1
|
Scaletti C, Russell PPS, Hebel KJ, Rickard MM, Boob M, Danksagmüller F, Taylor SA, Pogorelov TV, Gruebele M. Hydrogen bonding heterogeneity correlates with protein folding transition state passage time as revealed by data sonification. Proc Natl Acad Sci U S A 2024; 121:e2319094121. [PMID: 38768341 PMCID: PMC11145292 DOI: 10.1073/pnas.2319094121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 04/18/2024] [Indexed: 05/22/2024] Open
Abstract
Protein-protein and protein-water hydrogen bonding interactions play essential roles in the way a protein passes through the transition state during folding or unfolding, but the large number of these interactions in molecular dynamics (MD) simulations makes them difficult to analyze. Here, we introduce a state space representation and associated "rarity" measure to identify and quantify transition state passage (transit) events. Applying this representation to a long MD simulation trajectory that captured multiple folding and unfolding events of the GTT WW domain, a small protein often used as a model for the folding process, we identified three transition categories: Highway (faster), Meander (slower), and Ambiguous (intermediate). We developed data sonification and visualization tools to analyze hydrogen bond dynamics before, during, and after these transition events. By means of these tools, we were able to identify characteristic hydrogen bonding patterns associated with "Highway" versus "Meander" versus "Ambiguous" transitions and to design algorithms that can identify these same folding pathways and critical protein-water interactions directly from the data. Highly cooperative hydrogen bonding can either slow down or speed up transit. Furthermore, an analysis of protein-water hydrogen bond dynamics at the surface of WW domain shows an increase in hydrogen bond lifetime from folded to unfolded conformations with Ambiguous transitions as an outlier. In summary, hydrogen bond dynamics provide a direct window into the heterogeneity of transits, which can vary widely in duration (by a factor of 10) due to a complex energy landscape.
Collapse
Affiliation(s)
| | | | | | - Meredith M. Rickard
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, IL61801
| | - Mayank Boob
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, IL61801
| | | | - Stephen A. Taylor
- School of Music, University of Illinois Urbana-Champaign, Urbana, IL61801
| | - Taras V. Pogorelov
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, IL61801
- Center for Biophysics and Quantitative Biology, University of Illinois Urbana-Champaign, Urbana, IL61801
- School of Chemical Sciences, University of Illinois Urbana-Champaign, Urbana, IL61801
- Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, IL61801
- National Center for Supercomputer Applications, University of Illinois Urbana-Champaign, Urbana, IL61801
| | - Martin Gruebele
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, IL61801
- Center for Biophysics and Quantitative Biology, University of Illinois Urbana-Champaign, Urbana, IL61801
- Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, IL61801
- Department of Physics, University of Illinois Urbana-Champaign, Urbana, IL61801
| |
Collapse
|
2
|
Li C, Wei TY, Cheung MS, Tsai MY. Deciphering the Cofilin Oligomers via Intermolecular Disulfide Bond Formation: A Coarse-Grained Molecular Dynamics Approach to Understanding Cofilin's Regulation on Actin Filaments. J Phys Chem B 2024; 128:4590-4601. [PMID: 38701111 PMCID: PMC11104348 DOI: 10.1021/acs.jpcb.3c07938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 04/20/2024] [Accepted: 04/24/2024] [Indexed: 05/05/2024]
Abstract
Cofilin, a key actin-binding protein, orchestrates the dynamics of the actomyosin network through its actin-severing activity and by promoting the recycling of actin monomers. Recent experiments suggest that cofilin forms functionally distinct oligomers via thiol post-translational modifications (PTMs) that promote actin nucleation and assembly. Despite these advances, the structural conformations of cofilin oligomers that modulate actin activity remain elusive because there are combinatorial ways to oxidize thiols in cysteines to form disulfide bonds rapidly. This study employs molecular dynamics simulations to investigate human cofilin 1 as a case study for exploring cofilin dimers via disulfide bond formation. Utilizing a biasing scheme in simulations, we focus on analyzing dimer conformations conducive to disulfide bond formation. Additionally, we explore potential PTMs arising from the examined conformational ensemble. Using the free energy profiling, our simulations unveil a range of probable cofilin dimer structures not represented in current Protein Data Bank entries. These candidate dimers are characterized by their distinct population distributions and relative free energies. Of particular note is a dimer featuring an interface between cysteines 139 and 147 residues, which demonstrates stable free energy characteristics and intriguingly symmetrical geometry. In contrast, the experimentally proposed dimer structure exhibits a less stable free energy profile. We also evaluate frustration quantification based on the energy landscape theory in the protein-protein interactions at the dimer interfaces. Notably, the 39-39 dimer configuration emerges as a promising candidate for forming cofilin tetramers, as substantiated by frustration analysis. Additionally, docking simulations with actin filaments further evaluate the stability of these cofilin dimer-actin complexes. Our findings thus offer a computational framework for understanding the role of thiol PTM of cofilin proteins in regulating oligomerization, and the subsequent cofilin-mediated actin dynamics in the actomyosin network.
