1
|
Markthaler D, Fleck M, Stankiewicz B, Hansen N. Exploring the Effect of Enhanced Sampling on Protein Stability Prediction. J Chem Theory Comput 2022; 18:2569-2583. [PMID: 35298174 DOI: 10.1021/acs.jctc.1c01012] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Changes in protein stability due to side-chain mutations are evaluated by alchemical free-energy calculations based on classical molecular dynamics (MD) simulations in explicit solvent using the GROMOS force field. Three proteins of different complexity with a total number of 93 single-point mutations are analyzed, and the relative free-energy differences are discussed with respect to configurational sampling and (dis)agreement with experimental data. For the smallest protein studied, a 34-residue WW domain, the starting structure dependence of the alchemical free-energy changes, is discussed in detail. Deviations from previous simulations for the two other proteins are shown to result from insufficient sampling in the earlier studies. Hamiltonian replica exchange in combination with multiple starting structures and sufficient sampling time of more than 100 ns per intermediate alchemical state is required in some cases to reach convergence.
Collapse
Affiliation(s)
- Daniel Markthaler
- Institute of Thermodynamics and Thermal Process Engineering, University of Stuttgart, Pfaffenwaldring 9, 70569 Stuttgart, Germany
| | - Maximilian Fleck
- Institute of Thermodynamics and Thermal Process Engineering, University of Stuttgart, Pfaffenwaldring 9, 70569 Stuttgart, Germany
| | - Bartosz Stankiewicz
- Institute of Thermodynamics and Thermal Process Engineering, University of Stuttgart, Pfaffenwaldring 9, 70569 Stuttgart, Germany
| | - Niels Hansen
- Institute of Thermodynamics and Thermal Process Engineering, University of Stuttgart, Pfaffenwaldring 9, 70569 Stuttgart, Germany
| |
Collapse
|
2
|
Exposing the distinctive modular behavior of β-strands and α-helices in folded proteins. Proc Natl Acad Sci U S A 2020; 117:28775-28783. [PMID: 33148805 PMCID: PMC7682573 DOI: 10.1073/pnas.1920455117] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Although folded proteins are commonly depicted as simplistic combinations of β-strands and α-helices, the actual properties and functions of these secondary-structure elements in their native contexts are just partly understood. The principal reason is that the behavior of individual β- and α-elements is obscured by the global folding cooperativity. In this study, we have circumvented this problem by designing frustrated variants of the mixed α/β-protein S6, which allow the structural behavior of individual β-strands and α-helices to be targeted selectively by stopped-flow kinetics, X-ray crystallography, and solution-state NMR. Essentially, our approach is based on provoking intramolecular "domain swap." The results show that the α- and β-elements have quite different characteristics: The swaps of β-strands proceed via global unfolding, whereas the α-helices are free to swap locally in the native basin. Moreover, the α-helices tend to hybridize and to promote protein association by gliding over to neighboring molecules. This difference in structural behavior follows directly from hydrogen-bonding restrictions and suggests that the protein secondary structure defines not only tertiary geometry, but also maintains control in function and structural evolution. Finally, our alternative approach to protein folding and native-state dynamics presents a generally applicable strategy for in silico design of protein models that are computationally testable in the microsecond-millisecond regime.
