1
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Zhang Y, Li S, Gong X, Chen J. Toward Accurate Simulation of Coupling between Protein Secondary Structure and Phase Separation. J Am Chem Soc 2024; 146:342-357. [PMID: 38112495 PMCID: PMC10842759 DOI: 10.1021/jacs.3c09195] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
Intrinsically disordered proteins (IDPs) frequently mediate phase separation that underlies the formation of a biomolecular condensate. Together with theory and experiment, efficient coarse-grained (CG) simulations have been instrumental in understanding the sequence-specific phase separation of IDPs. However, the widely used Cα-only models are limited in capturing the peptide nature of IDPs, particularly backbone-mediated interactions and effects of secondary structures, in phase separation. Here, we describe a hybrid resolution (HyRes) protein model toward a more accurate description of the backbone and transient secondary structures in phase separation. With an atomistic backbone and coarse-grained side chains, HyRes can semiquantitatively capture the residue helical propensity and overall chain dimension of monomeric IDPs. Using GY-23 as a model system, we show that HyRes is efficient enough for the direct simulation of spontaneous phase separation and, at the same time, appears accurate enough to resolve the effects of single His to Lys mutations. HyRes simulations also successfully predict increased β-structure formation in the condensate, consistent with available experimental CD data. We further utilize HyRes to study the phase separation of TPD-43, where several disease-related mutants in the conserved region (CR) have been shown to affect residual helicities and modulate the phase separation propensity as measured by the saturation concentration. The simulations successfully recapitulate the effect of these mutants on the helicity and phase separation propensity of TDP-43 CR. Analyses reveal that the balance between backbone and side chain-mediated interactions, but not helicity itself, actually determines phase separation propensity. These results support that HyRes represents an effective protein model for molecular simulation of IDP phase separation and will help to elucidate the coupling between transient secondary structures and phase separation.
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Affiliation(s)
| | | | - Xiping Gong
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA
| | - Jianhan Chen
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA
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2
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Zhang Y, Li S, Gong X, Chen J. Accurate Simulation of Coupling between Protein Secondary Structure and Liquid-Liquid Phase Separation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.22.554378. [PMID: 37662293 PMCID: PMC10473686 DOI: 10.1101/2023.08.22.554378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Intrinsically disordered proteins (IDPs) frequently mediate liquid-liquid phase separation (LLPS) that underlies the formation of membraneless organelles. Together with theory and experiment, efficient coarse-grained (CG) simulations have been instrumental in understanding sequence-specific phase separation of IDPs. However, the widely-used Cα-only models are severely limited in capturing the peptide nature of IDPs, including backbone-mediated interactions and effects of secondary structures, in LLPS. Here, we describe a hybrid resolution (HyRes) protein model for accurate description of the backbone and transient secondary structures in LLPS. With an atomistic backbone and coarse-grained side chains, HyRes accurately predicts the residue helical propensity and chain dimension of monomeric IDPs. Using GY-23 as a model system, we show that HyRes is efficient enough for direct simulation of spontaneous phase separation, and at the same time accurate enough to resolve the effects of single mutations. HyRes simulations also successfully predict increased beta-sheet formation in the condensate, consistent with available experimental data. We further utilize HyRes to study the phase separation of TPD-43, where several disease-related mutants in the conserved region (CR) have been shown to affect residual helicities and modulate LLPS propensity. The simulations successfully recapitulate the effect of these mutants on the helicity and LLPS propensity of TDP-43 CR. Analyses reveal that the balance between backbone and sidechain-mediated interactions, but not helicity itself, actually determines LLPS propensity. We believe that the HyRes model represents an important advance in the molecular simulation of LLPS and will help elucidate the coupling between IDP transient secondary structures and phase separation.
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Affiliation(s)
| | | | - Xiping Gong
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA
| | - Jianhan Chen
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA
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3
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Yu J, Zhang ZW, Yang HY, Liu CJ, Lu WC. Study of fusion peptide release for the spike protein of SARS-CoV-2. RSC Adv 2023; 13:16970-16983. [PMID: 37288377 PMCID: PMC10242618 DOI: 10.1039/d3ra01764h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 05/11/2023] [Indexed: 06/09/2023] Open
Abstract
The spike protein of SARS-CoV-2 can recognize the ACE2 membrane protein on the host cell and plays a key role in the membrane fusion process between the virus envelope and the host cell membrane. However, to date, the mechanism for the spike protein recognizing host cells and initiating membrane fusion remains unknown. In this study, based on the general assumption that all three S1/S2 junctions of the spike protein are cleaved, structures with different forms of S1 subunit stripping and S2' site cleavage were constructed. Then, the minimum requirement for the release of the fusion peptide was studied by all-atom structure-based MD simulations. The results from simulations showed that stripping an S1 subunit from the A-, B- or C-chain of the spike protein and cleaving the specific S2' site on the B-chain (C-chain or A-chain) may result in the release of the fusion peptide, suggesting that the requirement for the release of FP may be more relaxed than previously expected.
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Affiliation(s)
- Jie Yu
- College of Physics, Qingdao University Qingdao 266071 Shandong P. R. China
| | - Zhi-Wei Zhang
- College of Physics, Qingdao University Qingdao 266071 Shandong P. R. China
| | - Han-Yu Yang
- College of Physics, Qingdao University Qingdao 266071 Shandong P. R. China
| | - Chong-Jin Liu
- College of Physics, Qingdao University Qingdao 266071 Shandong P. R. China
| | - Wen-Cai Lu
- College of Physics, Qingdao University Qingdao 266071 Shandong P. R. China
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4
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Hsueh SCC, Aina A, Plotkin SS. Ensemble Generation for Linear and Cyclic Peptides Using a Reservoir Replica Exchange Molecular Dynamics Implementation in GROMACS. J Phys Chem B 2022; 126:10384-10399. [PMID: 36410027 DOI: 10.1021/acs.jpcb.2c05470] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The profile of shapes presented by a cyclic peptide modulates its therapeutic efficacy and is represented by the ensemble of its sampled conformations. Although some algorithms excel at creating a diverse ensemble of cyclic peptide conformations, they seldom address the entropic contribution of flexible conformations and often have significant practical difficulty producing an ensemble with converged and reliable thermodynamic properties. In this study, an accelerated molecular dynamics (MD) method, namely, reservoir replica exchange MD (R-REMD or Res-REMD), was implemented in GROMACS ver. 4.6.7 and benchmarked on two small cyclic peptide model systems: a cyclized furin cleavage site of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike (cyclo-(CGPRRARSG)) and oxytocin (disulfide-bonded CYIQNCPLG). Additionally, we also benchmarked Res-REMD on alanine dipeptide and Trpzip2 to demonstrate its validity and efficiency over REMD. For Trpzip2, Res-REMD coupled with an umbrella-sampling-derived reservoir generated similar folded fractions as regular REMD but on a much faster time scale. For cyclic peptides, Res-REMD appeared to be marginally faster than REMD in ensemble generation. Finally, Res-REMD was more effective in sampling rare events such as trans to cis peptide bond isomerization. We provide a GitHub page with the modified GROMACS source code for running Res-REMD at https://github.com/PlotkinLab/Reservoir-REMD.
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Affiliation(s)
- Shawn C C Hsueh
- Department of Physics and Astronomy, The University of British Columbia, Vancouver, BCV6T 1Z1, Canada
| | - Adekunle Aina
- Department of Physics and Astronomy, The University of British Columbia, Vancouver, BCV6T 1Z1, Canada
| | - Steven S Plotkin
- Department of Physics and Astronomy, The University of British Columbia, Vancouver, BCV6T 1Z1, Canada.,Genome Science and Technology Program, The University of British Columbia, Vancouver, BCV6T 1Z1, Canada
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5
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Pal S, Mitra RK. Nonpolar hydrophobic amino acids tune the enzymatic activity of lysozyme. Biophys Chem 2022; 288:106842. [PMID: 35696897 DOI: 10.1016/j.bpc.2022.106842] [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: 02/15/2022] [Revised: 05/19/2022] [Accepted: 05/26/2022] [Indexed: 11/02/2022]
Abstract
We have used five different hydrophobic L-amino acids (Gly, Ala, Val, Leu, Ile) as molecular crowders to investigate their role on the enzymatic activity of lysozyme towards Micrococcus lysodeikticus (M. lys.)cell as substrate. We found that except Ile, all other amino acids show a bell like profile of catalytic efficiency (kcat/Km) with their increasing concentration whereas for Ile, the value is gradually increasing. The trend of activation energy (Ea) is also well correlated with the catalytic efficiency of lysozyme. At low concentration of amino acids, soft interaction predominates whereas at higher concentration range, excluded volume, viscosity, hydrophobicity combinedly decrease the activity of lysozyme.
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Affiliation(s)
- Saikat Pal
- Department of Chemical, Biological and Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake, Kolkata 700106, India
| | - Rajib Kumar Mitra
- Department of Chemical, Biological and Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake, Kolkata 700106, India.