Collapse
Affiliation(s)
- Chengxuan Li
- Department
of Physics, University of Washington, Seattle, Washington 98195, United States
- Center
for Theoretical Biological Physics, Rice
University, Houston, Texas 77005, United States
| | - Ting-Yi Wei
- Department
of Chemistry and Biochemistry, National
Chung Cheng University, Minhsiung, Chiayi 621301, Taiwan
| | - Margaret S. Cheung
- Department
of Physics, University of Washington, Seattle, Washington 98195, United States
- Center
for Theoretical Biological Physics, Rice
University, Houston, Texas 77005, United States
- Pacific
Northwest National Laboratory, Seattle, Washington 98109, United States
| | - Min-Yeh Tsai
- Department
of Chemistry and Biochemistry, National
Chung Cheng University, Minhsiung, Chiayi 621301, Taiwan
- Division
of Physics, National Center for Theoretical Sciences, National Taiwan University, Taipei 106319, Taiwan
| |
Collapse
|
3
|
Especial JNC, Faísca PFN. Effects of sequence-dependent non-native interactions in equilibrium and kinetic folding properties of knotted proteins. J Chem Phys 2023; 159:065101. [PMID: 37551809 DOI: 10.1063/5.0160886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 07/24/2023] [Indexed: 08/09/2023] Open
Abstract
Determining the role of non-native interactions in folding dynamics, kinetics, and mechanisms is a classic problem in protein folding. More recently, this question has witnessed a renewed interest in light of the hypothesis that knotted proteins require the assistance of non-native interactions to fold efficiently. Here, we conduct extensive equilibrium and kinetic Monte Carlo simulations of a simple off-lattice C-alpha model to explore the role of non-native interactions in the thermodynamics and kinetics of three proteins embedding a trefoil knot in their native structure. We find that equilibrium knotted conformations are stabilized by non-native interactions that are non-local, and proximal to native ones, thus enhancing them. Additionally, non-native interactions increase the knotting frequency at high temperatures, and in partially folded conformations below the transition temperatures. Although non-native interactions clearly enhance the efficiency of transition from an unfolded conformation to a partially folded knotted one, they are not required to efficiently fold a knotted protein. Indeed, a native-centric interaction potential drives the most efficient folding transition, provided that the simulation temperature is well below the transition temperature of the considered model system.
Collapse
Affiliation(s)
- João N C Especial
- Departamento de Física, Faculdade de Ciências, Ed. C8, Universidade de Lisboa, Campo Grande, Lisboa, Portugal
- BioISI-Biosystems and Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Lisboa, Portugal
| | - Patrícia F N Faísca
- Departamento de Física, Faculdade de Ciências, Ed. C8, Universidade de Lisboa, Campo Grande, Lisboa, Portugal
- BioISI-Biosystems and Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Lisboa, Portugal
| |
Collapse
|
4
|
da Silva FB, Martins de Oliveira V, de Oliveira Junior AB, Contessoto VDG, Leite VBP. Probing the Energy Landscape of Spectrin R15 and R16 and the Effects of Non-native Interactions. J Phys Chem B 2023; 127:1291-1300. [PMID: 36723393 DOI: 10.1021/acs.jpcb.2c06178] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Understanding the details of a protein folding mechanism can be a challenging and complex task. One system with an interesting folding behavior is the α-spectrin domain, where the R15 folds three-orders of magnitude faster than its homologues R16 and R17, despite having similar structures. The molecular origins that explain these folding rate differences remain unclear, but our previous work revealed that a combined effect produced by non-native interactions could be a reasonable cause for these differences. In this study, we explore further the folding process by identifying the molecular paths, metastable states, and the collective motions that lead these unfolded proteins to their native state conformation. Our results uncovered the differences between the folding pathways for the wild-type R15 and R16 and an R16 mutant. The metastable ensembles that speed down the folding were identified using an energy landscape visualization method (ELViM). These ensembles correspond to similar experimentally reported configurations. Our observations indicate that the non-native interactions are also associated with secondary structure misdocking. This computational methodology can be used as a fast, straightforward protocol for shedding light on systems with unclear folding or conformational traps.