Collapse
|
3
|
Bansal R, Srivastava P, Rathore AS, Chokshi P. Population balance modelling of aggregation of monoclonal antibody based therapeutic proteins. Chem Eng Sci 2020. [DOI: 10.1016/j.ces.2020.115479] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
|
4
|
Becerra D, Butyaev A, Waldispühl J. Fast and flexible coarse-grained prediction of protein folding routes using ensemble modeling and evolutionary sequence variation. Bioinformatics 2020; 36:1420-1428. [PMID: 31584628 DOI: 10.1093/bioinformatics/btz743] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 09/22/2019] [Accepted: 09/28/2019] [Indexed: 11/15/2022] Open
Abstract
MOTIVATION Protein folding is a dynamic process through which polypeptide chains reach their native 3D structures. Although the importance of this mechanism is widely acknowledged, very few high-throughput computational methods have been developed to study it. RESULTS In this paper, we report a computational platform named P3Fold that combines statistical and evolutionary information for predicting and analyzing protein folding routes. P3Fold uses coarse-grained modeling and efficient combinatorial schemes to predict residue contacts and evaluate the folding routes of a protein sequence within minutes or hours. To facilitate access to this technology, we devise graphical representations and implement an interactive web interface that allows end-users to leverage P3Fold predictions. Finally, we use P3Fold to conduct large and short scale experiments on the human proteome that reveal the broad conservation and variations of structural intermediates within protein families. AVAILABILITY AND IMPLEMENTATION A Web server of P3Fold is freely available at http://csb.cs.mcgill.ca/P3Fold. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- David Becerra
- School of Computer Science, McGill University, Montréal, QC H3A 0E9, Canada
| | - Alexander Butyaev
- School of Computer Science, McGill University, Montréal, QC H3A 0E9, Canada
| | - Jérôme Waldispühl
- School of Computer Science, McGill University, Montréal, QC H3A 0E9, Canada
| |
Collapse
|
5
|
Trotter D, Wallin S. Effects of Topology and Sequence in Protein Folding Linked via Conformational Fluctuations. Biophys J 2020; 118:1370-1380. [PMID: 32061276 DOI: 10.1016/j.bpj.2020.01.020] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 12/17/2019] [Accepted: 01/13/2020] [Indexed: 01/18/2023] Open
Abstract
Experiments have compared the folding of proteins with different amino acid sequences but the same basic structure, or fold. Results indicate that folding is robust to sequence variations for proteins with some nonlocal folds, such as all-β, whereas the folding of more local, all-α proteins typically exhibits a stronger sequence dependence. Here, we use a coarse-grained model to systematically study how variations in sequence perturb the folding energy landscapes of three model sequences with 3α, 4β + α, and β-barrel folds, respectively. These three proteins exhibit folding features in line with experiments, including expected rank order in the cooperativity of the folding transition and stability-dependent shifts in the location of the free-energy barrier to folding. Using a generalized-ensemble simulation approach, we determine the thermodynamics of around 2000 sequence variants representing all possible hydrophobic or polar single- and double-point mutations. From an analysis of the subset of stability-neutral mutations, we find that folding is perturbed in a topology-dependent manner, with the β-barrel protein being the most robust. Our analysis shows, in particular, that the magnitude of mutational perturbations of the transition state is controlled in part by the size or "width" of the underlying conformational ensemble. This result suggests that the mutational robustness of the folding of the β-barrel protein is underpinned by its conformationally restricted transition state ensemble, revealing a link between sequence and topological effects in protein folding.
Collapse
Affiliation(s)
- Daniel Trotter
- Department of Physics and Physical Oceanography, Memorial University of Newfoundland, St. John's, Newfoundland, Canada
| | - Stefan Wallin
- Department of Physics and Physical Oceanography, Memorial University of Newfoundland, St. John's, Newfoundland, Canada.
| |
Collapse
|
6
|
Visconti L, Malagrinò F, Broggini L, De Luca CMG, Moda F, Gianni S, Ricagno S, Toto A. Investigating the Molecular Basis of the Aggregation Propensity of the Pathological D76N Mutant of Beta-2 Microglobulin: Role of the Denatured State. Int J Mol Sci 2019; 20:E396. [PMID: 30669253 PMCID: PMC6359115 DOI: 10.3390/ijms20020396] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 01/09/2019] [Accepted: 01/11/2019] [Indexed: 12/23/2022] Open
Abstract
Beta-2 microglobulin (β2m) is a protein responsible for a pathologic condition, known as dialysis-related amyloidosis (DRA), caused by its aggregation and subsequent amyloid formation. A naturally occurring mutation of β2m, D76N, presents a higher amyloidogenic propensity compared to the wild type counterpart. Since the three-dimensional structure of the protein is essentially unaffected by the mutation, the increased aggregation propensity of D76N has been generally ascribed to its lower thermodynamic stability and increased dynamics. In this study we compare the equilibrium unfolding and the aggregation propensity of wild type β2m and D76N variant at different experimental conditions. Our data revealed a surprising effect of the D76N mutation in the residual structure of the denatured state, which appears less compact than that of the wild type protein. A careful investigation of the structural malleability of the denatured state of wild type β2m and D76N pinpoint a clear role of the denatured state in triggering the amyloidogenic propensity of the protein. The experimental results are discussed in the light of the previous work on β2m and its role in disease.