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6
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Leavens MJ, Spang LE, Cherney MM, Bowler BE. Denatured State Conformational Biases in Three-Helix Bundles Containing Divergent Sequences Localize near Turns and Helix Capping Residues. Biochemistry 2021; 60:3071-3085. [PMID: 34606713 PMCID: PMC8751257 DOI: 10.1021/acs.biochem.1c00400] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Rhodopseudomonas palustris cytochrome c', a four-helix bundle, and the second ubiquitin-associated domain, UBA(2), a three-helix bundle from the human homologue of yeast Rad23, HHR23A, deviate from random coil behavior under denaturing conditions in a fold-specific manner. The random coil deviations in each of these folds occur near interhelical turns and loops in their tertiary structures. Here, we examine an additional three-helix bundle with an identical fold to UBA(2), but a highly divergent sequence, the first ubiquitin-associated domain, UBA(1), of HHR23A. We use histidine-heme loop formation methods, employing eight single histidine variants, to probe for denatured state conformational bias of a UBA(1) domain fused to the N-terminus of iso-1-cytochrome c (iso-1-Cytc). Guanidine hydrochloride (GuHCl) denaturation shows that the iso-1-Cytc domain unfolds first, followed by the UBA(1) domain. Denatured state (4 and 6 M GuHCl) histidine-heme loop formation studies show that as the size of the histidine-heme loop increases, loop stability decreases, as expected for the Jacobson-Stockmayer relationship. However, loops formed with His35, His31, and His15, of UBA(1), are 0.6-1.1 kcal/mol more stable than expected from the Jacobson-Stockmayer relationship, confirming the importance of deviations of the denatured state from random coil behavior near interhelical turns of helical domains for facilitating folding to the correct topology. For UBA(1) and UBA(2), hydrophobic clusters on either side of the turns partially explain deviations from random coil behavior; however, helix capping also appears to be important.
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Affiliation(s)
- Moses J. Leavens
- Department of Chemistry & Biochemistry, University of Montana, Missoula, Montana 59812, United States
- Center for Biomolecular Structure & Dynamics, University of Montana, Missoula, Montana 59812, United States
| | - Lisa E. Spang
- Department of Chemistry & Biochemistry, University of Montana, Missoula, Montana 59812, United States
- Center for Biomolecular Structure & Dynamics, University of Montana, Missoula, Montana 59812, United States
| | - Melisa M. Cherney
- Department of Chemistry & Biochemistry, University of Montana, Missoula, Montana 59812, United States
- Center for Biomolecular Structure & Dynamics, University of Montana, Missoula, Montana 59812, United States
| | - Bruce E. Bowler
- Department of Chemistry & Biochemistry, University of Montana, Missoula, Montana 59812, United States
- Center for Biomolecular Structure & Dynamics, University of Montana, Missoula, Montana 59812, United States
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7
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Dodero-Rojas E, Onuchic JN, Whitford PC. Sterically confined rearrangements of SARS-CoV-2 Spike protein control cell invasion. eLife 2021; 10:70362. [PMID: 34463614 PMCID: PMC8456623 DOI: 10.7554/elife.70362] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 08/06/2021] [Indexed: 12/13/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is highly contagious, and transmission involves a series of processes that may be targeted by vaccines and therapeutics. During transmission, host cell invasion is controlled by a large-scale (200–300 Å) conformational change of the Spike protein. This conformational rearrangement leads to membrane fusion, which creates transmembrane pores through which the viral genome is passed to the host. During Spike-protein-mediated fusion, the fusion peptides must be released from the core of the protein and associate with the host membrane. While infection relies on this transition between the prefusion and postfusion conformations, there has yet to be a biophysical characterization reported for this rearrangement. That is, structures are available for the endpoints, though the intermediate conformational processes have not been described. Interestingly, the Spike protein possesses many post-translational modifications, in the form of branched glycans that flank the surface of the assembly. With the current lack of data on the pre-to-post transition, the precise role of glycans during cell invasion has also remained unclear. To provide an initial mechanistic description of the pre-to-post rearrangement, an all-atom model with simplified energetics was used to perform thousands of simulations in which the protein transitions between the prefusion and postfusion conformations. These simulations indicate that the steric composition of the glycans can induce a pause during the Spike protein conformational change. We additionally show that this glycan-induced delay provides a critical opportunity for the fusion peptides to capture the host cell. In contrast, in the absence of glycans, the viral particle would likely fail to enter the host. This analysis reveals how the glycosylation state can regulate infectivity, while providing a much-needed structural framework for studying the dynamics of this pervasive pathogen.
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Affiliation(s)
- Esteban Dodero-Rojas
- Center for Theoretical Biological Physics, Rice University, Houston, United States
| | - Jose N Onuchic
- Center for Theoretical Biological Physics, Rice University, Houston, United States.,Department of Physics and Astronomy, Rice University, Houston, United States.,Department of Chemistry, Rice University, Houston, United States.,Department of Biosciences, Rice University, Houston, United States
| | - Paul Charles Whitford
- Center for Theoretical Biological Physics, Northeastern University, Boston, United States.,Department of Physics, Northeastern University, Boston, United States
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8
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Lu J, Zhang X, Wu Y, Sheng Y, Li W, Wang W. Energy landscape remodeling mechanism of Hsp70-chaperone-accelerated protein folding. Biophys J 2021; 120:1971-1983. [PMID: 33745889 PMCID: PMC8204389 DOI: 10.1016/j.bpj.2021.03.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 02/02/2021] [Accepted: 03/12/2021] [Indexed: 11/29/2022] Open
Abstract
Hsp70 chaperone is one of the key protein machines responsible for the quality control of protein production in cells. Facilitating in vivo protein folding by counteracting misfolding and aggregation is the essence of its biological function. Although the allosteric cycle during its functional actions has been well characterized both experimentally and computationally, the mechanism by which Hsp70 assists protein folding is still not fully understood. In this work, we studied the Hsp70-mediated folding of model proteins with rugged energy landscape by using molecular simulations. Different from the canonical scenario of Hsp70 functioning, which assumes that folding of substrate proteins occurs spontaneously after releasing from chaperones, our results showed that the substrate protein remains in contacts with the chaperone during its folding process. The direct chaperone-substrate interactions in the open conformation of Hsp70 tend to shield the substrate sites prone to form non-native contacts, which therefore avoids the frustrated folding pathway, leading to a higher folding rate and less probability of misfolding. Our results suggest that in addition to the unfoldase and holdase functions widely addressed in previous studies, Hsp70 can facilitate the folding of its substrate proteins by remodeling the folding energy landscape and directing the folding processes, demonstrating the foldase scenario. These findings add new, to our knowledge, insights into the general molecular mechanisms of chaperone-mediated protein folding.
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Affiliation(s)
- Jiajun Lu
- Department of Physics, National Laboratory of Solid State Microstructure, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing, China
| | - Xiaoyi Zhang
- Department of Physics, National Laboratory of Solid State Microstructure, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing, China
| | - Yichao Wu
- Department of Physics, National Laboratory of Solid State Microstructure, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing, China
| | - Yuebiao Sheng
- Department of Physics, National Laboratory of Solid State Microstructure, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing, China
| | - Wenfei Li
- Department of Physics, National Laboratory of Solid State Microstructure, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing, China.
| | - Wei Wang
- Department of Physics, National Laboratory of Solid State Microstructure, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing, China.
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9
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Zhang H, Zhang H, Chen C. Investigating the folding mechanism of the N-terminal domain of ribosomal protein L9. Proteins 2021; 89:832-844. [PMID: 33576138 DOI: 10.1002/prot.26062] [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: 10/07/2020] [Revised: 01/04/2021] [Accepted: 01/31/2021] [Indexed: 11/10/2022]
Abstract
Protein folding is a popular topic in the life science. However, due to the limited sampling ability of experiments and simulations, the general folding mechanism is not yet clear to us. In this work, we study the folding of the N-terminal domain of ribosomal protein L9 (NTL9) in detail by a mixing replica exchange molecular dynamics method. The simulation results are close to previous experimental observations. According to the Markov state model, the folding of the protein follows a nucleation-condensation path. Moreover, after the comparison to its 39-residue β-α-β motif, we find that the helix at the C-terminal has a great influence on the folding process of the intact protein, including the nucleation of the key residues in the transition state ensemble and the packing of the hydrophobic residues in the native state.
