1
|
Müller L, Hoppe T. UPS-dependent strategies of protein quality control degradation. Trends Biochem Sci 2024:S0968-0004(24)00149-X. [PMID: 38945729 DOI: 10.1016/j.tibs.2024.06.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 05/29/2024] [Accepted: 06/10/2024] [Indexed: 07/02/2024]
Abstract
The degradation of damaged proteins is critical for tissue integrity and organismal health because damaged proteins have a high propensity to form aggregates. E3 ubiquitin ligases are key regulators of protein quality control (PQC) and mediate the selective degradation of damaged proteins, a process termed 'PQC degradation' (PQCD). The degradation signals (degrons) that trigger PQCD are based on hydrophobic sites that are normally buried within the native protein structure. However, an open question is how PQCD-specialized E3 ligases distinguish between transiently misfolded proteins, which can be efficiently refolded, and permanently damaged proteins, which must be degraded. While significant progress has been made in characterizing degradation determinants, understanding the key regulatory signals of cellular and organismal PQCD pathways remains a challenge.
Collapse
Affiliation(s)
- Leonie Müller
- Institute for Genetics, University of Cologne, 50674 Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, 50931 Cologne, Germany; Center for Molecular Medicine Cologne (CMMC), Faculty of Medicine and University Hospital of Cologne, 50931 Cologne, Germany
| | - Thorsten Hoppe
- Institute for Genetics, University of Cologne, 50674 Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, 50931 Cologne, Germany; Center for Molecular Medicine Cologne (CMMC), Faculty of Medicine and University Hospital of Cologne, 50931 Cologne, Germany.
| |
Collapse
|
2
|
Ghosh D, Biswas A, Radhakrishna M. Advanced computational approaches to understand protein aggregation. BIOPHYSICS REVIEWS 2024; 5:021302. [PMID: 38681860 PMCID: PMC11045254 DOI: 10.1063/5.0180691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 03/18/2024] [Indexed: 05/01/2024]
Abstract
Protein aggregation is a widespread phenomenon implicated in debilitating diseases like Alzheimer's, Parkinson's, and cataracts, presenting complex hurdles for the field of molecular biology. In this review, we explore the evolving realm of computational methods and bioinformatics tools that have revolutionized our comprehension of protein aggregation. Beginning with a discussion of the multifaceted challenges associated with understanding this process and emphasizing the critical need for precise predictive tools, we highlight how computational techniques have become indispensable for understanding protein aggregation. We focus on molecular simulations, notably molecular dynamics (MD) simulations, spanning from atomistic to coarse-grained levels, which have emerged as pivotal tools in unraveling the complex dynamics governing protein aggregation in diseases such as cataracts, Alzheimer's, and Parkinson's. MD simulations provide microscopic insights into protein interactions and the subtleties of aggregation pathways, with advanced techniques like replica exchange molecular dynamics, Metadynamics (MetaD), and umbrella sampling enhancing our understanding by probing intricate energy landscapes and transition states. We delve into specific applications of MD simulations, elucidating the chaperone mechanism underlying cataract formation using Markov state modeling and the intricate pathways and interactions driving the toxic aggregate formation in Alzheimer's and Parkinson's disease. Transitioning we highlight how computational techniques, including bioinformatics, sequence analysis, structural data, machine learning algorithms, and artificial intelligence have become indispensable for predicting protein aggregation propensity and locating aggregation-prone regions within protein sequences. Throughout our exploration, we underscore the symbiotic relationship between computational approaches and empirical data, which has paved the way for potential therapeutic strategies against protein aggregation-related diseases. In conclusion, this review offers a comprehensive overview of advanced computational methodologies and bioinformatics tools that have catalyzed breakthroughs in unraveling the molecular basis of protein aggregation, with significant implications for clinical interventions, standing at the intersection of computational biology and experimental research.