Collapse
Affiliation(s)
- Lorenzo Visconti
- Istituto Pasteur-Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche "A. Rossi Fanelli" and Istituto di Biologia e Patologia Molecolari del CNR, Sapienza Università di Roma, 00185 Rome, Italy.
| | - Francesca Malagrinò
- Istituto Pasteur-Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche "A. Rossi Fanelli" and Istituto di Biologia e Patologia Molecolari del CNR, Sapienza Università di Roma, 00185 Rome, Italy.
| | - Luca Broggini
- Dipartimento di Bioscienze, Università degli Studi di Milano, 20133 Milano, Italy.
| | - Chiara Maria Giulia De Luca
- Fondazione IRCCS Istituto Neurologico Carlo Besta, Divisione di Neurologia 5-Neuropatologia, 20133 Milano, Italy.
| | - Fabio Moda
- Fondazione IRCCS Istituto Neurologico Carlo Besta, Divisione di Neurologia 5-Neuropatologia, 20133 Milano, Italy.
| | - Stefano Gianni
- Istituto Pasteur-Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche "A. Rossi Fanelli" and Istituto di Biologia e Patologia Molecolari del CNR, Sapienza Università di Roma, 00185 Rome, Italy.
| | - Stefano Ricagno
- Dipartimento di Bioscienze, Università degli Studi di Milano, 20133 Milano, Italy.
| | - Angelo Toto
- Istituto Pasteur-Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche "A. Rossi Fanelli" and Istituto di Biologia e Patologia Molecolari del CNR, Sapienza Università di Roma, 00185 Rome, Italy.
| |
Collapse
|
7
|
Gianni S, McCully ME, Malagrinò F, Bonetti D, De Simone A, Brunori M, Daggett V. A Carboxylate to Amide Substitution That Switches Protein Folds. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201807723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Stefano Gianni
- Istituto Pasteur-Fondazione Cenci Bolognetti and; Ist. for Mol. Biol. Pat. of CNR, Dept. Biochemical Sci.; Sapienza, University of Rome; 00185 Rome Italy
| | - Michelle E. McCully
- Department of Bioengineering; University of Washington; Seattle WA 98195-5013 USA
- Department of Biology; Santa Clara University; Santa Clara CA 95050-0268 USA
| | - Francesca Malagrinò
- Istituto Pasteur-Fondazione Cenci Bolognetti and; Ist. for Mol. Biol. Pat. of CNR, Dept. Biochemical Sci.; Sapienza, University of Rome; 00185 Rome Italy
| | - Daniela Bonetti
- Istituto Pasteur-Fondazione Cenci Bolognetti and; Ist. for Mol. Biol. Pat. of CNR, Dept. Biochemical Sci.; Sapienza, University of Rome; 00185 Rome Italy
| | - Alfonso De Simone
- Department of Life Sciences; Imperial College London; South Kensington SW7 2AZ UK
| | - Maurizio Brunori
- Istituto Pasteur-Fondazione Cenci Bolognetti and; Ist. for Mol. Biol. Pat. of CNR, Dept. Biochemical Sci.; Sapienza, University of Rome; 00185 Rome Italy
| | - Valerie Daggett
- Department of Bioengineering; University of Washington; Seattle WA 98195-5013 USA
| |
Collapse
|
8
|
Gianni S, McCully ME, Malagrinò F, Bonetti D, De Simone A, Brunori M, Daggett V. A Carboxylate to Amide Substitution That Switches Protein Folds. Angew Chem Int Ed Engl 2018; 57:12795-12798. [DOI: 10.1002/anie.201807723] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 07/31/2018] [Indexed: 11/11/2022]
Affiliation(s)
- Stefano Gianni
- Istituto Pasteur-Fondazione Cenci Bolognetti and; Ist. for Mol. Biol. Pat. of CNR, Dept. Biochemical Sci.; Sapienza, University of Rome; 00185 Rome Italy
| | - Michelle E. McCully
- Department of Bioengineering; University of Washington; Seattle WA 98195-5013 USA
- Department of Biology; Santa Clara University; Santa Clara CA 95050-0268 USA
| | - Francesca Malagrinò
- Istituto Pasteur-Fondazione Cenci Bolognetti and; Ist. for Mol. Biol. Pat. of CNR, Dept. Biochemical Sci.; Sapienza, University of Rome; 00185 Rome Italy
| | - Daniela Bonetti
- Istituto Pasteur-Fondazione Cenci Bolognetti and; Ist. for Mol. Biol. Pat. of CNR, Dept. Biochemical Sci.; Sapienza, University of Rome; 00185 Rome Italy
| | - Alfonso De Simone
- Department of Life Sciences; Imperial College London; South Kensington SW7 2AZ UK
| | - Maurizio Brunori
- Istituto Pasteur-Fondazione Cenci Bolognetti and; Ist. for Mol. Biol. Pat. of CNR, Dept. Biochemical Sci.; Sapienza, University of Rome; 00185 Rome Italy
| | - Valerie Daggett
- Department of Bioengineering; University of Washington; Seattle WA 98195-5013 USA
| |
Collapse
|
9
|
Ge B, Jiang X, Chen Y, Sun T, Yang Q, Huang F. Kinetic and thermodynamic studies reveal chemokine homologues CC11 and CC24 with an almost identical tertiary structure have different folding pathways. BMC BIOPHYSICS 2017; 10:7. [PMID: 28919974 PMCID: PMC5596964 DOI: 10.1186/s13628-017-0039-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 09/06/2017] [Indexed: 11/10/2022]
Abstract