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Affiliation(s)
- Haozhe Zhang
- Biomolecular Physics and Modeling Group, School of Physics, Huazhong University of Science and Technology, Wuhan, China
| | - Haomiao Zhang
- Biomolecular Physics and Modeling Group, School of Physics, Huazhong University of Science and Technology, Wuhan, China
| | - Changjun Chen
- Biomolecular Physics and Modeling Group, School of Physics, Huazhong University of Science and Technology, Wuhan, China
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10
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Dong S, Luo S, Huang K, Zhao X, Duan L, Li H. Insights into four helical proteins folding via self-guided Langevin dynamics simulation. Mol Phys 2021. [DOI: 10.1080/00268976.2021.1874558] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Shuheng Dong
- School of Physics and Electronics, Shandong Normal University, Jinan, People’s Republic of China
| | - Song Luo
- School of Physics and Electronics, Shandong Normal University, Jinan, People’s Republic of China
| | - Kaifang Huang
- School of Physics and Electronics, Shandong Normal University, Jinan, People’s Republic of China
| | - Xiaoyu Zhao
- School of Physics and Electronics, Shandong Normal University, Jinan, People’s Republic of China
| | - Lili Duan
- School of Physics and Electronics, Shandong Normal University, Jinan, People’s Republic of China
| | - Hao Li
- School of Physics and Electronics, Shandong Normal University, Jinan, People’s Republic of China
- Department of Science and Technology, Shandong Normal University, Jinan, People’s Republic of China
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11
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Neelamraju S, Wales DJ, Gosavi S. Protein energy landscape exploration with structure-based models. Curr Opin Struct Biol 2020; 64:145-151. [DOI: 10.1016/j.sbi.2020.07.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 06/30/2020] [Accepted: 07/15/2020] [Indexed: 12/11/2022]
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12
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Perego C, Potestio R. Searching the Optimal Folding Routes of a Complex Lasso Protein. Biophys J 2019; 117:214-228. [PMID: 31235180 PMCID: PMC6700606 DOI: 10.1016/j.bpj.2019.05.025] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 04/29/2019] [Accepted: 05/30/2019] [Indexed: 10/27/2022] Open
Abstract
Understanding how polypeptides can efficiently and reproducibly attain a self-entangled conformation is a compelling biophysical challenge that might shed new light on our general knowledge of protein folding. Complex lassos, namely self-entangled protein structures characterized by a covalent loop sealed by a cysteine bridge, represent an ideal test system in the framework of entangled folding. Indeed, because cysteine bridges form in oxidizing conditions, they can be used as on/off switches of the structure topology to investigate the role played by the backbone entanglement in the process. In this work, we have used molecular dynamics to simulate the folding of a complex lasso glycoprotein, granulocyte-macrophage colony-stimulating factor, modeling both reducing and oxidizing conditions. Together with a well-established Gō-like description, we have employed the elastic folder model, a coarse-grained, minimalistic representation of the polypeptide chain driven by a structure-based angular potential. The purpose of this study is to assess the kinetically optimal pathways in relation to the formation of the native topology. To this end, we have implemented an evolutionary strategy that tunes the elastic folder model potentials to maximize the folding probability within the early stages of the dynamics. The resulting protein model is capable of folding with high success rate, avoiding the kinetic traps that hamper the efficient folding in the other tested models. Employing specifically designed topological descriptors, we could observe that the selected folding routes avoid the topological bottleneck by locking the cysteine bridge after the topology is formed. These results provide valuable insights on the selection of mechanisms in self-entangled protein folding while, at the same time, the proposed methodology can complement the usage of established minimalistic models and draw useful guidelines for more detailed simulations.
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Affiliation(s)
- Claudio Perego
- Polymer Theory Department, Max Planck Institute for Polymer Research, Mainz, Germany.
| | - Raffaello Potestio
- Department of Physics, University of Trento, Trento, Italy; INFN-TIFPA, Trento Institute for Fundamental Physics and Applications, Trento, Italy
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13
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Peter EK, Černý J. A Hybrid Hamiltonian for the Accelerated Sampling along Experimental Restraints. Int J Mol Sci 2019; 20:E370. [PMID: 30654563 PMCID: PMC6359555 DOI: 10.3390/ijms20020370] [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: 12/17/2018] [Revised: 01/07/2019] [Accepted: 01/10/2019] [Indexed: 12/25/2022] Open
Abstract
In this article, we present an enhanced sampling method based on a hybrid Hamiltonian which combines experimental distance restraints with a bias dependent from multiple path-dependent variables. This simulation method determines the bias-coordinates on the fly and does not require a priori knowledge about reaction coordinates. The hybrid Hamiltonian accelerates the sampling of proteins, and, combined with experimental distance information, the technique considers the restraints adaptively and in dependency of the system's intrinsic dynamics. We validate the methodology on the dipole relaxation of two water models and the conformational landscape of dialanine. Using experimental NMR-restraint data, we explore the folding landscape of the TrpCage mini-protein and in a second example apply distance restraints from chemical crosslinking/mass spectrometry experiments for the sampling of the conformation space of the Killer Cell Lectin-like Receptor Subfamily B Member 1A (NKR-P1A). The new methodology has the potential to adaptively introduce experimental restraints without affecting the conformational space of the system along an ergodic trajectory. Since only a limited number of input- and no-order parameters are required for the setup of the simulation, the method is broadly applicable and has the potential to be combined with coarse-graining methods.
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Affiliation(s)
- Emanuel K Peter
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Průmyslová 595, 252 50 Vestec, Prague West, Czech Republic.
| | - Jiří Černý
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Průmyslová 595, 252 50 Vestec, Prague West, Czech Republic.
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14
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Peter EK, Cerny J. Enriched Conformational Sampling of DNA and Proteins with a Hybrid Hamiltonian Derived from the Protein Data Bank. Int J Mol Sci 2018; 19:E3405. [PMID: 30380800 PMCID: PMC6274895 DOI: 10.3390/ijms19113405] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2018] [Revised: 10/22/2018] [Accepted: 10/27/2018] [Indexed: 12/26/2022] Open
Abstract
In this article, we present a method for the enhanced molecular dynamics simulation of protein and DNA systems called potential of mean force (PMF)-enriched sampling. The method uses partitions derived from the potentials of mean force, which we determined from DNA and protein structures in the Protein Data Bank (PDB). We define a partition function from a set of PDB-derived PMFs, which efficiently compensates for the error introduced by the assumption of a homogeneous partition function from the PDB datasets. The bias based on the PDB-derived partitions is added in the form of a hybrid Hamiltonian using a renormalization method, which adds the PMF-enriched gradient to the system depending on a linear weighting factor and the underlying force field. We validated the method using simulations of dialanine, the folding of TrpCage, and the conformational sampling of the Dickerson⁻Drew DNA dodecamer. Our results show the potential for the PMF-enriched simulation technique to enrich the conformational space of biomolecules along their order parameters, while we also observe a considerable speed increase in the sampling by factors ranging from 13.1 to 82. The novel method can effectively be combined with enhanced sampling or coarse-graining methods to enrich conformational sampling with a partition derived from the PDB.
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Affiliation(s)
- Emanuel K Peter
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Průmyslová 595, 252 50 Vestec, Czech Republic.
| | - Jiri Cerny
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Průmyslová 595, 252 50 Vestec, Czech Republic.
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15
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Terse VL, Gosavi S. The Sensitivity of Computational Protein Folding to Contact Map Perturbations: The Case of Ubiquitin Folding and Function. J Phys Chem B 2018; 122:11497-11507. [PMID: 30234303 DOI: 10.1021/acs.jpcb.8b07409] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Ubiquitin is a small model protein, commonly used in protein folding experiments and simulations. We simulated ubiquitin using a well-tested structure-based model coarse-grained to a Cα level (Cα-SBM) and found that the simulated folding route did not agree with the experimentally observed one. Simulating the Cα-SBM with a cutoff contact map, instead of a screened contact map, switched the folding route with the new route matching the experimental route. Thus, the simulated folding of ubiquitin is sensitive to contact map definition. The screened contact map, which is used in folding simulations because it captures protein folding cooperativity, removes contacts in which the atoms in contact are occluded by a third atom and is less sensitive to the value of the cutoff distance in well-packed regions of the protein. In sparsely packed regions, the larger cutoff distance creates bridging contacts between atoms which are separated by voids. Such contacts do not seem to affect the folding of most proteins, including those of the ubiquitin fold. However, the surface of ubiquitin has several protruding functional side chains which naturally create bridging contacts. Together, our results show that subtle structural features of a protein that may not be apparent by mere observation can be identified by comparing folding simulations of SBMs in which these features are differently encoded. When such structural features are preserved for functional reasons, differences in computational folding can be leveraged to identify functional features. Notably, such features are accessible to a gradation of SBMs even in commonly studied proteins such as ubiquitin.
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Affiliation(s)
- Vishram L Terse
- Simons Centre for the Study of Living Machines , National Centre for Biological Sciences , Tata Institute of Fundamental Research, Bangalore 560065 , India
| | - Shachi Gosavi
- Simons Centre for the Study of Living Machines , National Centre for Biological Sciences , Tata Institute of Fundamental Research, Bangalore 560065 , India
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16
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Simulations Reveal Multiple Intermediates in the Unzipping Mechanism of Neuronal SNARE Complex. Biophys J 2018; 115:1470-1480. [PMID: 30268539 DOI: 10.1016/j.bpj.2018.08.043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 07/26/2018] [Accepted: 08/16/2018] [Indexed: 11/22/2022] Open
Abstract
The assembling of the soluble N-ethylmaleimide-sensitive factor attachment protein receptor protein complex is a fundamental step in neuronal exocytosis, and it has been extensively studied in the last two decades. Yet, many details of this process remain inaccessible with the current experimental space and time resolution. Here, we study the zipping mechanism of the soluble N-ethylmaleimide-sensitive factor attachment protein receptor complex computationally by using a coarse-grained model. We explore the different pathways available and analyze their dependence on the computational model employed. We reveal and characterize multiple intermediate states, in agreement with previous experimental findings. We use our model to analyze the influence of single-residue mutations on the thermodynamics of the folding process.
