folding may occur during elongation of the nascent peptide chain. We show that the binding abilities of the intact enzyme and its seven fragments to the monoclonal antibodies are not simply proportional to the length of the peptide chain, suggesting that there may be continuous conformational adjustment in the nascent peptide chain as new C-terminal amino acids are added. A folding intermediate close in structure to the native state but with structural features in common with SNR121 is highly populated in 0.6 M GuHCl, and is also formed transiently during folding.
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Affiliation(s)
- Z J Qin
- National Laboratory of Biomacromolecules, Institute of Biophysics, Academia Sinica, Beijing, PR China
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34
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Lin E, Lin SW, Lin A. The participation of 5S rRNA in the co-translational formation of a eukaryotic 5S ribonucleoprotein complex. Nucleic Acids Res 2001; 29:2510-6. [PMID: 11410658 PMCID: PMC55736 DOI: 10.1093/nar/29.12.2510] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The eukaryotic ribosomal 5S RNA-protein complex (5S rRNP) is formed by a co-translational event that requires 5S rRNA binding to the nascent peptide chain of eukaryotic ribosomal protein L5. Binding between 5S rRNA and the nascent chain is specific: neither the 5S rRNA nor the nascent chain of L5 protein can be substituted by other RNAs or other ribosomal proteins. The region responsible for binding 5S rRNA is located at positions 35-50 with amino acid sequence RLVIQDIKNKYNTPKYRM. Eukaryotic 5S rRNA binds a nascent chain having this sequence, but such binding is not substantive enough to form a 5S-associated RNP complex, suggesting that 5S rRNA binding to the nascent chain is amino acid sequence dependent and that formation of the 5S rRNP complex is L5 protein specific. Microinjection of 5S rRNP complex into the cytoplasm of Xenopus oocytes results in both an increase in the initial rate and also in the extent of net nuclear import of L5. This suggests that the 5S rRNP complex enhances nuclear transport of L5. We propose that 5S rRNA plays a chaperone-like role in folding of the nascent chain of L5 and directs L5 into a 5S rRNP complex for nuclear entry.
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Affiliation(s)
- E Lin
- Institute of Genetics, National Yang-Ming University, Shih-Pai, Taipei, Taiwan, Republic of China
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35
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Abstract
When a protein folds or unfolds, it passes through many half-folded microstates. Only a few of them can accumulate and be seen experimentally, and this happens only when the folding (or unfolding) occurs far from the point of thermodynamic equilibrium between the native and denatured states. The universal features of folding, though, are observed just close to the equilibrium point. Here the 'two-state' transition proceeds without any accumulation of metastable intermediates, and only the transition state ('folding nucleus') is outlined by its key influence on the folding-unfolding kinetics. Our aim is to review recent experimental and theoretical studies of the folding nuclei.
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Affiliation(s)
- O V Galzitskaya
- Institute of Protein Research, Russian Academy of Sciences, 142290, Moscow Region, Pushchino, Russia
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36
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Loomis WP, Koo JT, Cheung TP, Moseley SL. A tripeptide sequence within the nascent DaaP protein is required for mRNA processing of a fimbrial operon in Escherichia coli. Mol Microbiol 2001; 39:693-707. [PMID: 11169109 DOI: 10.1046/j.1365-2958.2001.02241.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The biogenesis of F1845 fimbriae, a member of the Dr family of Escherichia coli adhesins, is regulated by endonucleolytic cleavage of the daaABCDPE primary transcript and differential stability of the resulting cleavage products. Processing of daa mRNA is dependent upon translation of a small open reading frame, designated daaP, which flanks the daa processing site. Here, we demonstrate that daa mRNA processing is directly coupled to daaP translation. Cleavage of the daaA-E mRNA was shown to require the tripeptide Gly-Pro-Pro (GPP), encoded by daaP codons 49-51 downstream of the processing site. Processing also required active translation through RNA located upstream of the processing site; however, processing did not depend on the amino acid sequence encoded by the region of daaP upstream of the processing site. Finally, determination of the processing site was shown to involve its location relative to the codons encoding the GPP tripeptide. These data show that translation of daaP is required in cis to promote RNA processing. These data suggest a model involving interaction of the nascent GPP tripeptide portion of the DaaP polypeptide with the ribosome, triggering cleavage of the associated mRNA at a fixed distance upstream. A model of active involvement of the ribosome in this process is proposed.