BACKGROUND Proteins with low sequence identity but almost identical tertiary structure and function have been valuable to uncover the relationship between sequence, tertiary structure, folding mechanism and functions. Two homologous chemokines, CCL11 and CCL24, with low sequence identity but similar tertiary structure and function, provide an excellent model system for respective studies. RESULTS The kinetics and thermodynamics of the two homologous chemokines were systematically characterized. Despite their similar tertiary structures, CCL11 and CCL24 show different thermodynamic stability in guanidine hydrochloride titration, with D50% = 2.20 M and 4.96 M, respectively. The kinetics curves clearly show two phases in the folding/unfolding processes of both CCL11 and CCL24, which suggests the existence of an intermediate state in their folding/unfolding processes. The folding pathway of both CCL11 and CCL24 could be well described using a folding model with an on-pathway folding intermediate. However, the folding kinetics and stability of the intermediate state of CCL11 and CCL24 are obviously different. CONCLUSION Our results suggest homologous proteins with low sequence identity can display almost identical tertiary structure, but very different folding mechanisms, which applies to homologues in the chemokine protein family, extending the general applicability of the above observation.
Collapse
Affiliation(s)
- Baosheng Ge
- Center for Bioengineering and Biotechnology, China University of Petroleum (East China), Qingdao, 266580 People's Republic of China
| | - Xiaoyong Jiang
- Center for Bioengineering and Biotechnology, China University of Petroleum (East China), Qingdao, 266580 People's Republic of China
| | - Yao Chen
- Center for Bioengineering and Biotechnology, China University of Petroleum (East China), Qingdao, 266580 People's Republic of China
| | - Tingting Sun
- Center for Bioengineering and Biotechnology, China University of Petroleum (East China), Qingdao, 266580 People's Republic of China
| | - Qiuxia Yang
- Center for Bioengineering and Biotechnology, China University of Petroleum (East China), Qingdao, 266580 People's Republic of China
| | - Fang Huang
- Center for Bioengineering and Biotechnology, China University of Petroleum (East China), Qingdao, 266580 People's Republic of China
| |
Collapse
|
10
|
Cieplak AS. Protein folding, misfolding and aggregation: The importance of two-electron stabilizing interactions. PLoS One 2017; 12:e0180905. [PMID: 28922400 PMCID: PMC5603215 DOI: 10.1371/journal.pone.0180905] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2017] [Accepted: 06/22/2017] [Indexed: 12/17/2022] Open
Abstract
Proteins associated with neurodegenerative diseases are highly pleiomorphic and may adopt an all-α-helical fold in one environment, assemble into all-β-sheet or collapse into a coil in another, and rapidly polymerize in yet another one via divergent aggregation pathways that yield broad diversity of aggregates’ morphology. A thorough understanding of this behaviour may be necessary to develop a treatment for Alzheimer’s and related disorders. Unfortunately, our present comprehension of folding and misfolding is limited for want of a physicochemical theory of protein secondary and tertiary structure. Here we demonstrate that electronic configuration and hyperconjugation of the peptide amide bonds ought to be taken into account to advance such a theory. To capture the effect of polarization of peptide linkages on conformational and H-bonding propensity of the polypeptide backbone, we introduce a function of shielding tensors of the Cα atoms. Carrying no information about side chain-side chain interactions, this function nonetheless identifies basic features of the secondary and tertiary structure, establishes sequence correlates of the metamorphic and pH-driven equilibria, relates binding affinities and folding rate constants to secondary structure preferences, and manifests common patterns of backbone density distribution in amyloidogenic regions of Alzheimer’s amyloid β and tau, Parkinson’s α-synuclein and prions. Based on those findings, a split-intein like mechanism of molecular recognition is proposed to underlie dimerization of Aβ, tau, αS and PrPC, and divergent pathways for subsequent association of dimers are outlined; a related mechanism is proposed to underlie formation of PrPSc fibrils. The model does account for: (i) structural features of paranuclei, off-pathway oligomers, non-fibrillar aggregates and fibrils; (ii) effects of incubation conditions, point mutations, isoform lengths, small-molecule assembly modulators and chirality of solid-liquid interface on the rate and morphology of aggregation; (iii) fibril-surface catalysis of secondary nucleation; and (iv) self-propagation of infectious strains of mammalian prions.