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17
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Nonnative Energetic Frustrations in Protein Folding at Residual Level: A Simulation Study of Homologous Immunoglobulin-like β-Sandwich Proteins. Int J Mol Sci 2018; 19:ijms19051515. [PMID: 29783701 PMCID: PMC5983731 DOI: 10.3390/ijms19051515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 05/08/2018] [Accepted: 05/09/2018] [Indexed: 11/16/2022] Open
Abstract
Nonnative interactions cause energetic frustrations in protein folding and were found to dominate key events in folding intermediates. However, systematically characterizing energetic frustrations that are caused by nonnative intra-residue interactions at residual resolution is still lacking. Recently, we studied the folding of a set of homologous all-α proteins and found that nonnative-contact-based energetic frustrations are highly correlated to topology of the protein native-contact network. Here, we studied the folding of nine homologous immunoglobulin-like (Ig-like) β-sandwich proteins, and examined nonnative-contact-based energetic frustrations Gō-like model. Our calculations showed that nonnative-interaction-based energetic frustrations in β-sandwich proteins are much more complicated than those in all-α proteins, and they exhibit highly heterogeneous effects on the folding of secondary structures. Further, the nonnative interactions introduced distinct correlations in the folding of different folding-patches of β-sandwich proteins. Taken together, a strong interplay might exist between nonnative-interaction energetic frustrations and the protein native-contact networks, which ensures that β-sandwich domains adopt a common folding mechanism.
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18
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Huynh L, Neale C, Pomès R, Chan HS. Molecular recognition and packing frustration in a helical protein. PLoS Comput Biol 2017; 13:e1005909. [PMID: 29261665 PMCID: PMC5757960 DOI: 10.1371/journal.pcbi.1005909] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Revised: 01/08/2018] [Accepted: 11/28/2017] [Indexed: 01/25/2023] Open
Abstract
Biomolecular recognition entails attractive forces for the functional native states and discrimination against potential nonnative interactions that favor alternate stable configurations. The challenge posed by the competition of nonnative stabilization against native-centric forces is conceptualized as frustration. Experiment indicates that frustration is often minimal in evolved biological systems although nonnative possibilities are intuitively abundant. Much of the physical basis of minimal frustration in protein folding thus remains to be elucidated. Here we make progress by studying the colicin immunity protein Im9. To assess the energetic favorability of nonnative versus native interactions, we compute free energies of association of various combinations of the four helices in Im9 (referred to as H1, H2, H3, and H4) by extensive explicit-water molecular dynamics simulations (total simulated time > 300 μs), focusing primarily on the pairs with the largest native contact surfaces, H1-H2 and H1-H4. Frustration is detected in H1-H2 packing in that a nonnative packing orientation is significantly stabilized relative to native, whereas such a prominent nonnative effect is not observed for H1-H4 packing. However, in contrast to the favored nonnative H1-H2 packing in isolation, the native H1-H2 packing orientation is stabilized by H3 and loop residues surrounding H4. Taken together, these results showcase the contextual nature of molecular recognition, and suggest further that nonnative effects in H1-H2 packing may be largely avoided by the experimentally inferred Im9 folding transition state with native packing most developed at the H1-H4 rather than the H1-H2 interface. Biomolecules need to recognize one another with high specificity: promoting “native” functional intermolecular binding events while avoiding detrimental “nonnative” bound configurations; i.e., “frustration”—the tendency for nonnative interactions—has to be minimized. Folding of globular proteins entails a similar discrimination. To gain physical insight, we computed the binding affinities of helical structures of the protein Im9 in various native or nonnative configurations by atomic simulations, discovering that partial packing of the Im9 core is frustrated. This frustration is overcome when the entire core of the protein is assembled, consistent with experiment indicating no significant kinetic trapping in Im9 folding. Our systematic analysis thus reveals a subtle, contextual aspect of biomolecular recognition and provides a general approach to characterize folding frustration.
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Affiliation(s)
- Loan Huynh
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Chris Neale
- Department of Physics, Applied Physics, and Astronomy, Rensselaer Polytechnic Institute, Troy, New York, United States of America
| | - Régis Pomès
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
- Molecular Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
- * E-mail: (HSC); (RP)
| | - Hue Sun Chan
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- * E-mail: (HSC); (RP)
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19
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Niewieczerzal S, Sulkowska JI. Knotting and unknotting proteins in the chaperonin cage: Effects of the excluded volume. PLoS One 2017; 12:e0176744. [PMID: 28489858 PMCID: PMC5425179 DOI: 10.1371/journal.pone.0176744] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Accepted: 04/14/2017] [Indexed: 11/18/2022] Open
Abstract
Molecular dynamics simulations are used to explore the effects of chaperonin-like cages on knotted proteins with very low sequence similarity, different depths of a knot but with a similar fold, and the same type of topology. The investigated proteins are VirC2, DndE and MJ0366 with two depths of a knot. A comprehensive picture how encapsulation influences folding rates is provided based on the analysis of different cage sizes and temperature conditions. Neither of these two effects with regard to knotted proteins has been studied by means of molecular dynamics simulations with coarse-grained structure-based models before. We show that encapsulation in a chaperonin is sufficient to self-tie and untie small knotted proteins (VirC2, DndE), for which the equilibrium process is not accessible in the bulk solvent. Furthermore, we find that encapsulation reduces backtracking that arises from the destabilisation of nucleation sites, smoothing the free energy landscape. However, this effect can also be coupled with temperature rise. Encapsulation facilitates knotting at the early stage of folding and can enhance an alternative folding route. Comparison to unknotted proteins with the same fold shows directly how encapsulation influences the free energy landscape. In addition, we find that as the size of the cage decreases, folding times increase almost exponentially in a certain range of cage sizes, in accordance with confinement theory and experimental data for unknotted proteins.
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Affiliation(s)
- Szymon Niewieczerzal
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland
| | - Joanna I. Sulkowska
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland
- Department of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
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20
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Zhu G, Saw WG, Nalaparaju A, Grüber G, Lu L. Coarse-Grained Molecular Modeling of the Solution Structure Ensemble of Dengue Virus Nonstructural Protein 5 with Small-Angle X-ray Scattering Intensity. J Phys Chem B 2017; 121:2252-2264. [DOI: 10.1021/acs.jpcb.7b00051] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Guanhua Zhu
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551 Singapore
| | - Wuan Geok Saw
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551 Singapore
| | - Anjaiah Nalaparaju
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551 Singapore
| | - Gerhard Grüber
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551 Singapore
| | - Lanyuan Lu
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551 Singapore
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21
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Evidence for the principle of minimal frustration in the evolution of protein folding landscapes. Proc Natl Acad Sci U S A 2017; 114:E1627-E1632. [PMID: 28196883 DOI: 10.1073/pnas.1613892114] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Theoretical and experimental studies have firmly established that protein folding can be described by a funneled energy landscape. This funneled energy landscape is the result of foldable protein sequences evolving following the principle of minimal frustration, which allows proteins to rapidly fold to their native biologically functional conformations. For a protein family with a given functional fold, the principle of minimal frustration suggests that, independent of sequence, all proteins within this family should fold with similar rates. However, depending on the optimal living temperature of the organism, proteins also need to modulate their thermodynamic stability. Consequently, the difference in thermodynamic stability should be primarily caused by differences in the unfolding rates. To test this hypothesis experimentally, we performed comprehensive thermodynamic and kinetic analyses of 15 different proteins from the thioredoxin family. Eight of these thioredoxins were extant proteins from psychrophilic, mesophilic, or thermophilic organisms. The other seven protein sequences were obtained using ancestral sequence reconstruction and can be dated back over 4 billion years. We found that all studied proteins fold with very similar rates but unfold with rates that differ up to three orders of magnitude. The unfolding rates correlate well with the thermodynamic stability of the proteins. Moreover, proteins that unfold slower are more resistant to proteolysis. These results provide direct experimental support to the principle of minimal frustration hypothesis.