Collapse
Affiliation(s)
- Fernando Bruno da Silva
- Department of Physics, São Paulo State University (UNESP), Institute of Biosciences, Humanities and Exact Sciences, São José do Rio Preto, São Paulo15054-000, Brazil
| | - Vinícius Martins de Oliveira
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland21201, United States
| | | | | | - Vitor B P Leite
- Department of Physics, São Paulo State University (UNESP), Institute of Biosciences, Humanities and Exact Sciences, São José do Rio Preto, São Paulo15054-000, Brazil
| |
Collapse
|
5
|
Mouro PR, Sanches MN, Leite VBP, Chahine J. Exploring the Folding Mechanism of Dimeric Superoxide Dismutase. J Phys Chem B 2023; 127:1338-1349. [PMID: 36716437 DOI: 10.1021/acs.jpcb.2c08877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The Cu/Zn Human Superoxide Dismutase (SOD1) is a dimeric metalloenzyme whose genetic mutations are directly related to amyotrophic lateral sclerosis (ALS), so understanding its folding mechanism is of fundamental importance. Currently, the SOD1 dimer formation is studied via molecular dynamics simulations using a simplified structure-based model and an all-atom model. Results from the simplified model reveal a mechanism dependent on distances between monomers, which are limited by constraints to mimic concentration dependence. The stability of intermediates (during the int state) is significantly affected by this distance, as well as by the presence of two folded monomers prior to dimer formation. The kinetics of interface formation are also highly dependent on the separation distance. The folding temperature of the dimer is about 4.2% higher than that of the monomer, a value not too different from experimental data. All-atom simulations on the apo dimer give binding free energy between monomers similar to experimental values. An intermediate state is evident for the apo form at a separation distance between monomers slightly larger than the native distance which has little formed interface between monomers. We have shown that this intermediate is stabilized by non-native intra- and intercontacts.
Collapse
Affiliation(s)
- Paulo R Mouro
- São Paulo State University (UNESP), IBILCE, São José do Rio Preto15054-000, Brazil
| | - Murilo N Sanches
- São Paulo State University (UNESP), IBILCE, São José do Rio Preto15054-000, Brazil
| | - Vitor B P Leite
- São Paulo State University (UNESP), IBILCE, São José do Rio Preto15054-000, Brazil
| | - Jorge Chahine
- São Paulo State University (UNESP), IBILCE, São José do Rio Preto15054-000, Brazil
| |
Collapse
|
6
|
Galaz‐Davison P, Ferreiro DU, Ramírez‐Sarmiento CA. Coevolution-derived native and non-native contacts determine the emergence of a novel fold in a universally conserved family of transcription factors. Protein Sci 2022; 31:e4337. [PMID: 35634768 PMCID: PMC9123645 DOI: 10.1002/pro.4337] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 04/18/2022] [Accepted: 05/03/2022] [Indexed: 11/07/2022]
Abstract
The NusG protein family is structurally and functionally conserved in all domains of life. Its members directly bind RNA polymerases and regulate transcription processivity and termination. RfaH, a divergent sub-family in its evolutionary history, is known for displaying distinct features than those in NusG proteins, which allows them to regulate the expression of virulence factors in enterobacteria in a DNA sequence-dependent manner. A striking feature is its structural interconversion between an active fold, which is the canonical NusG three-dimensional structure, and an autoinhibited fold, which is distinctively novel. How this novel fold is encoded within RfaH sequence to encode a metamorphic protein remains elusive. In this work, we used publicly available genomic RfaH protein sequences to construct a complete multiple sequence alignment, which was further augmented with metagenomic sequences and curated by predicting their secondary structure propensities using JPred. Coevolving pairs of residues were calculated from these sequences using plmDCA and GREMLIN, which allowed us to detect the enrichment of key metamorphic contacts after sequence filtering. Finally, we combined our coevolutionary predictions with molecular dynamics to demonstrate that these interactions are sufficient to predict the structures of both native folds, where coevolutionary-derived non-native contacts may play a key role in achieving the compact RfaH novel fold. All in all, emergent coevolutionary signals found within RfaH sequences encode the autoinhibited and active folds of this protein, shedding light on the key interactions responsible for the action of this metamorphic protein.
Collapse
Affiliation(s)
- Pablo Galaz‐Davison
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological SciencesPontificia Universidad Católica de ChileSantiagoChile
- ANID—Millennium Science Initiative Program—Millennium Institute for Integrative Biology (iBio)SantiagoChile
| | - Diego U. Ferreiro
- Protein Physiology Lab, Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales (IQUIBICEN‐CONICET)Universidad de Buenos AiresBuenos AiresArgentina
| | - César A. Ramírez‐Sarmiento
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological SciencesPontificia Universidad Católica de ChileSantiagoChile
- ANID—Millennium Science Initiative Program—Millennium Institute for Integrative Biology (iBio)SantiagoChile
| |
Collapse
|
7
|
Freitas FC, Maldonado M, Oliveira Junior AB, Onuchic JN, Oliveira RJD. Biotin-painted proteins have thermodynamic stability switched by kinetic folding routes. J Chem Phys 2022; 156:195101. [PMID: 35597640 DOI: 10.1063/5.0083875] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Biotin-labeled proteins are widely used as tools to study protein-protein interactions and proximity in living cells. Proteomic methods broadly employ proximity-labeling technologies based on protein biotinylation in order to investigate the transient encounters of biomolecules in subcellular compartments. Biotinylation is a post-translation modification in which the biotin molecule is attached to lysine or tyrosine residues. So far, biotin-based technologies proved to be effective instruments as affinity and proximity tags. However, the influence of biotinylation on aspects such as folding, binding, mobility, thermodynamic stability, and kinetics needs to be investigated. Here, we selected two proteins [biotin carboxyl carrier protein (BCCP) and FKBP3] to test the influence of biotinylation on thermodynamic and kinetic properties. Apo (without biotin) and holo (biotinylated) protein structures were used separately to generate all-atom structure-based model simulations in a wide range of temperatures. Holo BCCP contains one biotinylation site, and FKBP3 was modeled with up to 23 biotinylated lysines. The two proteins had their estimated thermodynamic stability changed by altering their energy landscape. In all cases, after comparison between the apo and holo simulations, differences were observed on the free-energy profiles and folding routes. Energetic barriers were altered with the density of states clearly showing changes in the transition state. This study suggests that analysis of large-scale datasets of biotinylation-based proximity experiments might consider possible alterations in thermostability and folding mechanisms imposed by the attached biotins.