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Affiliation(s)
- W P Loomis
- Department of Microbiology, University of Washington, Box 357242, Seattle, WA 98195-7242, USA
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37
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Eggers DK, Valentine JS. Molecular confinement influences protein structure and enhances thermal protein stability. Protein Sci 2001; 10:250-61. [PMID: 11266611 PMCID: PMC2373941 DOI: 10.1110/ps.36201] [Citation(s) in RCA: 291] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Abstract
The sol-gel method of encapsulating proteins in a silica matrix was investigated as a potential experimental system for testing the effects of molecular confinement on the structure and stability of proteins. We demonstrate that silica entrapment (1) is fully compatible with structure analysis by circular dichroism, (2) allows conformational studies in contact with solvents that would otherwise promote aggregation in solution, and (3) generally enhances thermal protein stability. Lysozyme, alpha-lactalbumin, and metmyoglobin retained native-like solution structures following sol-gel encapsulation, but apomyoglobin was found to be largely unfolded within the silica matrix under control buffer conditions. The secondary structure of encapsulated apomyoglobin was unaltered by changes in pH and ionic strength of KCl. Intriguingly, the addition of other neutral salts resulted in an increase in the alpha-helical content of encapsulated apomyoglobin in accordance with the Hofmeister ion series. We hypothesize that protein conformation is influenced directly by the properties of confined water in the pores of the silica. Further work is needed to differentiate the steric effects of the silica matrix from the solvent effects of confined water on protein structure and to determine the extent to which this experimental system mimics the effects of crowding and confinement on the function of macromolecules in vivo.
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Affiliation(s)
- D K Eggers
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095-1569, USA.
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38
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Wattenberg B, Lithgow T. Targeting of C-terminal (tail)-anchored proteins: understanding how cytoplasmic activities are anchored to intracellular membranes. Traffic 2001; 2:66-71. [PMID: 11208169 DOI: 10.1034/j.1600-0854.2001.20108.x] [Citation(s) in RCA: 160] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
A class of integral membrane proteins, referred to as 'tail-anchored proteins', are inserted into phospholipid bilayers via a single segment of hydrophobic amino acids at the C-terminus, thereby displaying a large functional domain in the cytosol. This membrane attachment strategy allows eukaryotic cells to position a wide range of cytoplasmic activities close to the surface of an intracellular membrane. Tail-anchored proteins often, but not always, demonstrate a selective distribution to specific intracellular organelles. This membrane-specific distribution is required for the large number of targeting proteins that are tail-anchored, but may or may not be critical for the numerous tail-anchored pro-apoptotic and anti-apoptotic proteins of the Bcl-2 family. Recent work has begun to address the mechanism for targeting tail-anchored proteins to their resident membranes, but questions remain. What targeting signals determine each protein's intracellular location? Are there receptors for these signals and, if so, how do they function? What steps are required to integrate tail-anchored proteins into the phospholipid bilayers? In this Traffic interchange, we summarise what is known about tail-anchored proteins, and outline the areas that are currently under study.
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Affiliation(s)
- B Wattenberg
- Hanson Centre for Cancer Research, Box 14 Rundle Mall Post Office, Adelaide 5000, Australia.
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39
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Chen LY, Lin B, Pan CJ, Hiraiwa H, Chou JY. Structural requirements for the stability and microsomal transport activity of the human glucose 6-phosphate transporter. J Biol Chem 2000; 275:34280-6. [PMID: 10940311 DOI: 10.1074/jbc.m006439200] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Deficiencies in glucose 6-phosphate (G6P) transporter (G6PT), a 10-helical endoplasmic reticulum transmembrane protein of 429 amino acids, cause glycogen storage disease type 1b. To date, only three missense mutations in G6PT have been shown to abolish microsomal G6P transport activity. Here, we report the results of structure-function studies on human G6PT and demonstrate that 15 missense mutations and a codon deletion (delta F93) mutation abolish microsomal G6P uptake activity and that two splicing mutations cause exon skipping. While most missense mutants support the synthesis of G6PT protein similar to that of the wild-type transporter, immunoblot analysis shows that G20D, delta F93, and I278N mutations, located in helix 1, 2, and 6, respectively, destabilize the G6PT. Further, we demonstrate that G6PT mutants lacking an intact helix 10 are misfolded and undergo degradation within cells. Moreover, amino acids 415-417 in the cytoplasmic tail of the carboxyl-domain, extending from helix 10, also play a critical role in the correct folding of the transporter. However, the last 12 amino acids of the cytoplasmic tail play no essential role(s) in functional integrity of the G6PT. Our results, for the first time, elucidate the structural requirements for the stability and transport activity of the G6PT protein.
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Affiliation(s)
- L Y Chen
- Heritable Disorders Branch, NICHD, National Institutes of Health, Bethesda, Maryland 20892, USA
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40
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Chen W, Helenius A. Role of ribosome and translocon complex during folding of influenza hemagglutinin in the endoplasmic reticulum of living cells. Mol Biol Cell 2000; 11:765-72. [PMID: 10679029 PMCID: PMC14808 DOI: 10.1091/mbc.11.2.765] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Protein folding in the living cell begins cotranslationally. To analyze how it is influenced by the ribosome and by the translocon complex during translocation into the endoplasmic reticulum, we expressed a mutant influenza hemagglutinin (a type I membrane glycoprotein) with a C-terminal extension. Analysis of the nascent chains by two-dimensional SDS-PAGE showed that ribosome attachment as such had little effect on ectodomain folding or trimer assembly. However, as long as the chains were ribosome bound and inside the translocon complex, formation of disulfides was partially suppressed, trimerization was inhibited, and the protein protected against aggregation.