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22
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Harada R, Takano Y, Shigeta Y. Common folding processes of mini-proteins: Partial formations of secondary structures initiate the immediate protein folding. J Comput Chem 2017; 38:790-797. [DOI: 10.1002/jcc.24748] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Revised: 12/20/2016] [Accepted: 01/12/2017] [Indexed: 11/10/2022]
Affiliation(s)
- Ryuhei Harada
- Center for Computational Sciences, University of Tsukuba; 1-1-1 Tennodai Tsukuba Ibaraki 305-8577 Japan
| | - Yu Takano
- Department of Biomedical Information Sciences; Graduate School of Information Sciences, Hiroshima City University; 3-4-1 Ozuka-Higashi, Asa-Minami-Ku Hiroshima 731-3194 Japan
| | - Yasuteru Shigeta
- Center for Computational Sciences, University of Tsukuba; 1-1-1 Tennodai Tsukuba Ibaraki 305-8577 Japan
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23
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Makhatadze GI. Linking computation and experiments to study the role of charge-charge interactions in protein folding and stability. Phys Biol 2017; 14:013002. [PMID: 28169222 DOI: 10.1088/1478-3975/14/1/013002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Over the past two decades there has been an increase in appreciation for the role of surface charge-charge interactions in protein folding and stability. The perception shifted from the belief that charge-charge interactions are not important for protein folding and stability to the near quantitative understanding of how these interactions shape the folding energy landscape. This led to the ability of computational approaches to rationally redesign surface charge-charge interactions to modulate thermodynamic properties of proteins. Here we summarize our progress in understanding the role of charge-charge interactions for protein stability using examples drawn from my own laboratory and touch upon unanswered questions.
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Affiliation(s)
- George I Makhatadze
- Center for Biotechnology and Interdisciplinary Studies, and Department of Biological Sciences, Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, 110 8th Street, Troy, NY 12180 USA
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24
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SMOG 2: A Versatile Software Package for Generating Structure-Based Models. PLoS Comput Biol 2016; 12:e1004794. [PMID: 26963394 PMCID: PMC4786265 DOI: 10.1371/journal.pcbi.1004794] [Citation(s) in RCA: 191] [Impact Index Per Article: 23.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Accepted: 02/07/2016] [Indexed: 12/01/2022] Open
Abstract
Molecular dynamics simulations with coarse-grained or simplified Hamiltonians have proven to be an effective means of capturing the functionally important long-time and large-length scale motions of proteins and RNAs. Originally developed in the context of protein folding, structure-based models (SBMs) have since been extended to probe a diverse range of biomolecular processes, spanning from protein and RNA folding to functional transitions in molecular machines. The hallmark feature of a structure-based model is that part, or all, of the potential energy function is defined by a known structure. Within this general class of models, there exist many possible variations in resolution and energetic composition. SMOG 2 is a downloadable software package that reads user-designated structural information and user-defined energy definitions, in order to produce the files necessary to use SBMs with high performance molecular dynamics packages: GROMACS and NAMD. SMOG 2 is bundled with XML-formatted template files that define commonly used SBMs, and it can process template files that are altered according to the needs of each user. This computational infrastructure also allows for experimental or bioinformatics-derived restraints or novel structural features to be included, e.g. novel ligands, prosthetic groups and post-translational/transcriptional modifications. The code and user guide can be downloaded at http://smog-server.org/smog2.
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25
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Microscopic interpretation of folding ϕ-values using the transition path ensemble. Proc Natl Acad Sci U S A 2016; 113:3263-8. [PMID: 26957599 DOI: 10.1073/pnas.1520864113] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
All-atom molecular dynamics simulations now allow us to create movies of proteins folding and unfolding. However, it is difficult to assess the accuracy of the folding mechanisms observed because experiments cannot yet directly resolve events occurring along the transition paths between unfolded and folded states. Protein folding ϕ-values provide residue-resolved information about folding mechanisms by comparing the effects of mutations on folding rates and stability, but determining ϕ-values by separately simulating mutant proteins would be computationally demanding and prone to large statistical errors. Here we use transition path theory to develop a method for computing ϕ-values directly from the transition path ensemble, without the need for additional simulations. This path-based approach uses the full transition path information available from equilibrium folding and unfolding trajectories, or from transition path sampling, and does not require identification of folding transition states. Applying our approach to a set of simulations of 10 small proteins by Shaw and coworkers [Lindorff-Larsen K, Piana S, Dror RO, Shaw DE (2011) Science 334(6055):517-520; Piana S, Lindorff-Larsen K, Shaw DE (2011) Biophys J100(9):L47-L49; and Piana S, Lindorff-Larsen K, Shaw DE (2013) Proc Natl Acad Sci USA 110(15):5915-5920], we find good agreement with experiments in most cases where data are available. We can further resolve the contributions to fractional ϕ-values coming from partial contact formation versus transition path heterogeneity. Although in some cases, there is substantial heterogeneity of folding mechanism, in others, such as Ubiquitin, the mechanism is strongly conserved.
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26
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Baruah A, Biswas P. Globular–disorder transition in proteins: a compromise between hydrophobic and electrostatic interactions? Phys Chem Chem Phys 2016; 18:23207-14. [DOI: 10.1039/c6cp03185d] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Protein disorder, like protein folding, satisfies the principle of minimal frustration.
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27
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Böker A, Paul W. Wang-Landau simulation of Gō model molecules. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2016; 39:5. [PMID: 26810395 DOI: 10.1140/epje/i2016-16005-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Accepted: 01/04/2016] [Indexed: 06/05/2023]
Abstract
Gō-like models are one of the oldest protein modeling concepts in computational physics and have proven their value over and over for forty years. The essence of a Gō model is to define a native contact matrix for a well-defined low-energy polymer configuration, e.g., the native state in the case of proteins or peptides. Many different potential shapes and many different cut-off distances in the definition of this native contact matrix have been proposed and applied. We investigate here the physical consequences of the choice for this cut-off distance in the Gō models derived for a square-well tangent sphere homopolymer chain. For this purpose we are performing flat-histogram Monte Carlo simulations of Wang-Landau type, obtaining the thermodynamic and structural properties of such models over the complete temperature range. Differences and similarities with Gō models for proteins and peptides are discussed.
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Affiliation(s)
- Arne Böker
- Institut für Physik, Martin-Luther-Universität, D-06099, Halle (Saale), Germany
| | - Wolfgang Paul
- Institut für Physik, Martin-Luther-Universität, D-06099, Halle (Saale), Germany.
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28
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Zhang Z, Ouyang Y, Chen T. Influences of heterogeneous native contact energy and many-body interactions on the prediction of protein folding mechanisms. Phys Chem Chem Phys 2016; 18:31304-31311. [DOI: 10.1039/c6cp06181h] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Combining heterogenous native contact energies and many-body interactions could improve the prediction of Brønsted plots using a structure-based model.
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Affiliation(s)
- Zhuqing Zhang
- College of Life Sciences
- University of Chinese Academy of Sciences
- Beijing
- China
| | - Yanhua Ouyang
- College of Life Sciences
- University of Chinese Academy of Sciences
- Beijing
- China
| | - Tao Chen
- College of Chemistry and Materials Science
- Northwest University
- Xi’an
- China
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29
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Tripathi S, Garcìa AE, Makhatadze GI. Alterations of Nonconserved Residues Affect Protein Stability and Folding Dynamics through Charge–Charge Interactions. J Phys Chem B 2015; 119:13103-12. [DOI: 10.1021/acs.jpcb.5b08527] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Swarnendu Tripathi
- Department
of Physics, University of Houston, Houston, Texas 77204, United States
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30
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Zheng W, De Sancho D, Hoppe T, Best RB. Dependence of internal friction on folding mechanism. J Am Chem Soc 2015; 137:3283-90. [PMID: 25721133 PMCID: PMC4379956 DOI: 10.1021/ja511609u] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Indexed: 12/25/2022]
Abstract
An outstanding challenge in protein folding is understanding the origin of "internal friction" in folding dynamics, experimentally identified from the dependence of folding rates on solvent viscosity. A possible origin suggested by simulation is the crossing of local torsion barriers. However, it was unclear why internal friction varied from protein to protein or for different folding barriers of the same protein. Using all-atom simulations with variable solvent viscosity, in conjunction with transition-path sampling to obtain reaction rates and analysis via Markov state models, we are able to determine the internal friction in the folding of several peptides and miniproteins. In agreement with experiment, we find that the folding events with greatest internal friction are those that mainly involve helix formation, while hairpin formation exhibits little or no evidence of friction. Via a careful analysis of folding transition paths, we show that internal friction arises when torsion angle changes are an important part of the folding mechanism near the folding free energy barrier. These results suggest an explanation for the variation of internal friction effects from protein to protein and across the energy landscape of the same protein.