Collapse
Affiliation(s)
- Deepshikha Ghosh
- Department of Biological Sciences and Engineering, Indian Institute of Technology (IIT) Gandhinagar, Palaj, Gujarat 382355, India
| | - Anushka Biswas
- Department of Chemical Engineering, Indian Institute of Technology (IIT) Gandhinagar, Palaj, Gujarat 382355, India
| | | |
Collapse
|
3
|
Lan PD, Nissley DA, Sitarik I, Vu QV, Jiang Y, To P, Xia Y, Fried SD, Li MS, O'Brien EP. Synonymous Mutations Can Alter Protein Dimerization Through Localized Interface Misfolding Involving Self-entanglements. J Mol Biol 2024; 436:168487. [PMID: 38341172 PMCID: PMC11260358 DOI: 10.1016/j.jmb.2024.168487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 01/10/2024] [Accepted: 02/06/2024] [Indexed: 02/12/2024]
Abstract
Synonymous mutations in messenger RNAs (mRNAs) can reduce protein-protein binding substantially without changing the protein's amino acid sequence. Here, we use coarse-grain simulations of protein synthesis, post-translational dynamics, and dimerization to understand how synonymous mutations can influence the dimerization of two E. coli homodimers, oligoribonuclease and ribonuclease T. We synthesize each protein from its wildtype, fastest- and slowest-translating synonymous mRNAs in silico and calculate the ensemble-averaged interaction energy between the resulting dimers. We find synonymous mutations alter oligoribonuclease's dimer properties. Relative to wildtype, the dimer interaction energy becomes 4% and 10% stronger, respectively, when translated from its fastest- and slowest-translating mRNAs. Ribonuclease T dimerization, however, is insensitive to synonymous mutations. The structural and kinetic origin of these changes are misfolded states containing non-covalent lasso-entanglements, many of which structurally perturb the dimer interface, and whose probability of occurrence depends on translation speed. These entangled states are kinetic traps that persist for long time scales. Entanglements cause altered dimerization energies for oligoribonuclease, as there is a large association (odds ratio: 52) between the co-occurrence of non-native self-entanglements and weak-binding dimer conformations. Simulated at all-atom resolution, these entangled structures persist for long timescales, indicating the conclusions are independent of model resolution. Finally, we show that regions of the protein we predict to have changes in entanglement are also structurally perturbed during refolding, as detected by limited-proteolysis mass spectrometry. Thus, non-native changes in entanglement at dimer interfaces is a mechanism through which oligomer structure and stability can be altered.
Collapse
Affiliation(s)
- Pham Dang Lan
- Institute for Computational Sciences and Technology, Ho Chi Minh City, Viet Nam; Faculty of Physics and Engineering Physics, VNUHCM-University of Science, 227, Nguyen Van Cu Street, District 5, Ho Chi Minh City, Viet Nam
| | - Daniel Allen Nissley
- Department of Chemistry, Pennsylvania State University, University Park, PA 16802, USA
| | - Ian Sitarik
- Department of Chemistry, Pennsylvania State University, University Park, PA 16802, USA
| | - Quyen V Vu
- Institute of Physics, Polish Academy of Sciences, 02-668 Warsaw, Poland
| | - Yang Jiang
- Department of Chemistry, Pennsylvania State University, University Park, PA 16802, USA
| | - Philip To
- Department of Chemistry, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Yingzi Xia
- Department of Chemistry, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Stephen D Fried
- Department of Chemistry, Johns Hopkins University, Baltimore, MD 21218, USA; Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Mai Suan Li
- Institute for Computational Sciences and Technology, Ho Chi Minh City, Viet Nam; Institute of Physics, Polish Academy of Sciences, 02-668 Warsaw, Poland
| | - Edward P O'Brien
- Department of Chemistry, Pennsylvania State University, University Park, PA 16802, USA; Bioinformatics and Genomics Graduate Program, The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA; Institute for Computational and Data Sciences, Pennsylvania State University, University Park, PA 16802, USA.
| |
Collapse
|
4
|
Rana V, Sitarik I, Petucci J, Jiang Y, Song H, O'Brien EP. Non-covalent Lasso Entanglements in Folded Proteins: Prevalence, Functional Implications, and Evolutionary Significance. J Mol Biol 2024; 436:168459. [PMID: 38296158 PMCID: PMC11265471 DOI: 10.1016/j.jmb.2024.168459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Revised: 01/23/2024] [Accepted: 01/24/2024] [Indexed: 02/17/2024]
Abstract
One-third of protein domains in the CATH database contain a recently discovered tertiary topological motif: non-covalent lasso entanglements, in which a segment of the protein backbone forms a loop closed by non-covalent interactions between residues and is threaded one or more times by the N- or C-terminal backbone segment. Unknown is how frequently this structural motif appears across the proteomes of organisms. And the correlation of these motifs with various classes of protein function and biological processes have not been quantified. Here, using a combination of protein crystal structures, AlphaFold2 predictions, and Gene Ontology terms we show that in E. coli, S. cerevisiae and H. sapiens that 71%, 52% and 49% of globular proteins contain one-or-more non-covalent lasso entanglements in their native fold, and that some of these are highly complex with multiple threading events. Further, proteins containing these tertiary motifs are consistently enriched in certain functions and biological processes across these organisms and depleted in others, strongly indicating an influence of evolutionary selection pressures acting positively and negatively on the distribution of these motifs. Together, these results demonstrate that non-covalent lasso entanglements are widespread and indicate they may be extensively utilized for protein function and subcellular processes, thus impacting phenotype.