Collapse
Affiliation(s)
- Andrzej Stanisław Cieplak
- Department of Chemistry, Bilkent University, Ankara, Turkey
- Department of Chemistry, Yale University, New Haven, Connecticut, United States of America
- Department of Chemistry, Brandeis University, Waltham, Massachusetts, United States of America
- * E-mail:
| |
Collapse
|
11
|
Lella M, Mahalakshmi R. Metamorphic Proteins: Emergence of Dual Protein Folds from One Primary Sequence. Biochemistry 2017; 56:2971-2984. [DOI: 10.1021/acs.biochem.7b00375] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Muralikrishna Lella
- Molecular Biophysics Laboratory,
Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal 462066, India
| | - Radhakrishnan Mahalakshmi
- Molecular Biophysics Laboratory,
Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal 462066, India
| |
Collapse
|
12
|
Kukic P, Pustovalova Y, Camilloni C, Gianni S, Korzhnev DM, Vendruscolo M. Structural Characterization of the Early Events in the Nucleation–Condensation Mechanism in a Protein Folding Process. J Am Chem Soc 2017; 139:6899-6910. [DOI: 10.1021/jacs.7b01540] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Predrag Kukic
- Department
of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K
| | - Yulia Pustovalova
- Department
of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, Connecticut 06030, United States
| | - Carlo Camilloni
- Department
of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K
- Technische Universität Mun̈chen Institute for Advanced Study & Department of Chemistry, Lichtenbergstr. 4, 85748 Garching, Germany
| | - Stefano Gianni
- Istituto
Pasteur - Fondazione Cenci Bolognetti and Istituto di Biologia e Patologia
Molecolari del CNR, Dipartimento di Scienze Biochimiche “A.
Rossi Fanelli”, Sapienza Università di Roma, Rome 00185, Italy
| | - Dmitry M. Korzhnev
- Department
of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, Connecticut 06030, United States
| | | |
Collapse
|
13
|
Malhotra P, Udgaonkar JB. How cooperative are protein folding and unfolding transitions? Protein Sci 2016; 25:1924-1941. [PMID: 27522064 PMCID: PMC5079258 DOI: 10.1002/pro.3015] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Revised: 08/09/2016] [Accepted: 08/09/2016] [Indexed: 11/12/2022]
Abstract
A thermodynamically and kinetically simple picture of protein folding envisages only two states, native (N) and unfolded (U), separated by a single activation free energy barrier, and interconverting by cooperative two-state transitions. The folding/unfolding transitions of many proteins occur, however, in multiple discrete steps associated with the formation of intermediates, which is indicative of reduced cooperativity. Furthermore, much advancement in experimental and computational approaches has demonstrated entirely non-cooperative (gradual) transitions via a continuum of states and a multitude of small energetic barriers between the N and U states of some proteins. These findings have been instrumental towards providing a structural rationale for cooperative versus noncooperative transitions, based on the coupling between interaction networks in proteins. The cooperativity inherent in a folding/unfolding reaction appears to be context dependent, and can be tuned via experimental conditions which change the stabilities of N and U. The evolution of cooperativity in protein folding transitions is linked closely to the evolution of function as well as the aggregation propensity of the protein. A large activation energy barrier in a fully cooperative transition can provide the kinetic control required to prevent the accumulation of partially unfolded forms, which may promote aggregation. Nevertheless, increasing evidence for barrier-less "downhill" folding, as well as for continuous "uphill" unfolding transitions, indicate that gradual non-cooperative processes may be ubiquitous features on the free energy landscape of protein folding.