Collapse
Affiliation(s)
- Frederico Campos Freitas
- Laboratório de Biofísica Teórica, Departamento de Física, Instituto de Ciências Exatas, Naturais e Educação, Universidade Federal do Triângulo Mineiro, Uberaba, MG 38064-200, Brazil
| | - Michelli Maldonado
- Departamento de Matemática, Instituto de Ciências Exatas, Naturais e Educação, Universidade Federal do Triângulo Mineiro, Uberaba, MG 38064-200, Brazil
| | - Antonio Bento Oliveira Junior
- Center for Theoretical Biological Physics, Rice University, BioScience Research Collaborative, 6566 Main St., Houston, Texas 77030, USA
| | - José Nelson Onuchic
- Center for Theoretical Biological Physics, Rice University, BioScience Research Collaborative, 6566 Main St., Houston, Texas 77030, USA
| | - Ronaldo Junio de Oliveira
- Laboratório de Biofísica Teórica, Departamento de Física, Instituto de Ciências Exatas, Naturais e Educação, Universidade Federal do Triângulo Mineiro, Uberaba, MG 38064-200, Brazil
| |
Collapse
|
8
|
Contessoto VG, de Oliveira VM, Leite VBP. Coarse-Grained Simulations of Protein Folding: Bridging Theory and Experiments. Methods Mol Biol 2022; 2376:303-315. [PMID: 34845616 DOI: 10.1007/978-1-0716-1716-8_16] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Computational coarse-grained models play a fundamental role as a research tool in protein folding, and they are important in bridging theory and experiments. Folding mechanisms are generally discussed using the energy landscape framework, which is well mapped within a class of simplified structure-based models. In this chapter, simplified computer models are discussed with special focus on structure-based ones.
Collapse
Affiliation(s)
| | - Vinícius M de Oliveira
- Brazilian Biosciences National Laboratory, LNBio/CNPEM, Campinas, SP, Brazil
- São Paulo State University, IBILCE/UNESP, São José do Rio Preto, SP, Brazil
| | - Vitor B P Leite
- São Paulo State University, IBILCE/UNESP, São José do Rio Preto, SP, Brazil.
| |
Collapse
|
9
|
Contessoto VG, Ferreira PHB, Chahine J, Leite VBP, Oliveira RJ. Small Neutral Crowding Solute Effects on Protein Folding Thermodynamic Stability and Kinetics. J Phys Chem B 2021; 125:11673-11686. [PMID: 34644091 DOI: 10.1021/acs.jpcb.1c07663] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Molecular crowding is a ubiquitous phenomenon in biological systems, with significant consequences on protein folding and stability. Small compounds, such as the osmolyte trimethylamine N-oxide (TMAO), can also present similar effects. To analyze the effects arising from these solute-like molecules, we performed a series of crowded coarse-grained folding simulations. Two well-known proteins were chosen, CI2 and SH3, modeled by the alpha-carbon-structure-based model. In the simulations, the crowding molecules were represented by low-sized neutral atom beads in different concentrations. The results show that a low level of the volume fraction occupied by neutral agents can change protein stability and folding kinetics for the two systems. However, the kinetics were shown to be unaffected in their respective folding temperatures. The faster kinetics correlates with changes in the folding route for systems at the same temperature, where non-native contacts were shown to be relevant. The transition states of the two systems with and without crowders are similar. In the case of SH3, there are differences in the structuring of two strands, which may be associated with the increase in its folding rate, in addition to the destabilization of the denatured ensemble. The present study also detected a crossover in the thermodynamic stability behavior, previously observed experimentally and theoretically. As the temperature increases, crowders change from destabilizing to stabilizing agents.