Collapse
Affiliation(s)
- Viraj Rana
- Department of Chemistry, Pennsylvania State University, University Park, PA, United States
| | - Ian Sitarik
- Department of Chemistry, Pennsylvania State University, University Park, PA, United States
| | - Justin Petucci
- Institute for Computational and Data Sciences, Pennsylvania State University, University Park, PA, United States
| | - Yang Jiang
- Department of Chemistry, Pennsylvania State University, University Park, PA, United States
| | - Hyebin Song
- Bioinformatics and Genomics Graduate Program, The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, United States; Department of Statistics, Pennsylvania State University, University Park, PA, United States.
| | - Edward P O'Brien
- Department of Chemistry, Pennsylvania State University, University Park, PA, United States; Institute for Computational and Data Sciences, Pennsylvania State University, University Park, PA, United States; Bioinformatics and Genomics Graduate Program, The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, United States.
| |
Collapse
|
5
|
Jiang Y, Deane CM, Morris GM, O’Brien EP. It is theoretically possible to avoid misfolding into non-covalent lasso entanglements using small molecule drugs. PLoS Comput Biol 2024; 20:e1011901. [PMID: 38470915 PMCID: PMC10931463 DOI: 10.1371/journal.pcbi.1011901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 02/08/2024] [Indexed: 03/14/2024] Open
Abstract
A novel class of protein misfolding characterized by either the formation of non-native noncovalent lasso entanglements in the misfolded structure or loss of native entanglements has been predicted to exist and found circumstantial support through biochemical assays and limited-proteolysis mass spectrometry data. Here, we examine whether it is possible to design small molecule compounds that can bind to specific folding intermediates and thereby avoid these misfolded states in computer simulations under idealized conditions (perfect drug-binding specificity, zero promiscuity, and a smooth energy landscape). Studying two proteins, type III chloramphenicol acetyltransferase (CAT-III) and D-alanyl-D-alanine ligase B (DDLB), that were previously suggested to form soluble misfolded states through a mechanism involving a failure-to-form of native entanglements, we explore two different drug design strategies using coarse-grained structure-based models. The first strategy, in which the native entanglement is stabilized by drug binding, failed to decrease misfolding because it formed an alternative entanglement at a nearby region. The second strategy, in which a small molecule was designed to bind to a non-native tertiary structure and thereby destabilize the native entanglement, succeeded in decreasing misfolding and increasing the native state population. This strategy worked because destabilizing the entanglement loop provided more time for the threading segment to position itself correctly to be wrapped by the loop to form the native entanglement. Further, we computationally identified several FDA-approved drugs with the potential to bind these intermediate states and rescue misfolding in these proteins. This study suggests it is possible for small molecule drugs to prevent protein misfolding of this type.
Collapse
Affiliation(s)
- Yang Jiang
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Charlotte M. Deane
- Oxford Protein Informatics Group, Department of Statistics, University of Oxford, 24-29 St Giles’ Oxford, OX1 3LB United Kingdom
| | - Garrett M. Morris
- Oxford Protein Informatics Group, Department of Statistics, University of Oxford, 24-29 St Giles’ Oxford, OX1 3LB United Kingdom
| | - Edward P. O’Brien
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania, United States of America
- Bioinformatics and Genomics Graduate Program, The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, United States of America
- Institute for Computational and Data Sciences, Pennsylvania State University, University Park, Pennsylvania, United States of America
| |
Collapse
|
6
|
Salicari L, Baiesi M, Orlandini E, Trovato A. Folding kinetics of an entangled protein. PLoS Comput Biol 2023; 19:e1011107. [PMID: 37956216 PMCID: PMC10681328 DOI: 10.1371/journal.pcbi.1011107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Revised: 11/27/2023] [Accepted: 11/02/2023] [Indexed: 11/15/2023] Open
Abstract
The possibility of the protein backbone adopting lasso-like entangled motifs has attracted increasing attention. After discovering the surprising abundance of natively entangled protein domain structures, it was shown that misfolded entangled subpopulations might become thermosensitive or escape the homeostasis network just after translation. To investigate the role of entanglement in shaping folding kinetics, we introduce a novel indicator and analyze simulations of a coarse-grained, structure-based model for two small single-domain proteins. The model recapitulates the well-known two-state folding mechanism of a non-entangled SH3 domain. However, despite its small size, a natively entangled antifreeze RD1 protein displays a rich refolding behavior, populating two distinct kinetic intermediates: a short-lived, entangled, near-unfolded state and a longer-lived, non-entangled, near-native state. The former directs refolding along a fast pathway, whereas the latter is a kinetic trap, consistently with known experimental evidence of two different characteristic times. Upon trapping, the natively entangled loop folds without being threaded by the N-terminal residues. After trapping, the native entangled structure emerges by either backtracking to the unfolded state or threading through the already formed but not yet entangled loop. Along the fast pathway, trapping does not occur because the native contacts at the closure of the lasso-like loop fold after those involved in the N-terminal thread, confirming previous predictions. Despite this, entanglement may appear already in unfolded configurations. Remarkably, a longer-lived, near-native intermediate, with non-native entanglement properties, recalls what was observed in cotranslational folding.