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Affiliation(s)
- Wenwei Zheng
- Laboratory
of Chemical Physics, National Institute of Diabetes and Digestive
and Kidney Diseases, National Institutes
of Health, Bethesda, Maryland 20892, United
States
| | - David De Sancho
- Department
of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
- CIC
nanoGUNE, 20018 Donostia−San Sebastián, Spain
- IKERBASQUE,
Basque Foundation for Science, Maria Diaz de Haro 3, 48013 Bilbao, Spain
| | - Travis Hoppe
- Laboratory
of Chemical Physics, National Institute of Diabetes and Digestive
and Kidney Diseases, National Institutes
of Health, Bethesda, Maryland 20892, United
States
| | - Robert B. Best
- Laboratory
of Chemical Physics, National Institute of Diabetes and Digestive
and Kidney Diseases, National Institutes
of Health, Bethesda, Maryland 20892, United
States
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31
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Modulation of folding energy landscape by charge-charge interactions: linking experiments with computational modeling. Proc Natl Acad Sci U S A 2015; 112:E259-66. [PMID: 25564663 DOI: 10.1073/pnas.1410424112] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
The kinetics of folding-unfolding of a structurally diverse set of four proteins optimized for thermodynamic stability by rational redesign of surface charge-charge interactions is characterized experimentally. The folding rates are faster for designed variants compared with their wild-type proteins, whereas the unfolding rates are largely unaffected. A simple structure-based computational model, which incorporates the Debye-Hückel formalism for the electrostatics, was used and found to qualitatively recapitulate the experimental results. Analysis of the energy landscapes of the designed versus wild-type proteins indicates the differences in refolding rates may be correlated with the degree of frustration of their respective energy landscapes. Our simulations indicate that naturally occurring wild-type proteins have frustrated folding landscapes due to the surface electrostatics. Optimization of the surface electrostatics seems to remove some of that frustration, leading to enhanced formation of native-like contacts in the transition-state ensembles (TSE) and providing a less frustrated energy landscape between the unfolded and TS ensembles. Macroscopically, this results in faster folding rates. Furthermore, analyses of pairwise distances and radii of gyration suggest that the less frustrated energy landscapes for optimized variants are a result of more compact unfolded and TS ensembles. These findings from our modeling demonstrates that this simple model may be used to: (i) gain a detailed understanding of charge-charge interactions and their effects on modulating the energy landscape of protein folding and (ii) qualitatively predict the kinetic behavior of protein surface electrostatic interactions.
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32
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Abstract
The kinase-inducible domain interacting (KIX) domain of the CREB binding protein (CBP) is capable of simultaneously binding two intrinsically disordered transcription factors, such as the mixed-lineage leukemia (MLL) and c-Myb peptides, at isolated interaction sites. In vitro, the affinity for binding c-Myb is approximately doubled when KIX is in complex with MLL, which suggests a positive cooperative binding mechanism, and the affinity for MLL is also slightly increased when KIX is first bound by c-Myb. Expanding the scope of recent NMR and computational studies, we explore the allosteric mechanism at a detailed molecular level that directly connects the microscopic structural dynamics to the macroscopic shift in binding affinities. To this end, we have performed molecular dynamics simulations of free KIX, KIX-c-Myb, MLL-KIX, and MLL-KIX-c-Myb using a topology-based Gō-like model. Our results capture an increase in affinity for the peptide in the allosteric site when KIX is prebound by a complementary effector and both peptides follow an effector-independent folding-and-binding mechanism. More importantly, we discover that MLL binding lowers the entropic cost for c-Myb binding, and vice versa, by stabilizing the L12-G2 loop and the C-terminal region of the α3 helix on KIX. This work demonstrates the importance of entropy in allosteric signaling between promiscuous molecular recognition sites and can inform the rational design of small molecule stabilizers to target important regions of conformationally dynamic proteins.
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33
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Savol AJ, Chennubhotla CS. Quantifying the Sources of Kinetic Frustration in Folding Simulations of Small Proteins. J Chem Theory Comput 2014; 10:2964-2974. [PMID: 25136267 PMCID: PMC4132847 DOI: 10.1021/ct500361w] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2014] [Indexed: 11/28/2022]
Abstract
![]()
Experiments
and atomistic simulations of polypeptides have revealed
structural intermediates that promote or inhibit conformational transitions
to the native state during folding. We invoke a concept of “kinetic
frustration” to quantify the prevalence and impact of these
behaviors on folding rates within a large set of atomistic simulation
data for 10 fast-folding proteins, where each protein’s conformational
space is represented as a Markov state model of conformational transitions.
Our graph theoretic approach addresses what conformational features
correlate with folding inhibition and therefore permits comparison
among features within a single protein network and also more generally
between proteins. Nonnative contacts and nonnative secondary structure
formation can thus be quantitatively implicated in inhibiting folding
for several of the tested peptides.
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Affiliation(s)
- Andrej J Savol
- Dept. of Computational and Systems Biology, School of Medicine, University of Pittsburgh , Pittsburgh, Pennsylvania 15260, United States ; Joint Carnegie Mellon University-University of Pittsburgh PhD Program in Computational Biology, Pittsburgh, Pennsylvania 15260, United States
| | - Chakra S Chennubhotla
- Dept. of Computational and Systems Biology, School of Medicine, University of Pittsburgh , Pittsburgh, Pennsylvania 15260, United States
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34
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Leioatts N, Suresh P, Romo TD, Grossfield A. Structure-based simulations reveal concerted dynamics of GPCR activation. Proteins 2014; 82:2538-51. [PMID: 24889093 DOI: 10.1002/prot.24617] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Revised: 05/06/2014] [Accepted: 05/20/2014] [Indexed: 11/08/2022]
Abstract
G protein-coupled receptors (GPCRs) are a vital class of proteins that transduce biological signals across the cell membrane. However, their allosteric activation mechanism is not fully understood; crystal structures of active and inactive receptors have been reported, but the functional pathway between these two states remains elusive. Here, we use structure-based (Gō-like) models to simulate activation of two GPCRs, rhodopsin and the β₂ adrenergic receptor (β₂AR). We used data-derived reaction coordinates that capture the activation mechanism for both proteins, showing that activation proceeds through quantitatively different paths in the two systems. Both reaction coordinates are determined from the dominant concerted motions in the simulations so the technique is broadly applicable. There were two surprising results. First, the main structural changes in the simulations were distributed throughout the transmembrane bundle, and not localized to the obvious areas of interest, such as the intracellular portion of Helix 6. Second, the activation (and deactivation) paths were distinctly nonmonotonic, populating states that were not simply interpolations between the inactive and active structures. These transitions also suggest a functional explanation for β₂AR's basal activity: it can proceed through a more broadly defined path during the observed transitions.
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Affiliation(s)
- Nicholas Leioatts
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, New York, 14642
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35
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Peter EK, Shea JE. A hybrid MD-kMC algorithm for folding proteins in explicit solvent. Phys Chem Chem Phys 2014; 16:6430-40. [PMID: 24499973 DOI: 10.1039/c3cp55251a] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We present a novel hybrid MD-kMC algorithm that is capable of efficiently folding proteins in explicit solvent. We apply this algorithm to the folding of a small protein, Trp-Cage. Different kMC move sets that capture different possible rate limiting steps are implemented. The first uses secondary structure formation as a relevant rate event (a combination of dihedral rotations and hydrogen-bonding formation and breakage). The second uses tertiary structure formation events through formation of contacts via translational moves. Both methods fold the protein, but via different mechanisms and with different folding kinetics. The first method leads to folding via a structured helical state, with kinetics fit by a single exponential. The second method leads to folding via a collapsed loop, with kinetics poorly fit by single or double exponentials. In both cases, folding times are faster than experimentally reported values, The secondary and tertiary move sets are integrated in a third MD-kMC implementation, which now leads to folding of the protein via both pathways, with single and double-exponential fits to the rates, and to folding rates in good agreement with experimental values. The competition between secondary and tertiary structure leads to a longer search for the helix-rich intermediate in the case of the first pathway, and to the emergence of a kinetically trapped long-lived molten-globule collapsed state in the case of the second pathway. The algorithm presented not only captures experimentally observed folding intermediates and kinetics, but yields insights into the relative roles of local and global interactions in determining folding mechanisms and rates.
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Affiliation(s)
- Emanuel Karl Peter
- University of California Santa Barbara, Department of Chemistry and Biochemistry, Department of Physics, Santa Barbara, CA 93106, USA.
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36
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Sun Y, Ming D. Energetic frustrations in protein folding at residue resolution: a homologous simulation study of Im9 proteins. PLoS One 2014; 9:e87719. [PMID: 24498176 PMCID: PMC3909201 DOI: 10.1371/journal.pone.0087719] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2013] [Accepted: 01/02/2014] [Indexed: 11/18/2022] Open
Abstract
Energetic frustration is becoming an important topic for understanding the mechanisms of protein folding, which is a long-standing big biological problem usually investigated by the free energy landscape theory. Despite the significant advances in probing the effects of folding frustrations on the overall features of protein folding pathways and folding intermediates, detailed characterizations of folding frustrations at an atomic or residue level are still lacking. In addition, how and to what extent folding frustrations interact with protein topology in determining folding mechanisms remains unclear. In this paper, we tried to understand energetic frustrations in the context of protein topology structures or native-contact networks by comparing the energetic frustrations of five homologous Im9 alpha-helix proteins that share very similar topology structures but have a single hydrophilic-to-hydrophobic mutual mutation. The folding simulations were performed using a coarse-grained Gō-like model, while non-native hydrophobic interactions were introduced as energetic frustrations using a Lennard-Jones potential function. Energetic frustrations were then examined at residue level based on φ-value analyses of the transition state ensemble structures and mapped back to native-contact networks. Our calculations show that energetic frustrations have highly heterogeneous influences on the folding of the four helices of the examined structures depending on the local environment of the frustration centers. Also, the closer the introduced frustration is to the center of the native-contact network, the larger the changes in the protein folding. Our findings add a new dimension to the understanding of protein folding the topology determination in that energetic frustrations works closely with native-contact networks to affect the protein folding.