Collapse
Affiliation(s)
- Vinícius G Contessoto
- Department of Physics, Institute of Biosciences, Letters and Exact Sciences, São Paulo State University, São José do Rio Preto 15054-000, Brazil
| | - Paulo H B Ferreira
- Laboratório de Biofísica Teórica, Departamento de Física, Instituto de Ciências Exatas, Naturais e Educação, Universidade Federal do Triângulo Mineiro, Uberaba 38064-200, Brazil
| | - Jorge Chahine
- Department of Physics, Institute of Biosciences, Letters and Exact Sciences, São Paulo State University, São José do Rio Preto 15054-000, Brazil
| | - Vitor B P Leite
- Department of Physics, Institute of Biosciences, Letters and Exact Sciences, São Paulo State University, São José do Rio Preto 15054-000, Brazil
| | - Ronaldo J Oliveira
- Laboratório de Biofísica Teórica, Departamento de Física, Instituto de Ciências Exatas, Naturais e Educação, Universidade Federal do Triângulo Mineiro, Uberaba 38064-200, Brazil
| |
Collapse
|
10
|
Ngo K, Bruno da Silva F, Leite VBP, Contessoto VG, Onuchic JN. Improving the Thermostability of Xylanase A from Bacillus subtilis by Combining Bioinformatics and Electrostatic Interactions Optimization. J Phys Chem B 2021; 125:4359-4367. [PMID: 33887137 DOI: 10.1021/acs.jpcb.1c01253] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The rational improvement of the enzyme catalytic activity is one of the most significant challenges in biotechnology. Most conventional strategies used to engineer enzymes involve selecting mutations to increase their thermostability. Determining good criteria for choosing these substitutions continues to be a challenge. In this work, we combine bioinformatics, electrostatic analysis, and molecular dynamics to predict beneficial mutations that may improve the thermostability of XynA from Bacillus subtilis. First, the Tanford-Kirkwood surface accessibility method is used to characterize each ionizable residue contribution to the protein native state stability. Residues identified to be destabilizing were mutated with the corresponding residues determined by the consensus or ancestral sequences at the same locations. Five mutants (K99T/N151D, K99T, S31R, N151D, and K154A) were investigated and compared with 12 control mutants derived from experimental approaches from the literature. Molecular dynamics results show that the mutants exhibited folding temperatures in the order K99T > K99T/N151D > S31R > N151D > WT > K154A. The combined approaches employed provide an effective strategy for low-cost enzyme optimization needed for large-scale biotechnological and medical applications.
Collapse
Affiliation(s)
- Khoa Ngo
- Department of Physics, University of Houston, Houston, Texas 77004, United States
| | - Fernando Bruno da Silva
- Departamento de Física, Instituto de Biociências, Letras e Ciências Exatas UNESP - Univ. Estadual Paulista, São José do Rio Preto, SP, Brazil
| | - Vitor B P Leite
- Departamento de Física, Instituto de Biociências, Letras e Ciências Exatas UNESP - Univ. Estadual Paulista, São José do Rio Preto, SP, Brazil
| | - Vinícius G Contessoto
- Departamento de Física, Instituto de Biociências, Letras e Ciências Exatas UNESP - Univ. Estadual Paulista, São José do Rio Preto, SP, Brazil
| | | |
Collapse
|
11
|
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
| |
Collapse
|
12
|
Ferreira PHB, Freitas FC, McCully ME, Slade GG, de Oliveira RJ. The Role of Electrostatics and Folding Kinetics on the Thermostability of Homologous Cold Shock Proteins. J Chem Inf Model 2020; 60:546-561. [PMID: 31910002 DOI: 10.1021/acs.jcim.9b00797] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Understanding which aspects contribute to the thermostability of proteins is a challenge that has persisted for decades, and it is of great relevance for protein engineering. Several types of interactions can influence the thermostability of a protein. Among them, the electrostatic interactions have been a target of particular attention. Aiming to explore how this type of interaction can affect protein thermostability, this paper investigated four homologous cold shock proteins from psychrophilic, mesophilic, thermophilic, and hyperthermophilic organisms using a set of theoretical methodologies. It is well-known that electrostatics as well as hydrophobicity are key-elements for the stabilization of these proteins. Therefore, both interactions were initially analyzed in the native structure of each protein. Electrostatic interactions present in the native structures were calculated with the Tanford-Kirkwood model with solvent accessibility, and the amount of hydrophobic surface area buried upon folding was estimated by measuring both folded and extended structures. On the basis of Energy Landscape Theory, the local frustration and the simplified alpha-carbon structure-based model were modeled with a Debye-Hückel potential to take into account the electrostatics and the effects of an implicit solvent. Thermodynamic data for the structure-based model simulations were collected and analyzed using the Weighted Histogram Analysis and Stochastic Diffusion methods. Kinetic quantities including folding times, transition path times, folding routes, and Φ values were also obtained. As a result, we found that the methods are able to qualitatively infer that electrostatic interactions play an important role on the stabilization of the most stable thermophilic cold shock proteins, showing agreement with the experimental data.