Collapse
Affiliation(s)
- Leonardo Salicari
- Department of Physics and Astronomy “G. Galilei”, University of Padova, Padova, Italy
- National Institute of Nuclear Physics (INFN), Padova Section, Padova, Italy
| | - Marco Baiesi
- Department of Physics and Astronomy “G. Galilei”, University of Padova, Padova, Italy
- National Institute of Nuclear Physics (INFN), Padova Section, Padova, Italy
| | - Enzo Orlandini
- Department of Physics and Astronomy “G. Galilei”, University of Padova, Padova, Italy
- National Institute of Nuclear Physics (INFN), Padova Section, Padova, Italy
| | - Antonio Trovato
- Department of Physics and Astronomy “G. Galilei”, University of Padova, Padova, Italy
- National Institute of Nuclear Physics (INFN), Padova Section, Padova, Italy
| |
Collapse
|
7
|
Chen JP, Gong JS, Su C, Li H, Xu ZH, Shi JS. Improving the soluble expression of difficult-to-express proteins in prokaryotic expression system via protein engineering and synthetic biology strategies. Metab Eng 2023; 78:99-114. [PMID: 37244368 DOI: 10.1016/j.ymben.2023.05.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2023] [Accepted: 05/23/2023] [Indexed: 05/29/2023]
Abstract
Solubility and folding stability are key concerns for difficult-to-express proteins (DEPs) restricted by amino acid sequences and superarchitecture, resolved by the precise distribution of amino acids and molecular interactions as well as the assistance of the expression system. Therefore, an increasing number of tools are available to achieve efficient expression of DEPs, including directed evolution, solubilization partners, chaperones, and affluent expression hosts, among others. Furthermore, genome editing tools, such as transposons and CRISPR Cas9/dCas9, have been developed and expanded to construct engineered expression hosts capable of efficient expression ability of soluble proteins. Accounting for the accumulated knowledge of the pivotal factors in the solubility and folding stability of proteins, this review focuses on advanced technologies and tools of protein engineering, protein quality control systems, and the redesign of expression platforms in prokaryotic expression systems, as well as advances of the cell-free expression technologies for membrane proteins production.
Collapse
Affiliation(s)
- Jin-Ping Chen
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, 214122, PR China; Yixing Institute of Food and Biotechnology Co., Ltd, Yixing, 214200, PR China
| | - Jin-Song Gong
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, 214122, PR China; Yixing Institute of Food and Biotechnology Co., Ltd, Yixing, 214200, PR China.
| | - Chang Su
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, 214122, PR China
| | - Heng Li
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, 214122, PR China
| | - Zheng-Hong Xu
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, School of Biotechnology, Jiangnan University, Wuxi, 214122, PR China; Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, 214122, PR China; Yixing Institute of Food and Biotechnology Co., Ltd, Yixing, 214200, PR China
| | - Jin-Song Shi
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, 214122, PR China; Yixing Institute of Food and Biotechnology Co., Ltd, Yixing, 214200, PR China
| |
Collapse
|
8
|
Halder R, Nissley DA, Sitarik I, Jiang Y, Rao Y, Vu QV, Li MS, Pritchard J, O'Brien EP. How soluble misfolded proteins bypass chaperones at the molecular level. Nat Commun 2023; 14:3689. [PMID: 37344452 DOI: 10.1038/s41467-023-38962-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 05/24/2023] [Indexed: 06/23/2023] Open
Abstract
Subpopulations of soluble, misfolded proteins can bypass chaperones within cells. The extent of this phenomenon and how it happens at the molecular level are unknown. Through a meta-analysis of the experimental literature we find that in all quantitative protein refolding studies there is always a subpopulation of soluble but misfolded protein that does not fold in the presence of one or more chaperones, and can take days or longer to do so. Thus, some misfolded subpopulations commonly bypass chaperones. Using multi-scale simulation models we observe that the misfolded structures that bypass various chaperones can do so because their structures are highly native like, leading to a situation where chaperones do not distinguish between the folded and near-native-misfolded states. More broadly, these results provide a mechanism by which long-time scale changes in protein structure and function can persist in cells because some misfolded states can bypass components of the proteostasis machinery.