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Affiliation(s)
- W Chen
- Department of Cell Biology, Yale University School of Medicine, New Haven, Connecticut 06520-8002, USA
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41
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Hayhurst A. Improved expression characteristics of single-chain Fv fragments when fused downstream of the Escherichia coli maltose-binding protein or upstream of a single immunoglobulin-constant domain. Protein Expr Purif 2000; 18:1-10. [PMID: 10648163 DOI: 10.1006/prep.1999.1164] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The expression of single-chain Fv fragments (scFv) targeted to the periplasm of Escherichia coli often results in very low yields of soluble protein frequently accompanied by host cell growth arrest and sometimes lysis. Single-chain antibody fragments (scAb) are scFv with a human kappa light chain constant (HuCkappa) domain attached C-terminally and share similar problems of expression. By fusing the E. coli maltose-binding protein (mbp) gene either 3' or 5' to a scAb specific for the herbicide atrazine, a reduction in growth arrest was observed that was dependent on the order of gene fusion. The scAb-mbp fusion delayed the onset of growth arrest following induction while the mbp-scAb fusion appeared to ablate growth arrest completely. Cell fractionation revealed barely detectable levels of scAb-mbp in the periplasm while mbp-scAb was detected at equivalent levels as scAb in the periplasmic compartment, indicating that periplasmic scAb solubility is unrelated to propensity to cause growth arrest. IMAC purification of scAb and mbp-scAb proteins followed by liquid competition ELISA revealed the IC(50) for atrazine to be approximately 1 nM for both proteins demonstrating that 5'-mbp fusion does not alter antigen binding. The equivalent scFv and mbp-scFv vectors expressed far less material in both periplasmic and insoluble fractions indicating that the HuCkappa domain can have a positive effect on scFv expression when expressed either alone or as a mbp fusion. The ablation of growth arrest by a 5'-mbp fusion and enhancement of expression by a 3'-HuCkappa domain fusion were extended to a second scFv specific for the herbicide diuron. Therefore, by expressing scFv as tripartite fusions (mbp-scFv-HuCkappa) enhanced levels of soluble periplasmic expression can be achieved without causing growth arrest of the host cell, realizing the potential for constitutive expression of hapten-binding scFv in the E. coli periplasm.
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Affiliation(s)
- A Hayhurst
- Department of Molecular and Cell Biology, Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen, AB25 2SZ, Scotland
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Caldas T, Laalami S, Richarme G. Chaperone properties of bacterial elongation factor EF-G and initiation factor IF2. J Biol Chem 2000; 275:855-60. [PMID: 10625618 DOI: 10.1074/jbc.275.2.855] [Citation(s) in RCA: 116] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Elongation factor G(EF-G) and initiation factor 2 (IF2) are involved in the translocation of ribosomes on mRNA and in the binding of initiator tRNA to the 30 S ribosomal subunit, respectively. Here we report that the Escherichia coli EF-G and IF2 interact with unfolded and denatured proteins, as do molecular chaperones that are involved in protein folding and protein renaturation after stress. EF-G and IF2 promote the functional folding of citrate synthase and alpha-glucosidase after urea denaturation. They prevent the aggregation of citrate synthase under heat shock conditions, and they form stable complexes with unfolded proteins such as reduced carboxymethyl alpha-lactalbumin. Furthermore, the EF-G and IF2-dependent renaturations of citrate synthase are stimulated by GTP, and the GTPase activity of EF-G and IF2 is stimulated by the permanently unfolded protein, reduced carboxymethyl alpha-lactalbumin. The concentrations at which these chaperone-like functions occur are lower than the cellular concentrations of EF-G and IF2. These results suggest that EF-G and IF2, in addition to their role in translation, might be implicated in protein folding and protection from stress.
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Affiliation(s)
- T Caldas
- Biochimie Génétique, Institut Jacques Monod, Université Paris 7, 2 place Jussieu, 75005 Paris, France
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Komar AA, Lesnik T, Reiss C. Synonymous codon substitutions affect ribosome traffic and protein folding during in vitro translation. FEBS Lett 1999; 462:387-91. [PMID: 10622731 DOI: 10.1016/s0014-5793(99)01566-5] [Citation(s) in RCA: 294] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
To investigate the possible influence of the local rates of translation on protein folding, 16 consecutive rare (in Escherichia coli) codons in the chloramphenicol acetyltransferase (CAT) gene have been replaced by frequent ones. Site-directed silent mutagenesis reduced the pauses in translation of CAT in E. coli S30 extract cell-free system and led to the acceleration of the overall rate of CAT protein synthesis. At the same time, the silently mutated protein (with unaltered protein sequence) synthesized in the E. coli S30 extract system was shown to possess 20% lower specific activity. The data suggest that kinetics of protein translation can affect the in vivo protein-folding pathway, leading to increased levels of protein misfolding.
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Affiliation(s)
- A A Komar
- Centre de Génétique Moléculaire, CNRS, Gif-sur-Yvette, France.
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