Collapse
Affiliation(s)
- Paulo Henrique Borges Ferreira
- Laboratório de Biofísica Teórica, Departamento de Física, Instituto de Ciências Exatas, Naturais e Educação , Universidade Federal do Triângulo Mineiro , Uberaba , Minas Gerais 38064200 , Brazil
| | - Frederico Campos Freitas
- Laboratório de Biofísica Teórica, Departamento de Física, Instituto de Ciências Exatas, Naturais e Educação , Universidade Federal do Triângulo Mineiro , Uberaba , Minas Gerais 38064200 , Brazil
| | - Michelle E McCully
- Department of Biology , Santa Clara University , Santa Clara , California 95050 , United States
| | - Gabriel Gouvêa Slade
- Laboratório de Biofísica Teórica, Departamento de Física, Instituto de Ciências Exatas, Naturais e Educação , Universidade Federal do Triângulo Mineiro , Uberaba , Minas Gerais 38064200 , Brazil
| | - Ronaldo Junio de Oliveira
- Laboratório de Biofísica Teórica, Departamento de Física, Instituto de Ciências Exatas, Naturais e Educação , Universidade Federal do Triângulo Mineiro , Uberaba , Minas Gerais 38064200 , Brazil
| |
Collapse
|
13
|
Mouro PR, Povinelli APR, Leite VBP, Chahine J. Exploring Folding Aspects of Monomeric Superoxide Dismutase. J Phys Chem B 2020; 124:650-661. [DOI: 10.1021/acs.jpcb.9b09640] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Paulo R. Mouro
- São Paulo State University (UNESP), IBILCE, São José do Rio Preto 15054-000, Brazil
| | - Ana P. R. Povinelli
- São Paulo State University (UNESP), IBILCE, São José do Rio Preto 15054-000, Brazil
| | - Vitor B. P. Leite
- São Paulo State University (UNESP), IBILCE, São José do Rio Preto 15054-000, Brazil
- Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, United States
| | - Jorge Chahine
- São Paulo State University (UNESP), IBILCE, São José do Rio Preto 15054-000, Brazil
| |
Collapse
|
14
|
B da Silva F, M de Oliveira V, Sanches MN, Contessoto VG, Leite VBP. Rational Design of Chymotrypsin Inhibitor 2 by Optimizing Non-Native Interactions. J Chem Inf Model 2019; 60:982-988. [PMID: 31794216 DOI: 10.1021/acs.jcim.9b00911] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Rational design of proteins via mutagenesis is crucial for several biotechnological applications. A significant challenge of the computational strategies used to predict optimized mutations is to understand the influence of each amino acid during the folding process. In the present work, chymotrypsin inhibitor 2 (CI2) and several of its designed mutants have been simulated using a non-native hydrophobic and electrostatic potential as a structure-based Cα model. Through these simulations, we could identify the most critical folding stage to accelerate CI2 and also the charged residues responsible for providing its thermostability. The replacement of ionizable residues for hydrophobic ones tended to promote the formation of the CI2 secondary structure in the early transition state, which speeds up folding. However, this same replacement destabilized the native structure, and there was a decrease in the protein thermostability. Such a simple method proved to be capable of providing valuable information about thermodynamics and kinetics of CI2 and its mutations, thus being a fast alternative to the study of rational protein design.
Collapse
Affiliation(s)
- Fernando B da Silva
- Department of Physics, Institute of Biosciences, Humanities and Exact Sciences , São Paulo State University (UNESP) , São José do Rio Preto , São Paulo 15054-000 , Brazil
| | - Vinícius M de Oliveira
- Brazilian Biosciences National Laboratory, Brazilian Center for Research in Energy and Materials , LNBio/CNPEM , Campinas , São Paulo 13083-970 , Brazil
| | - Murilo N Sanches
- Department of Physics, Institute of Biosciences, Humanities and Exact Sciences , São Paulo State University (UNESP) , São José do Rio Preto , São Paulo 15054-000 , Brazil
| | - Vinícius G Contessoto
- Brazilian Biorenewables National Laboratory - LNBR , Brazilian Center for Research in Energy and Materials - CNPEM , Campinas , São Paulo 13083-100 , Brazil.,Center for Theoretical Biological Physics , Rice University , Houston , Texas 77005 , United States
| | - Vitor B P Leite
- Department of Physics, Institute of Biosciences, Humanities and Exact Sciences , São Paulo State University (UNESP) , São José do Rio Preto , São Paulo 15054-000 , Brazil
| |
Collapse
|
15
|
Freitas FC, Lima AN, Contessoto VDG, Whitford PC, Oliveira RJD. Drift-diffusion (DrDiff) framework determines kinetics and thermodynamics of two-state folding trajectory and tunes diffusion models. J Chem Phys 2019; 151:114106. [DOI: 10.1063/1.5113499] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Affiliation(s)
- Frederico Campos Freitas
- Laboratório de Biofísica Teórica, Departamento de Física, Instituto de Ciências Exatas, Naturais e Educação, Universidade Federal do Triângulo Mineiro, Uberaba, MG, Brazil
| | - Angelica Nakagawa Lima
- Laboratório de Biofísica Teórica, Departamento de Física, Instituto de Ciências Exatas, Naturais e Educação, Universidade Federal do Triângulo Mineiro, Uberaba, MG, Brazil
- Laboratório de Biologia Computacional e Bioinformática, Universidade Federal do ABC, Santo André, SP, Brazil
| | - Vinícius de Godoi Contessoto
- Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, USA
- Departamento de Física, Universidade Estadual Paulista, São José do Rio Preto, SP, Brazil
- Brazilian Biorenewables National Laboratory - LNBR, Brazilian Center for Research in Energy and Materials - CNPEM, Campinas, SP, Brazil
| | - Paul C. Whitford
- Department of Physics, Northeastern University, Boston, Massachusetts 02115, USA
| | - Ronaldo Junio de Oliveira
- Laboratório de Biofísica Teórica, Departamento de Física, Instituto de Ciências Exatas, Naturais e Educação, Universidade Federal do Triângulo Mineiro, Uberaba, MG, Brazil
| |
Collapse
|
16
|
Abstract
The folding simulations of three ββα-motifs and β-barrel structured proteins (NTL9, NuG2b, and CspA) were performed to determine the important roles of native and nonnative contacts in protein folding.