Collapse
Affiliation(s)
- Ritaban Halder
- Department of Chemistry, Pennsylvania State University, University Park, PA, 16802, USA
| | - Daniel A Nissley
- Department of Chemistry, Pennsylvania State University, University Park, PA, 16802, USA
- Department of Statistics, University of Oxford, Oxford, OX1 3LB, UK
| | - Ian Sitarik
- Department of Chemistry, Pennsylvania State University, University Park, PA, 16802, USA
| | - Yang Jiang
- Department of Chemistry, Pennsylvania State University, University Park, PA, 16802, USA
| | - Yiyun Rao
- Molecular, Cellular and Integrative Biosciences Program, The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, 16802, USA
| | - Quyen V Vu
- Institute of Physics, Polish Academy of Sciences; Al. Lotnikow 32/46, 02-668, Warsaw, Poland
| | - Mai Suan Li
- Institute of Physics, Polish Academy of Sciences; Al. Lotnikow 32/46, 02-668, Warsaw, Poland
- Institute for Computational Sciences and Technology; Quang Trung Software City, Tan Chanh Hiep Ward, District 12, Ho Chi Minh City, Vietnam
| | - Justin Pritchard
- Department of Biomedical Engineering, Pennsylvania State University, State College, PA, 16802, USA
- Huck Institute for the Life Sciences, Pennsylvania State University, State College, PA, 16802, USA
| | - Edward P O'Brien
- Department of Chemistry, Pennsylvania State University, University Park, PA, 16802, USA.
- Bioinformatics and Genomics Graduate Program, The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, 16802, USA.
- Institute for Computational and Data Sciences, Pennsylvania State University, University Park, PA, 16802, USA.
| |
Collapse
|
9
|
Salicari L, Trovato A. Entangled Motifs in Membrane Protein Structures. Int J Mol Sci 2023; 24:ijms24119193. [PMID: 37298146 DOI: 10.3390/ijms24119193] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 05/18/2023] [Accepted: 05/20/2023] [Indexed: 06/12/2023] Open
Abstract
Entangled motifs are found in one-third of protein domain structures, a reference set that contains mostly globular proteins. Their properties suggest a connection with co-translational folding. Here, we wish to investigate the presence and properties of entangled motifs in membrane protein structures. From existing databases, we build a non-redundant data set of membrane protein domains, annotated with the monotopic/transmembrane and peripheral/integral labels. We evaluate the presence of entangled motifs using the Gaussian entanglement indicator. We find that entangled motifs appear in one-fifth of transmembrane and one-fourth of monotopic proteins. Surprisingly, the main features of the distribution of the values of the entanglement indicator are similar to the reference case of general proteins. The distribution is conserved across different organisms. Differences with respect to the reference set emerge when considering the chirality of entangled motifs. Although the same chirality bias is found for single-winding motifs in both membrane and reference proteins, the bias is reversed, strikingly, for double-winding motifs only in the reference set. We speculate that these observations can be rationalized in terms of the constraints exerted on the nascent chain by the co-translational bio-genesis machinery, which is different for membrane and globular proteins.
Collapse
Affiliation(s)
- Leonardo Salicari
- Department of Physics and Astronomy 'Galileo Galilei', University of Padova, Via Marzolo 8, 35031 Padova, PD, Italy
- National Institute of Nuclear Physics (INFN), Padova Section, Via Marzolo 8, 35131 Padova, PD, Italy
| | - Antonio Trovato
- Department of Physics and Astronomy 'Galileo Galilei', University of Padova, Via Marzolo 8, 35031 Padova, PD, Italy
- National Institute of Nuclear Physics (INFN), Padova Section, Via Marzolo 8, 35131 Padova, PD, Italy
| |
Collapse
|
10
|
Vu QV, Nissley DA, Jiang Y, O'Brien EP, Li MS. Is Posttranslational Folding More Efficient Than Refolding from a Denatured State: A Computational Study. J Phys Chem B 2023. [PMID: 37200608 DOI: 10.1021/acs.jpcb.3c01694] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The folding of proteins into their native conformation is a complex process that has been extensively studied over the past half-century. The ribosome, the molecular machine responsible for protein synthesis, is known to interact with nascent proteins, adding further complexity to the protein folding landscape. Consequently, it is unclear whether the folding pathways of proteins are conserved on and off the ribosome. The main question remains: to what extent does the ribosome help proteins fold? To address this question, we used coarse-grained molecular dynamics simulations to compare the mechanisms by which the proteins dihydrofolate reductase, type III chloramphenicol acetyltransferase, and d-alanine-d-alanine ligase B fold during and after vectorial synthesis on the ribosome to folding from the full-length unfolded state in bulk solution. Our results reveal that the influence of the ribosome on protein folding mechanisms varies depending on the size and complexity of the protein. Specifically, for a small protein with a simple fold, the ribosome facilitates efficient folding by helping the nascent protein avoid misfolded conformations. However, for larger and more complex proteins, the ribosome does not promote folding and may contribute to the formation of intermediate misfolded states cotranslationally. These misfolded states persist posttranslationally and do not convert to the native state during the 6 μs runtime of our coarse-grain simulations. Overall, our study highlights the complex interplay between the ribosome and protein folding and provides insight into the mechanisms of protein folding on and off the ribosome.