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Affiliation(s)
- Yunxiang Sun
- Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai, People's Republic of China
| | - Dengming Ming
- Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai, People's Republic of China
- * E-mail:
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37
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Baruah A, Biswas P. The role of site-directed point mutations in protein misfolding. Phys Chem Chem Phys 2014; 16:13964-73. [PMID: 24898496 DOI: 10.1039/c3cp55367a] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Mutations inducing higher clashing and lower matching residue pairs lead to misfolding.
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Affiliation(s)
- Anupaul Baruah
- Department of Chemistry
- University of Delhi
- Delhi-110007, India
| | - Parbati Biswas
- Department of Chemistry
- University of Delhi
- Delhi-110007, India
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38
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Ganguly D, Zhang W, Chen J. Electrostatically accelerated encounter and folding for facile recognition of intrinsically disordered proteins. PLoS Comput Biol 2013; 9:e1003363. [PMID: 24278008 PMCID: PMC3836701 DOI: 10.1371/journal.pcbi.1003363] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Accepted: 10/10/2013] [Indexed: 11/18/2022] Open
Abstract
Achieving facile specific recognition is essential for intrinsically disordered proteins (IDPs) that are involved in cellular signaling and regulation. Consideration of the physical time scales of protein folding and diffusion-limited protein-protein encounter has suggested that the frequent requirement of protein folding for specific IDP recognition could lead to kinetic bottlenecks. How IDPs overcome such potential kinetic bottlenecks to viably function in signaling and regulation in general is poorly understood. Our recent computational and experimental study of cell-cycle regulator p27 (Ganguly et al., J. Mol. Biol. (2012)) demonstrated that long-range electrostatic forces exerted on enriched charges of IDPs could accelerate protein-protein encounter via "electrostatic steering" and at the same time promote "folding-competent" encounter topologies to enhance the efficiency of IDP folding upon encounter. Here, we further investigated the coupled binding and folding mechanisms and the roles of electrostatic forces in the formation of three IDP complexes with more complex folded topologies. The surface electrostatic potentials of these complexes lack prominent features like those observed for the p27/Cdk2/cyclin A complex to directly suggest the ability of electrostatic forces to facilitate folding upon encounter. Nonetheless, similar electrostatically accelerated encounter and folding mechanisms were consistently predicted for all three complexes using topology-based coarse-grained simulations. Together with our previous analysis of charge distributions in known IDP complexes, our results support a prevalent role of electrostatic interactions in promoting efficient coupled binding and folding for facile specific recognition. These results also suggest that there is likely a co-evolution of IDP folded topology, charge characteristics, and coupled binding and folding mechanisms, driven at least partially by the need to achieve fast association kinetics for cellular signaling and regulation.
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Affiliation(s)
- Debabani Ganguly
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas, United States of America
| | - Weihong Zhang
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas, United States of America
| | - Jianhan Chen
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas, United States of America
- * E-mail:
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Markiewicz BN, Jo H, Culik RM, DeGrado WF, Gai F. Assessment of local friction in protein folding dynamics using a helix cross-linker. J Phys Chem B 2013; 117:14688-96. [PMID: 24205975 DOI: 10.1021/jp409334h] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Internal friction arising from local steric hindrance and/or the excluded volume effect plays an important role in controlling not only the dynamics of protein folding but also conformational transitions occurring within the native state potential well. However, experimental assessment of such local friction is difficult because it does not manifest itself as an independent experimental observable. Herein, we demonstrate, using the miniprotein trp-cage as a testbed, that it is possible to selectively increase the local mass density in a protein and hence the magnitude of local friction, thus making its effect directly measurable via folding kinetic studies. Specifically, we show that when a helix cross-linker, m-xylene, is placed near the most congested region of the trp-cage it leads to a significant decrease in both the folding rate (by a factor of 3.8) and unfolding rate (by a factor of 2.5 at 35 °C) but has little effect on protein stability. Thus, these results, in conjunction with those obtained with another cross-linked trp-cage and two uncross-linked variants, demonstrate the feasibility of using a nonperturbing cross-linker to help quantify the effect of internal friction. In addition, we estimate that a m-xylene cross-linker could lead to an increase in the roughness of the folding energy landscape by as much as 0.4-1.0k(B)T.
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Affiliation(s)
- Beatrice N Markiewicz
- Department of Chemistry and §Department of Biochemistry & Biophysics, University of Pennsylvania , Philadelphia, Pennsylvania 19104, United States
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40
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Best RB. How well does a funneled energy landscape capture the folding mechanism of spectrin domains? J Phys Chem B 2013; 117:13235-44. [PMID: 23947368 PMCID: PMC3808457 DOI: 10.1021/jp403305a] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Three structurally similar domains from α-spectrin have been shown to fold very differently. First, there is a contrast in the folding mechanism, as probed by Φ-value analysis, between the R15 domain and the R16 and R17 domains. Second, there are very different contributions from internal friction to folding: the folding rate of the R15 domain was found to be inversely proportional to solvent viscosity, showing no apparent frictional contribution from the protein, but in the other two domains, a large internal friction component was evident. Non-native misdocking of helices has been suggested to be responsible for this phenomenon. Here, I study the folding of these three proteins with minimalist coarse-grained models based on a funneled energy landscape. Remarkably, I find that, despite the absence of non-native interactions, the differences in folding mechanism of the domains are well captured by the model, and the agreement of the Φ-values with experiment is fairly good. On the other hand, within the context of this model, there are no significant differences in diffusion coefficient along the chosen folding coordinate, and the model cannot explain the large differences in folding rates between the proteins found experimentally. These results are nonetheless consistent with the expectations from the energy landscape perspective of protein folding, namely, that the folding mechanism is primarily determined by the native-like interactions present in the Gō-like model, with missing non-native interactions being required to explain the differences in "internal friction" seen in experiment.
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Affiliation(s)
- Robert B. Best
- Cambridge University, Department of Chemistry, Lensfield Road Cambridge CB2 1EW, and Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520
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41
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Native contacts determine protein folding mechanisms in atomistic simulations. Proc Natl Acad Sci U S A 2013; 110:17874-9. [PMID: 24128758 DOI: 10.1073/pnas.1311599110] [Citation(s) in RCA: 420] [Impact Index Per Article: 38.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The recent availability of long equilibrium simulations of protein folding in atomistic detail for more than 10 proteins allows us to identify the key interactions driving folding. We find that the collective fraction of native amino acid contacts, Q, captures remarkably well the transition states for all the proteins with a folding free energy barrier. Going beyond this global picture, we devise two different measures to quantify the importance of individual interresidue contacts in the folding mechanism: (i) the log-ratio of lifetimes of contacts during folding transition paths and in the unfolded state and (ii) a Bayesian measure of how predictive the formation of each contact is for being on a transition path. Both of these measures indicate that native, or near-native, contacts are important for determining mechanism, as might be expected. More remarkably, however, we found that for almost all the proteins, with the designed protein α3D being a notable exception, nonnative contacts play no significant part in determining folding mechanisms.
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42
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Kaya H, Uzunoğlu Z, Chan HS. Spatial ranges of driving forces are a key determinant of protein folding cooperativity and rate diversity. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2013; 88:044701. [PMID: 24229309 DOI: 10.1103/physreve.88.044701] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2013] [Revised: 08/21/2013] [Indexed: 06/02/2023]
Abstract
The physical basis of two-state-like folding transitions and the tremendous diversity in folding rates is elucidated by directly simulating the folding kinetics of 52 representative proteins. Relative to the results from a common modeling approach, the diversity of the simulated folding rates can be increased from ~10(2.1) to the experimental ~10(6.0) by a modest decrease in the spatial range of the attractive potential. The required theoretical range is consistent with desolvation physics and is notably much more permissive than that needed for two-state-like homopolymer collapse.