Collapse
Affiliation(s)
- Pooja Malhotra
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru, 560065, India
| | - Jayant B Udgaonkar
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru, 560065, India.
| |
Collapse
|
14
|
Song C, Wang Q, Xue T, Wang Y, Chen G. Molecular dynamics simulations on the conformational transitions from the G A 98 (G A 88) to G B 98 (G B 88) proteins. J Mol Recognit 2016; 29:580-595. [PMID: 27480925 DOI: 10.1002/jmr.2558] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Revised: 06/11/2016] [Accepted: 07/04/2016] [Indexed: 12/19/2022]
Abstract
We performed conventional and targeted molecular dynamics simulations to address the dynamic transition mechanisms of the conformational transitions from the GA 98 protein with only 1 mutation of Leu45Tyr to GB 98 and from the GA 88 protein with 7 mutations of Gly24Ala, Ile25Thr, Ile30Phe, Ile33Tyr, Leu45Tyr, Ile49Thr, and Leu50Lys to GB 88. The results show that the conformational transition mechanism from the mutated 3α GA 98 (GA 88) state to the α+4β GB 98 (GB 88) state via several intermediate conformations involves the bending of loops at the N and C termini firstly, the unfolding of αA and αC, then the traversing of αB, and the formation of the 4β layer with the conversion of the hydrophobic core. The bending of loops at the N and C termini and the formation of the crucial transition conformation with the full unfolded structure are key factors in their transition processes. The communication of the interaction network, the bending directions of loops, and the traversing site of αB in the transition of GA 98 to GB 98 are markedly different from those in GA 88 to GB 88 because of the different mutated residues. The analysis of the correlations and the calculated mass center distances between some segments further supported their conformational transition mechanisms. These results could help people to better understand the Paracelsus challenge. Copyright © 2016 John Wiley & Sons, Ltd.
Collapse
Affiliation(s)
- Chunnian Song
- College of Chemistry, Beijing Normal University, Beijing, China
| | - Qing Wang
- College of Chemistry, Beijing Normal University, Beijing, China
| | - Tuo Xue
- College of Chemistry, Beijing Normal University, Beijing, China
| | - Yan Wang
- College of Chemistry, Beijing Normal University, Beijing, China
| | - Guangju Chen
- College of Chemistry, Beijing Normal University, Beijing, China
| |
Collapse
|
15
|
Examination of the quality of various force fields and solvation models for the equilibrium simulations of GA88 and GB88. J Mol Model 2016; 22:177. [DOI: 10.1007/s00894-016-3027-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 05/31/2016] [Indexed: 10/21/2022]
|
16
|
Sikosek T, Krobath H, Chan HS. Theoretical Insights into the Biophysics of Protein Bi-stability and Evolutionary Switches. PLoS Comput Biol 2016; 12:e1004960. [PMID: 27253392 PMCID: PMC4890782 DOI: 10.1371/journal.pcbi.1004960] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Accepted: 05/04/2016] [Indexed: 11/18/2022] Open
Abstract
Deciphering the effects of nonsynonymous mutations on protein structure is central to many areas of biomedical research and is of fundamental importance to the study of molecular evolution. Much of the investigation of protein evolution has focused on mutations that leave a protein’s folded structure essentially unchanged. However, to evolve novel folds of proteins, mutations that lead to large conformational modifications have to be involved. Unraveling the basic biophysics of such mutations is a challenge to theory, especially when only one or two amino acid substitutions cause a large-scale conformational switch. Among the few such mutational switches identified experimentally, the one between the GA all-α and GB α+β folds is extensively characterized; but all-atom simulations using fully transferrable potentials have not been able to account for this striking switching behavior. Here we introduce an explicit-chain model that combines structure-based native biases for multiple alternative structures with a general physical atomic force field, and apply this construct to twelve mutants spanning the sequence variation between GA and GB. In agreement with experiment, we observe conformational switching from GA to GB upon a single L45Y substitution in the GA98 mutant. In line with the latent evolutionary potential concept, our model shows a gradual sequence-dependent change in fold preference in the mutants before this switch. Our analysis also indicates that a sharp GA/GB switch may arise from the orientation dependence of aromatic π-interactions. These findings provide physical insights toward rationalizing, predicting and designing evolutionary conformational switches. The biological functions of globular proteins are intimately related to their folded structures and their associated conformational fluctuations. Evolution of new structures is an important avenue to new functions. Although many mutations do not change the folded state, experiments indicate that a single amino acid substitution can lead to a drastic change in the folded structure. The physics of this switch-like behavior remains to be elucidated. Here we develop a computational model for the relevant physical forces, showing that mutations can lead to new folds by passing through intermediate sequences where the old and new folds occur with varying probabilities. Our approach helps provide a general physical account of conformational switching in evolution and mutational effects on conformational dynamics.