Collapse
Affiliation(s)
- Quyen V Vu
- Institute of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland
| | - Daniel A Nissley
- Department of Statistics, University of Oxford, Oxford OX1 3LB, U.K
| | - Yang Jiang
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802, 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 Computational and Data Sciences, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Mai Suan Li
- Institute of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland
- Institute for Computational Sciences and Technology, Quang Trung Software City, Tan Chanh Hiep Ward, District 12, Ho Chi Minh City 700000, Vietnam
| |
Collapse
|
11
|
Son A, Huizar Cabral V, Huang Z, Litberg TJ, Horowitz S. G-quadruplexes rescuing protein folding. Proc Natl Acad Sci U S A 2023; 120:e2216308120. [PMID: 37155907 PMCID: PMC10194009 DOI: 10.1073/pnas.2216308120] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 04/12/2023] [Indexed: 05/10/2023] Open
Abstract
Maintaining the health of the proteome is a critical cellular task. Recently, we found G-quadruplex (G4) nucleic acids are especially potent at preventing protein aggregation in vitro and could at least indirectly improve the protein folding environment of Escherichia coli. However, the roles of G4s in protein folding were not yet explored. Here, through in vitro protein folding experiments, we discover that G4s can accelerate protein folding by rescuing kinetically trapped intermediates to both native and near-native folded states. Time-course folding experiments in E. coli further demonstrate that these G4s primarily improve protein folding quality in E. coli as opposed to preventing protein aggregation. The ability of a short nucleic acid to rescue protein folding opens up the possibility of nucleic acids and ATP-independent chaperones to play considerable roles in dictating the ultimate folding fate of proteins.
Collapse
Affiliation(s)
- Ahyun Son
- Department of Chemistry & Biochemistry, Knoebel Institute for Healthy Aging, University of Denver, Denver, CO80208
| | - Veronica Huizar Cabral
- Department of Chemistry & Biochemistry, Knoebel Institute for Healthy Aging, University of Denver, Denver, CO80208
| | - Zijue Huang
- Department of Chemistry & Biochemistry, Knoebel Institute for Healthy Aging, University of Denver, Denver, CO80208
| | - Theodore J. Litberg
- Department of Chemistry & Biochemistry, Knoebel Institute for Healthy Aging, University of Denver, Denver, CO80208
| | - Scott Horowitz
- Department of Chemistry & Biochemistry, Knoebel Institute for Healthy Aging, University of Denver, Denver, CO80208
| |
Collapse
|
12
|
Jiang Y, Neti SS, Sitarik I, Pradhan P, To P, Xia Y, Fried SD, Booker SJ, O'Brien EP. How synonymous mutations alter enzyme structure and function over long timescales. Nat Chem 2023; 15:308-318. [PMID: 36471044 PMCID: PMC11267483 DOI: 10.1038/s41557-022-01091-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 10/17/2022] [Indexed: 12/12/2022]
Abstract
The specific activity of enzymes can be altered over long timescales in cells by synonymous mutations that alter a messenger RNA molecule's sequence but not the encoded protein's primary structure. How this happens at the molecular level is unknown. Here, we use multiscale modelling of three Escherichia coli enzymes (type III chloramphenicol acetyltransferase, D-alanine-D-alanine ligase B and dihydrofolate reductase) to understand experimentally measured changes in specific activity due to synonymous mutations. The modelling involves coarse-grained simulations of protein synthesis and post-translational behaviour, all-atom simulations to test robustness and quantum mechanics/molecular mechanics calculations to characterize enzymatic function. We show that changes in codon translation rates induced by synonymous mutations cause shifts in co-translational and post-translational folding pathways that kinetically partition molecules into subpopulations that very slowly interconvert to the native, functional state. Structurally, these states resemble the native state, with localized misfolding near the active sites of the enzymes. These long-lived states exhibit reduced catalytic activity, as shown by their increased activation energies for the reactions they catalyse.