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Affiliation(s)
- Hüseyin Kaya
- Department of Biophysics, Faculty of Medicine, University of Gaziantep, 27310 Gaziantep, Turkey
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43
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Tripathi S, Portman JJ. Allostery and Folding of the N-terminal Receiver Domain of Protein NtrC. J Phys Chem B 2013; 117:13182-93. [DOI: 10.1021/jp403181p] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Swarnendu Tripathi
- Department
of Physics, University of Houston, Houston, Texas 77204, United States
| | - John J. Portman
- Department
of Physics, Kent State University, Kent, Ohio 44242, United States
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44
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Ahlstrom LS, Dickson A, Brooks CL. Binding and folding of the small bacterial chaperone HdeA. J Phys Chem B 2013; 117:13219-25. [PMID: 23738772 DOI: 10.1021/jp403264s] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The small pH stress-sensing chaperone HdeA helps pathogenic enteric E. coli survive passage through the severely acidic environment of the mammalian stomach. Under stress conditions, HdeA transitions from an inactive folded dimer to a chaperone-active unfolded monomer to prevent the acid-induced aggregation of periplasmic proteins. Here we use a topology-based Gō-like model to delineate the relationship between dimer interface formation and monomer folding and to better understand the structural details of the chaperone activation mechanism. Free energy surfaces show that dimer interface formation and monomer folding proceed concurrently through an on-pathway dimeric intermediate in which one monomer is partially unfolded. The absence of a preexisting fully folded monomer in the proposed binding mechanism is in agreement with HdeA's rapid chaperone response. Binding between unfolded monomers exhibits an enhancement of molecular recognition reminiscent of the fly-casting mechanism. Overall, our simulations further highlight the efficient nature of HdeA's chaperone response and we anticipate that knowledge of a dimeric intermediate will facilitate the interpretation of experimental studies.
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Affiliation(s)
- Logan S Ahlstrom
- Department of Chemistry, The University of Michigan , Ann Arbor, Michigan, United States
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45
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Nanoscale imaging reveals laterally expanding antimicrobial pores in lipid bilayers. Proc Natl Acad Sci U S A 2013; 110:8918-23. [PMID: 23671080 DOI: 10.1073/pnas.1222824110] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Antimicrobial peptides are postulated to disrupt microbial phospholipid membranes. The prevailing molecular model is based on the formation of stable or transient pores although the direct observation of the fundamental processes is lacking. By combining rational peptide design with topographical (atomic force microscopy) and chemical (nanoscale secondary ion mass spectrometry) imaging on the same samples, we show that pores formed by antimicrobial peptides in supported lipid bilayers are not necessarily limited to a particular diameter, nor they are transient, but can expand laterally at the nano-to-micrometer scale to the point of complete membrane disintegration. The results offer a mechanistic basis for membrane poration as a generic physicochemical process of cooperative and continuous peptide recruitment in the available phospholipid matrix.
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46
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Irbäck A, Sjunnesson F, Wallin S. Hydrogen bonds, hydrophobicity forces and the character of the collapse transition. J Biol Phys 2013; 27:169-79. [PMID: 23345742 DOI: 10.1023/a:1013155018382] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
We study the thermodynamic behavior of a model protein with 54 amino acidsthat is designed to form a three-helix bundle in its native state. The model contains three types of amino acids and five to six atoms per amino acid, and has the Ramachandran torsion angles as its only degrees of freedom.The force field is based on hydrogen bonds and effective hydrophobicity forces. We study how the character of the collapse transition depends on the strengths of these forces. For a suitable choice of these two parameters, it is found that the collapse transition is first-order-like and coincides with the folding transition. Also shown is that the corresponding one- and two-helix segments make less stable secondary structure than the three-helix sequence.
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Affiliation(s)
- A Irbäck
- Complex Systems Division, Department of Theoretical Physics, Lund University, Sölvegatan 14A, S-223 62 Lund, Sweden
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47
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Tripathi S, Makhatadze GI, Garcia AE. Backtracking due to residual structure in the unfolded state changes the folding of the third fibronectin type III domain from tenascin-C. J Phys Chem B 2013; 117:800-10. [PMID: 23268597 DOI: 10.1021/jp310046k] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Residual structure in the unfolded state of a protein may play a crucial role in folding and stability. In the present study, using an all (heavy)-atom structure based model and replica exchange molecular dynamics simulations, we explored the folding landscape of the third fibronectin type III domain from tenascin-C (TNfn3). Specifically, both the wild type (WT) and a variant with two additional amino acids, Gly-Leu (GL), at the C-terminus (WT(+GL)) were studied. We found that, although both domains of TNfn3 are topologically frustrated, the early formation of the native contacts from the C-terminal end of WT(+GL) causes more "backtracking" than in the WT. As a result, the WT exhibits a two-state folding behavior with a broad transition-state ensemble, whereas the WT(+GL) folds through a metastable intermediate state. Furthermore, our study confirmed that the core of both proteins is conformationally heterogeneous and noncompact, and folds late mainly due to backtracking of the part of the core. Finally, in agreement with the previous experimental studies, our results clearly demonstrated distinct thermodynamic behavior of the two proteins with WT(+GL) being more stable.
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Affiliation(s)
- Swarnendu Tripathi
- Department of Biology, Rensselaer Polytechnic Institute, 110 8th Street, Troy, New York 12180, USA
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48
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De novo prediction of protein folding pathways and structure using the principle of sequential stabilization. Proc Natl Acad Sci U S A 2012; 109:17442-7. [PMID: 23045636 DOI: 10.1073/pnas.1209000109] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Motivated by the relationship between the folding mechanism and the native structure, we develop a unified approach for predicting folding pathways and tertiary structure using only the primary sequence as input. Simulations begin from a realistic unfolded state devoid of secondary structure and use a chain representation lacking explicit side chains, rendering the simulations many orders of magnitude faster than molecular dynamics simulations. The multiple round nature of the algorithm mimics the authentic folding process and tests the effectiveness of sequential stabilization (SS) as a search strategy wherein 2° structural elements add onto existing structures in a process of progressive learning and stabilization of structure found in prior rounds of folding. Because no a priori knowledge is used, we can identify kinetically significant non-native interactions and intermediates, sometimes generated by only two mutations, while the evolution of contact matrices is often consistent with experiments. Moreover, structure prediction improves substantially by incorporating information from prior rounds. The success of our simple, homology-free approach affirms the validity of our description of the primary determinants of folding pathways and structure, and the effectiveness of SS as a search strategy.
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49
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Ravikumar K, Huang W, Yang S. Coarse-grained simulations of protein-protein association: an energy landscape perspective. Biophys J 2012; 103:837-45. [PMID: 22947945 PMCID: PMC3443792 DOI: 10.1016/j.bpj.2012.07.013] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2012] [Revised: 07/10/2012] [Accepted: 07/12/2012] [Indexed: 01/15/2023] Open
Abstract
Understanding protein-protein association is crucial in revealing the molecular basis of many biological processes. Here, we describe a theoretical simulation pipeline to study protein-protein association from an energy landscape perspective. First, a coarse-grained model is implemented and its applications are demonstrated via molecular dynamics simulations for several protein complexes. Second, an enhanced search method is used to efficiently sample a broad range of protein conformations. Third, multiple conformations are identified and clustered from simulation data and further projected on a three-dimensional globe specifying protein orientations and interacting energies. Results from several complexes indicate that the crystal-like conformation is favorable on the energy landscape even if the landscape is relatively rugged with metastable conformations. A closer examination on molecular forces shows that the formation of associated protein complexes can be primarily electrostatics-driven, hydrophobics-driven, or a combination of both in stabilizing specific binding interfaces. Taken together, these results suggest that the coarse-grained simulations and analyses provide an alternative toolset to study protein-protein association occurring in functional biomolecular complexes.
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Affiliation(s)
| | | | - Sichun Yang
- Center for Proteomics and Department of Pharmacology, Case Western Reserve University, Cleveland, Ohio
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50
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Beharry AA, Chen T, Al-Abdul-Wahid MS, Samanta S, Davidov K, Sadovski O, Ali AM, Chen SB, Prosser RS, Chan HS, Woolley GA. Quantitative analysis of the effects of photoswitchable distance constraints on the structure of a globular protein. Biochemistry 2012; 51:6421-31. [PMID: 22803618 DOI: 10.1021/bi300685a] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Photoswitchable distance constraints in the form of photoisomerizable chemical cross-links offer a general approach to the design of reversibly photocontrolled proteins. To apply these effectively, however, one must have guidelines for the choice of cross-linker structure and cross-linker attachment sites. Here we investigate the effects of varying cross-linker structure on the photocontrol of folding of the Fyn SH3 domain, a well-studied model protein. We develop a theoretical framework based on an explicit-chain model of protein folding, modified to include detailed model linkers, that allows prediction of the effect of a given linker on the free energy of folding of a protein. Using this framework, we were able to quantitatively explain the experimental result that a longer, but somewhat flexible, cross-linker is less destabilizing to the folded state than a shorter more rigid cross-linker. The models also suggest how misfolded states may be generated by cross-linking, providing a rationale for altered dynamics seen in nuclear magnetic resonance analyses of these proteins. The theoretical framework is readily portable to any protein of known folded state structure and thus can be used to guide the design of photoswitchable proteins generally.
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Affiliation(s)
- Andrew A Beharry
- Department of Chemistry, University of Toronto, 80 Saint George Street, Toronto, Ontario M5S 3H6, Canada
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