Collapse
Affiliation(s)
- Tobias Sikosek
- Departments of Biochemistry and Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Heinrich Krobath
- Departments of Biochemistry and Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Hue Sun Chan
- Departments of Biochemistry and Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- * E-mail:
| |
Collapse
|
17
|
Gianni S, Jemth P. Protein folding: Vexing debates on a fundamental problem. Biophys Chem 2016; 212:17-21. [DOI: 10.1016/j.bpc.2016.03.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Revised: 02/25/2016] [Accepted: 03/07/2016] [Indexed: 11/24/2022]
|
18
|
Malhotra P, Udgaonkar JB. Secondary Structural Change Can Occur Diffusely and Not Modularly during Protein Folding and Unfolding Reactions. J Am Chem Soc 2016; 138:5866-78. [DOI: 10.1021/jacs.6b03356] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Pooja Malhotra
- National Centre for Biological
Sciences, Tata Institute of Fundamental Research, Bengaluru 560065, India
| | - Jayant B. Udgaonkar
- National Centre for Biological
Sciences, Tata Institute of Fundamental Research, Bengaluru 560065, India
| |
Collapse
|
19
|
Collins JC, Bedford JT, Greene LH. Elucidating the Key Determinants of Structure, Folding, and Stability for the ( 4β+ α ) Conformation of the B1 Domain of Protein G Using Bioinformatics Approaches. IEEE Trans Nanobioscience 2016; 15:140-7. [PMID: 27071185 DOI: 10.1109/tnb.2016.2546247] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The B1 domain of protein G (GB1) is a small, 56 amino acid bacterial immunoglobulin-binding protein with a 4β+ α fold. Architecturally, it is composed of a two-layer sandwich consisting of a four-stranded β -sheet that packs against an α -helix. Using several bioinformatics approaches, we investigated which residues may be key determinants of this fold. We identified nine structurally conserved amino acids using a conservation analysis and propose they are critical to forming and stabilizing the fold. The nine conserved residues form a predominantly hydrophobic nucleus within the core of GB1. A network analysis of all the long-range interactions in the structure of GB1 in concert with a betweenness centrality analysis revealed the relative significance of each conserved amino acid residue based on the number and location of the interactions. This bioinformatics analysis provides an important foundation for the design and interpretation of both computational and experimental work which may be helpful in solving the protein folding problem.
Collapse
|
20
|
Where the complex things are: single molecule and ensemble spectroscopic investigations of protein folding dynamics. Curr Opin Struct Biol 2015; 36:1-9. [PMID: 26687767 DOI: 10.1016/j.sbi.2015.11.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2015] [Accepted: 11/10/2015] [Indexed: 01/11/2023]
Abstract
Progress in our understanding of the simple folding dynamics of small proteins and the complex dynamics of large proteins is reviewed. Recent characterizations of the folding transition path of small proteins revealed a simple dynamics explainable by the native centric model. In contrast, the accumulated data showed the substates containing residual structures in the unfolded state and partially populated intermediates, causing complexity in the early folding dynamics of small proteins. The size of the unfolded proteins in the absence of denaturants is likely expanded but still controversial. The steady progress in the observation of folding of large proteins has clarified the rapid formation of long-range contacts that seem inconsistent with the native centric model, suggesting that the folding strategy of large proteins is distinct from that of small proteins.
Collapse
|
21
|
Dodson CA, Arbely E. Protein folding of the SAP domain, a naturally occurring two-helix bundle. FEBS Lett 2015; 589:1740-7. [PMID: 26073259 PMCID: PMC4509717 DOI: 10.1016/j.febslet.2015.06.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Revised: 06/01/2015] [Accepted: 06/01/2015] [Indexed: 11/25/2022]
Abstract
Thol SAP domain is one of the smallest model protein folding domains. SAP domain folds through a diffuse transition state in which helix 1 is most formed. Native state stability is dominated by contacts formed after the transition state.
The SAP domain from the Saccharomyces cerevisiae Tho1 protein is comprised of just two helices and a hydrophobic core and is one of the smallest proteins whose folding has been characterised. Φ-value analysis revealed that Tho1 SAP folds through a transition state where helix 1 is the most extensively formed element of secondary structure and flickering native-like core contacts from Leu35 are also present. The contacts that contribute most to native state stability of Tho1 SAP are not formed in the transition state.