Collapse
Affiliation(s)
- Yang Jiang
- Department of Chemistry, Pennsylvania State University, University Park, PA, USA
| | - Syam Sundar Neti
- Department of Chemistry, Pennsylvania State University, University Park, PA, USA
| | - Ian Sitarik
- Department of Chemistry, Pennsylvania State University, University Park, PA, USA
| | - Priya Pradhan
- Department of Chemistry, Pennsylvania State University, University Park, PA, USA
| | - Philip To
- Department of Chemistry, Johns Hopkins University, Baltimore, MD, USA
| | - Yingzi Xia
- Department of Chemistry, Johns Hopkins University, Baltimore, MD, USA
| | - Stephen D Fried
- Department of Chemistry, Johns Hopkins University, Baltimore, MD, USA
- Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD, USA
| | - Squire J Booker
- Department of Chemistry, Pennsylvania State University, University Park, PA, USA
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA
- Howard Hughes Medical Institute, Pennsylvania State University, University Park, PA, USA
| | - Edward P O'Brien
- Department of Chemistry, Pennsylvania State University, University Park, PA, USA.
- Bioinformatics and Genomics Graduate Program, The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, USA.
- Institute for Computational and Data Sciences, Pennsylvania State University, University Park, PA, USA.
| |
Collapse
|
13
|
Binhi VN. Statistical Amplification of the Effects of Weak Magnetic Fields in Cellular Translation. Cells 2023; 12:cells12050724. [PMID: 36899858 PMCID: PMC10000676 DOI: 10.3390/cells12050724] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 02/21/2023] [Accepted: 02/22/2023] [Indexed: 03/12/2023] Open
Abstract
We assume that the enzymatic processes of recognition of amino acids and their addition to the synthesized molecule in cellular translation include the formation of intermediate pairs of radicals with spin-correlated electrons. The mathematical model presented describes the changes in the probability of incorrectly synthesized molecules in response to a change in the external weak magnetic field. A relatively high chance of errors has been shown to arise from the statistical enhancement of the low probability of local incorporation errors. This statistical mechanism does not require a long thermal relaxation time of electron spins of about 1 μs-a conjecture often used to match theoretical models of magnetoreception with experiments. The statistical mechanism allows for experimental verification by testing the usual Radical Pair Mechanism properties. In addition, this mechanism localizes the site where magnetic effects originate, the ribosome, which makes it possible to verify it by biochemical methods. This mechanism predicts a random nature of the nonspecific effects caused by weak and hypomagnetic fields and agrees with the diversity of biological responses to a weak magnetic field.
Collapse
Affiliation(s)
- Vladimir N Binhi
- Prokhorov General Physics Institute of the Russian Academy of Sciences, 38 Vavilov St., 119991 Moscow, Russia
| |
Collapse
|
14
|
Zhang W, Xiang Y, Xu W. Probing protein higher-order structures by native capillary electrophoresis-mass spectrometry. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
15
|
A proteome-wide map of chaperone-assisted protein refolding in a cytosol-like milieu. Proc Natl Acad Sci U S A 2022; 119:e2210536119. [PMID: 36417429 PMCID: PMC9860312 DOI: 10.1073/pnas.2210536119] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
The journey by which proteins navigate their energy landscapes to their native structures is complex, involving (and sometimes requiring) many cellular factors and processes operating in partnership with a given polypeptide chain's intrinsic energy landscape. The cytosolic environment and its complement of chaperones play critical roles in granting many proteins safe passage to their native states; however, it is challenging to interrogate the folding process for large numbers of proteins in a complex background with most biophysical techniques. Hence, most chaperone-assisted protein refolding studies are conducted in defined buffers on single purified clients. Here, we develop a limited proteolysis-mass spectrometry approach paired with an isotope-labeling strategy to globally monitor the structures of refolding Escherichia coli proteins in the cytosolic medium and with the chaperones, GroEL/ES (Hsp60) and DnaK/DnaJ/GrpE (Hsp70/40). GroEL can refold the majority (85%) of the E. coli proteins for which we have data and is particularly important for restoring acidic proteins and proteins with high molecular weight, trends that come to light because our assay measures the structural outcome of the refolding process itself, rather than binding or aggregation. For the most part, DnaK and GroEL refold a similar set of proteins, supporting the view that despite their vastly different structures, these two chaperones unfold misfolded states, as one mechanism in common. Finally, we identify a cohort of proteins that are intransigent to being refolded with either chaperone. We suggest that these proteins may fold most efficiently cotranslationally, and then remain kinetically trapped in their native conformations.