Collapse
Affiliation(s)
- Qiang Shao
- Drug Discovery and Design Center
- CAS Key Laboratory of Receptor Research
- Shanghai Institute of Materia Medica
- Chinese Academy of Sciences
- Shanghai
| | - Weiliang Zhu
- Drug Discovery and Design Center
- CAS Key Laboratory of Receptor Research
- Shanghai Institute of Materia Medica
- Chinese Academy of Sciences
- Shanghai
| |
Collapse
|
17
|
Bruno da Silva F, Contessoto VG, de Oliveira VM, Clarke J, Leite VBP. Non-Native Cooperative Interactions Modulate Protein Folding Rates. J Phys Chem B 2018; 122:10817-10824. [DOI: 10.1021/acs.jpcb.8b08990] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Fernando Bruno da Silva
- Department of Physics, Institute of Biosciences, Humanities and Exact Sciences, São Paulo State University (UNESP), São José do Rio Preto - São Paulo 15054-000, Brazil
| | - Vinícius G. Contessoto
- Brazilian Bioethanol Science and Technology Laboratory - CTBE, Campinas - São Paulo 13083-100, Brazil
| | - Vinícius M. de Oliveira
- Department of Physics, Institute of Biosciences, Humanities and Exact Sciences, São Paulo State University (UNESP), São José do Rio Preto - São Paulo 15054-000, Brazil
| | - Jane Clarke
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Vitor B. P. Leite
- Department of Physics, Institute of Biosciences, Humanities and Exact Sciences, São Paulo State University (UNESP), São José do Rio Preto - São Paulo 15054-000, Brazil
| |
Collapse
|
18
|
Martins de Oliveira V, Godoi Contessoto VD, Bruno da Silva F, Zago Caetano DL, Jurado de Carvalho S, Pereira Leite VB. Effects of pH and Salt Concentration on Stability of a Protein G Variant Using Coarse-Grained Models. Biophys J 2018; 114:65-75. [PMID: 29320697 PMCID: PMC5984902 DOI: 10.1016/j.bpj.2017.11.012] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Revised: 10/20/2017] [Accepted: 11/13/2017] [Indexed: 11/18/2022] Open
Abstract
The importance of charge-charge interactions in the thermal stability of proteins is widely known. pH and ionic strength play a crucial role in these electrostatic interactions, as well as in the arrangement of ionizable residues in each protein-folding stage. In this study, two coarse-grained models were used to evaluate the effect of pH and salt concentration on the thermal stability of a protein G variant (1PGB-QDD), which was chosen due to the quantity of experimental data exploring these effects on its stability. One of these coarse-grained models, the TKSA, calculates the electrostatic free energy of the protein in the native state via the Tanford-Kirkwood approach for each residue. The other one, CpHMD-SBM, uses a Coulomb screening potential in addition to the structure-based model Cα. Both models simulate the system in constant pH. The comparison between the experimental stability analysis and the computational results obtained by these simple models showed a good agreement. Through the TKSA method, the role of each charged residue in the protein's thermal stability was inferred. Using CpHMD-SBM, it was possible to evaluate salt and pH effects throughout the folding process. Finally, the computational pKa values were calculated by both methods and presented a good level of agreement with the experiments. This study provides, to our knowledge, new information and a comprehensive description of the electrostatic contribution to protein G stability.