Collapse
Affiliation(s)
- Charlotte A Dodson
- MRC Centre for Protein Engineering, Hills Road, Cambridge CB2 0QH, UK; Molecular Medicine, National Heart & Lung Institute, Imperial College London, SAF Building, London SW7 2AZ, UK.
| | - Eyal Arbely
- MRC Centre for Protein Engineering, Hills Road, Cambridge CB2 0QH, UK
| |
Collapse
|
22
|
Foldase and inhibitor functionalities of the pepsinogen prosegment are encoded within discrete segments of the 44 residue domain. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1854:1300-6. [PMID: 26003941 DOI: 10.1016/j.bbapap.2015.05.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2015] [Revised: 05/09/2015] [Accepted: 05/13/2015] [Indexed: 11/22/2022]
Abstract
Pepsin is initially produced as the zymogen pepsinogen, containing a 44 residue prosegment (PS) domain. When folded without the PS, pepsin forms a thermodynamically stable denatured state (refolded pepsin, Rp). To guide native folding, the PS binds to Rp, stabilizes the folding transition state, and binds tightly to native pepsin (Np), thereby driving the folding equilibrium to favor the native state. It is unknown whether these functionalities of the PS are encoded within the entire sequence or within discrete segments. PS residues 1p-29p correspond to a highly conserved region in pepsin-like aspartic proteases and we hypothesized that this segment is critical to PS-catalyzed folding. This notion was tested in the present study by characterizing the ability of various truncated PS peptides to bind Rp, catalyze folding from Rp to Np, and to inhibit Np. Four PS truncations were examined, corresponding to PS residues 1p-16p (PS1-16), 1p-29p (PS1-29), 17p-44p (PS17-44) and 30p-44p (PS30-44). The three PS functionalities could be ascribed primarily to discrete regions within the highly conserved motif: 1p-16p dictated Rp binding, 17p-29p dictated Np binding/inhibition, while the entire 1p-29p dictated transition state binding/catalyzing folding. Conversely, PS30-44 played no obvious role in PS-catalyzed folding; it is hypothesized that this more variable region may serve as a linker between PS1-29 and the mature domain. The high sequence conservation of PS1-29 and its role in catalyzing pepsin folding strongly suggest that there is a conserved PS-catalyzed folding mechanism shared by pepsin-like aspartic proteases with this motif.
Collapse
|
23
|
Saravanan KM, Selvaraj S. Better theoretical models and protein design experiments can help to understand protein folding. J Nat Sci Biol Med 2015; 6:202-4. [PMID: 25810661 PMCID: PMC4367036 DOI: 10.4103/0976-9668.149122] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In our study, we have concluded that two proteins with 88% homology choose different energetically favorable pathways in the very early stage of the folding process to attain their native folds. Subsequent reports from other investigators by performing folding and unfolding kinetics experiments concur with our findings. We herewith discuss the key papers revealing computational and experimental analysis of two designed proteins with similar sequence distant folds. Further we suggest that the theoretical/computational analysis of protein sequences and structures along with the relevant experiments provide a better understanding of the relationship between protein sequence, folding, and structure.
Collapse
Affiliation(s)
- Konda Mani Saravanan
- Centre of Excellence in Bioinformatics, School of Biotechnology, Madurai Kamaraj University, Madurai, India
| | - Samuel Selvaraj
- Department of Bioinformatics, School of Life Sciences, Bharathidasan University, Tiruchirappalli, Tamil Nadu, India
| |
Collapse
|
24
|
Nickson AA, Wensley BG, Clarke J. Take home lessons from studies of related proteins. Curr Opin Struct Biol 2012; 23:66-74. [PMID: 23265640 PMCID: PMC3578095 DOI: 10.1016/j.sbi.2012.11.009] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2012] [Revised: 11/26/2012] [Accepted: 11/27/2012] [Indexed: 11/30/2022]
Abstract
The 'Fold Approach' involves a detailed analysis of the folding of several topologically, structurally and/or evolutionarily related proteins. Such studies can reveal determinants of the folding mechanism beyond the gross topology, and can dissect the residues required for folding from those required for stability or function. While this approach has not yet matured to the point where we can predict the native conformation of any polypeptide chain in silico, it has been able to highlight, amongst others, the specific residues that are responsible for nucleation, pathway malleability, kinetic intermediates, chain knotting, internal friction and Paracelsus switches. Some of the most interesting discoveries have resulted from the attempt to explain differences between homologues.
Collapse
Affiliation(s)
- Adrian A Nickson
- Department of Chemistry, University of Cambridge, Lensfield Rd, Cambridge CB2 1EW, UK.
| | | | | |
Collapse
|
25
|
|