Collapse
|
16
|
Hassell D, Denney A, Singer E, Benson A, Roth A, Ceglowski J, Steingesser M, McMurray M. Chaperone requirements for de novo folding of Saccharomyces cerevisiae septins. Mol Biol Cell 2022; 33:ar111. [PMID: 35947497 PMCID: PMC9635297 DOI: 10.1091/mbc.e22-07-0262] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 08/02/2022] [Indexed: 11/11/2022] Open
Abstract
Polymers of septin protein complexes play cytoskeletal roles in eukaryotic cells. The specific subunit composition within complexes controls functions and higher-order structural properties. All septins have globular GTPase domains. The other eukaryotic cytoskeletal NTPases strictly require assistance from molecular chaperones of the cytosol, particularly the cage-like chaperonins, to fold into oligomerization-competent conformations. We previously identified cytosolic chaperones that bind septins and influence the oligomerization ability of septins carrying mutations linked to human disease, but it was unknown to what extent wild-type septins require chaperone assistance for their native folding. Here we use a combination of in vivo and in vitro approaches to demonstrate chaperone requirements for de novo folding and complex assembly by budding yeast septins. Individually purified septins adopted nonnative conformations and formed nonnative homodimers. In chaperonin- or Hsp70-deficient cells, septins folded slower and were unable to assemble posttranslationally into native complexes. One septin, Cdc12, was so dependent on cotranslational chaperonin assistance that translation failed without it. Our findings point to distinct translation elongation rates for different septins as a possible mechanism to direct a stepwise, cotranslational assembly pathway in which general cytosolic chaperones act as key intermediaries.
Collapse
Affiliation(s)
- Daniel Hassell
- University of Colorado Anschutz Medical Campus, Aurora, CO 80045
| | - Ashley Denney
- University of Colorado Anschutz Medical Campus, Aurora, CO 80045
| | - Emily Singer
- University of Colorado Anschutz Medical Campus, Aurora, CO 80045
| | - Aleyna Benson
- University of Colorado Anschutz Medical Campus, Aurora, CO 80045
| | - Andrew Roth
- University of Colorado Anschutz Medical Campus, Aurora, CO 80045
| | - Julia Ceglowski
- University of Colorado Anschutz Medical Campus, Aurora, CO 80045
| | - Marc Steingesser
- University of Colorado Anschutz Medical Campus, Aurora, CO 80045
| | - Michael McMurray
- University of Colorado Anschutz Medical Campus, Aurora, CO 80045
| |
Collapse
|
17
|
Dahal N, Sharma S, Phan B, Eis A, Popa I. Mechanical regulation of talin through binding and history-dependent unfolding. SCIENCE ADVANCES 2022; 8:eabl7719. [PMID: 35857491 DOI: 10.1126/sciadv.abl7719] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Talin is a force-sensing multidomain protein and a major player in cellular mechanotransduction. Here, we use single-molecule magnetic tweezers to investigate the mechanical response of the R8 rod domain of talin. We find that under various force cycles, the R8 domain of talin can display a memory-dependent behavior: At the same low force (<10 pN), the same protein molecule shows vastly different unfolding kinetics. This history-dependent behavior indicates the evolution of a unique force-induced native state. We measure through mechanical unfolding that talin R8 domain binds one of its ligands, DLC1, with much higher affinity than previously reported. This strong interaction can explain the antitumor response of DLC1 by regulating inside-out activation of integrins. Together, our results paint a complex picture for the mechanical unfolding of talin in the physiological range and a new mechanism of function of DLC1 to regulate inside-out activation of integrins.
Collapse
Affiliation(s)
- Narayan Dahal
- Department of Physics, University of Wisconsin-Milwaukee, 3135 N. Maryland Ave., Milwaukee, WI 53211, USA
| | - Sabita Sharma
- Department of Physics, University of Wisconsin-Milwaukee, 3135 N. Maryland Ave., Milwaukee, WI 53211, USA
| | - Binh Phan
- Department of Physics, University of Wisconsin-Milwaukee, 3135 N. Maryland Ave., Milwaukee, WI 53211, USA
| | - Annie Eis
- Department of Physics, University of Wisconsin-Milwaukee, 3135 N. Maryland Ave., Milwaukee, WI 53211, USA
| | - Ionel Popa
- Department of Physics, University of Wisconsin-Milwaukee, 3135 N. Maryland Ave., Milwaukee, WI 53211, USA
| |
Collapse
|