Collapse
Affiliation(s)
- Vinícius Martins de Oliveira
- São Paulo State University (UNESP), Institute of Biosciences, Humanities and Exact Sciences (Ibilce), Campus São José do Rio Preto, Brazil
| | - Vinícius de Godoi Contessoto
- São Paulo State University (UNESP), Institute of Biosciences, Humanities and Exact Sciences (Ibilce), Campus São José do Rio Preto, Brazil; Brazilian Bioethanol Science and Technology Laboratory- (CTBE), Campinas, Brazil
| | - Fernando Bruno da Silva
- São Paulo State University (UNESP), Institute of Biosciences, Humanities and Exact Sciences (Ibilce), Campus São José do Rio Preto, Brazil
| | - Daniel Lucas Zago Caetano
- São Paulo State University (UNESP), Institute of Biosciences, Humanities and Exact Sciences (Ibilce), Campus São José do Rio Preto, Brazil
| | - Sidney Jurado de Carvalho
- São Paulo State University (UNESP), Institute of Biosciences, Humanities and Exact Sciences (Ibilce), Campus São José do Rio Preto, Brazil
| | - Vitor Barbanti Pereira Leite
- São Paulo State University (UNESP), Institute of Biosciences, Humanities and Exact Sciences (Ibilce), Campus São José do Rio Preto, Brazil.
| |
Collapse
|
19
|
Q Nguyen KK, Gomez YK, Bakhom M, Radcliffe A, La P, Rochelle D, Lee JW, Sorin EJ. Ensemble simulations: folding, unfolding and misfolding of a high-efficiency frameshifting RNA pseudoknot. Nucleic Acids Res 2017; 45:4893-4904. [PMID: 28115636 PMCID: PMC5416846 DOI: 10.1093/nar/gkx012] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Accepted: 01/11/2017] [Indexed: 12/11/2022] Open
Abstract
Massive all-atom molecular dynamics simulations were conducted across a distributed computing network to study the folding, unfolding, misfolding and conformational plasticity of the high-efficiency frameshifting double mutant of the 26 nt potato leaf roll virus RNA pseudoknot. Our robust sampling, which included over 40 starting structures spanning the spectrum from the extended unfolded state to the native fold, yielded nearly 120 μs of cumulative sampling time. Conformational microstate transitions on the 1.0 ns to 10.0 μs timescales were observed, with post-equilibration sampling providing detailed representations of the conformational free energy landscape and the complex folding mechanism inherent to the pseudoknot motif. Herein, we identify and characterize two alternative native structures, three intermediate states, and numerous misfolded states, the latter of which have not previously been characterized via atomistic simulation techniques. While in line with previous thermodynamics-based models of a general RNA folding mechanism, our observations indicate that stem-strand-sequence-separation may serve as an alternative predictor of the order of stem formation during pseudoknot folding. Our results contradict a model of frameshifting based on structural rigidity and resistance to mechanical unfolding, and instead strongly support more recent studies in which conformational plasticity is identified as a determining factor in frameshifting efficiency.
Collapse
Affiliation(s)
- Khai K Q Nguyen
- Department of Chemistry & Biochemistry, California State University Long Beach, Long Beach, CA 90840, USA.,Department of Computer Engineering & Computer Science, California State University Long Beach, Long Beach, CA 90840, USA
| | - Yessica K Gomez
- Department of Chemistry & Biochemistry, California State University Long Beach, Long Beach, CA 90840, USA.,Department of Physics & Astronomy, California State University Long Beach, Long Beach, CA 90840, USA
| | - Mona Bakhom
- Department of Chemistry & Biochemistry, California State University Long Beach, Long Beach, CA 90840, USA
| | - Amethyst Radcliffe
- Department of Physics & Astronomy, California State University Long Beach, Long Beach, CA 90840, USA
| | - Phuc La
- Department of Chemistry & Biochemistry, California State University Long Beach, Long Beach, CA 90840, USA
| | - Dakota Rochelle
- Department of Chemistry & Biochemistry, California State University Long Beach, Long Beach, CA 90840, USA
| | - Ji Won Lee
- Department of Chemistry & Biochemistry, California State University Long Beach, Long Beach, CA 90840, USA
| | - Eric J Sorin
- Department of Chemistry & Biochemistry, California State University Long Beach, Long Beach, CA 90840, USA
| |
Collapse
|
20
|
Wu J, Chen G, Zhang Z, Zhang P, Chen T. The low populated folding intermediate of a mutant of the Fyn SH3 domain identified by a simple model. Phys Chem Chem Phys 2017; 19:22321-22328. [DOI: 10.1039/c7cp04139j] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The low populated on-pathway folding intermediate of the A39V/N53P/V55L Fyn SH3 domain is captured by a native-centric model augmented by sequence-dependent nonnative hydrophobic interactions.
Collapse
Affiliation(s)
- Jing Wu
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry of the Ministry of Education
- College of Chemistry and Materials Science
- Northwest University
- Xi'an
- P. R. China
| | - Guojun Chen
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry of the Ministry of Education
- College of Chemistry and Materials Science
- Northwest University
- Xi'an
- P. R. China
| | - Zhuqing Zhang
- College of Life Sciences
- University of Chinese Academy of Sciences
- Beijing
- P. R. China
| | - Ping Zhang
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry of the Ministry of Education
- College of Chemistry and Materials Science
- Northwest University
- Xi'an
- P. R. China
| | - Tao Chen
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry of the Ministry of Education
- College of Chemistry and Materials Science
- Northwest University
- Xi'an
- P. R. China
| |
Collapse
|