1
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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.
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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
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2
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Shibata M, Lin X, Onuchic JN, Yura K, Cheng RR. Residue coevolution and mutational landscape for OmpR and NarL response regulator subfamilies. Biophys J 2024; 123:681-692. [PMID: 38291753 PMCID: PMC10995415 DOI: 10.1016/j.bpj.2024.01.028] [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: 11/10/2023] [Revised: 12/31/2023] [Accepted: 01/24/2024] [Indexed: 02/01/2024] Open
Abstract
DNA-binding response regulators (DBRRs) are a broad class of proteins that operate in tandem with their partner kinase proteins to form two-component signal transduction systems in bacteria. Typical DBRRs are composed of two domains where the conserved N-terminal domain accepts transduced signals and the evolutionarily diverse C-terminal domain binds to DNA. These domains are assumed to be functionally independent, and hence recombination of the two domains should yield novel DBRRs of arbitrary input/output response, which can be used as biosensors. This idea has been proved to be successful in some cases; yet, the error rate is not trivial. Improvement of the success rate of this technique requires a deeper understanding of the linker-domain and inter-domain residue interactions, which have not yet been thoroughly examined. Here, we studied residue coevolution of DBRRs of the two main subfamilies (OmpR and NarL) using large collections of bacterial amino acid sequences to extensively investigate the evolutionary signatures of linker-domain and inter-domain residue interactions. Coevolutionary analysis uncovered evolutionarily selected linker-domain and inter-domain residue interactions of known experimental structures, as well as previously unknown inter-domain residue interactions. We examined the possibility of these inter-domain residue interactions as contacts that stabilize an inactive conformation of the DBRR where DNA binding is inhibited for both subfamilies. The newly gained insights on linker-domain/inter-domain residue interactions and shared inactivation mechanisms improve the understanding of the functional mechanism of DBRRs, providing clues to efficiently create functional DBRR-based biosensors. Additionally, we show the feasibility of applying coevolutionary landscape models to predict the functionality of domain-swapped DBRR proteins. The presented result demonstrates that sequence information can be used to filter out bioengineered DBRR proteins that are predicted to be nonfunctional due to a high negative predictive value.
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Affiliation(s)
- Mayu Shibata
- Graduate School of Humanities and Sciences, Ochanomizu University, Bunkyo, Tokyo, Japan; Center for Theoretical Biological Physics, Rice University, Houston Texas
| | - Xingcheng Lin
- Department of Physics, North Carolina State University, Raleigh, North Carolina; Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina
| | - José N Onuchic
- Center for Theoretical Biological Physics, Rice University, Houston Texas; Department of Physics and Astronomy, Chemistry, and Biosciences, Rice University, Houston, Texas
| | - Kei Yura
- Graduate School of Humanities and Sciences, Ochanomizu University, Bunkyo, Tokyo, Japan; Center for Interdisciplinary AI and Data Science, Ochanomizu University, Bunkyo, Tokyo, Japan; Graduate School of Advanced Science and Engineering, Waseda University, Shinjuku, Tokyo, Japan
| | - Ryan R Cheng
- Department of Chemistry, University of Kentucky, Lexington, Kentucky.
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3
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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.
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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
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4
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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.
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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
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5
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Quiroz RCN, Philot EA, General IJ, Perahia D, Scott AL. Effect of phosphorylation on the structural dynamics, thermal stability of human dopamine transporter: A simulation study using normal modes, molecular dynamics and Markov State Model. J Mol Graph Model 2023; 118:108359. [PMID: 36279761 DOI: 10.1016/j.jmgm.2022.108359] [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: 07/26/2022] [Revised: 10/04/2022] [Accepted: 10/06/2022] [Indexed: 11/06/2022]
Abstract
The Human Dopamine Transporter (hDAT) plays an essential role in modulating the Influx/Efflux of dopamine, and it is involved in the mechanism of certain neurodegenerative diseases such as Parkinson's disease. Several studies have reported important states for Dopamine transport: outward-facing open state (OFo), the outward-facing closed state (OFc), the holo-occluded state closed (holo), and the inward-facing open state (IFo). Furthermore, experimental assays have shown that different phosphorylation conditions in hDAT can affect the rate of dopamine absorption. We present a protocol using hybrid simulation methods to study the conformational dynamics and stability of states of hDAT under different phosphorylation sites. With this protocol, we explored the conformational space of hDAT, identified the states, and evaluated the free energy differences and the transition probabilities between them in each of the phosphorylation cases. We also presented the conformational changes and correlated them with those described in the literature. There is a thesis/hypothesis that the phosphorylation condition corresponding to NP-333 system (where all sites Ser/Thr from residue 2 to 62 and 254 to 613 are phosphorylated, except residue 333) would decrease the rate of dopamine transport from the extracellular medium to the intracellular medium by hDAT as previously described in the literature by Lin et al., 2003. Our results corroborated this thesis/hypothesis and the data reported. It is probably due to the affectation/changes/alteration of the conformational dynamics of this system that makes the intermediate states more likely and makes it difficult to initial states associated with the uptake of dopamine in the extracellular medium, corroborating the experimental results. Furthermore, our results showed that just single phosphorylation/dephosphorylation could alter intrinsic protein motions affecting the sampling of one or more states necessary for dopamine transport. In this sense, the modification of phosphorylation influences protein movements and conformational preferences, affecting the stability of states and the transition between them and, therefore, the transport.
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Affiliation(s)
- R C N Quiroz
- Biossistemas, Universidade Federal do ABC, CCNH, Santo André, Brazil; Centro de Matemática, Computação e Cognição. Laboratório de Biofísica e Biologia Computacional. Universidade Federal do ABC, Santo André, São Paulo, Brazil
| | - E A Philot
- Centro de Matemática, Computação e Cognição. Laboratório de Biofísica e Biologia Computacional. Universidade Federal do ABC, Santo André, São Paulo, Brazil
| | - I J General
- School of Science and Technology, Universidad Nacional de San Martin, ICIFI and CONICET, 25 de Mayo y Francia, San Martín, 1650, Buenos Aires, Argentina
| | - D Perahia
- Laboratoire de Biologie et Pharmacologie Appliquée, Ecole Normale Supérieure Paris-Saclay, UMR 8113, CNRS, 4 avenue des Sciences, 91190 Gif-sur-Yvette, France
| | - A L Scott
- UFABC - Universidade Federal Do ABC, Centro de Matemática, Computação e Cognição, Laboratório de Biofísica e Biologia Computacional, Brazil.
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6
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Oliveira RJD. Coordinate-Dependent Drift-Diffusion Reveals the Kinetic Intermediate Traps of Top7-Based Proteins. J Phys Chem B 2022; 126:10854-10869. [PMID: 36519977 DOI: 10.1021/acs.jpcb.2c07031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The computer-designed Top7 served as a scaffold to produce immunoreactive proteins by grafting of the 2F5 HIV-1 antibody epitope (Top7-2F5) followed by biotinylation (Top7-2F5-biotin). The resulting nonimmunoglobulin affinity proteins were effective in inducing and detecting the HIV-1 antibody. However, the grafted Top7-2F5 design led to protein aggregation, as opposed to the soluble biotinylated Top7-2F5-biotin. The structure-based model predicted that the thermodynamic cooperativity of Top7 increases after grafting and biotin-labeling, reducing their intermediate state populations. In this work, the folding kinetic traps that might contribute to the aggregation propensity are investigated by the diffusion theory. Since the engineered proteins have similar sequence and structural homology, they served as protein models to study the kinetic intermediate traps that were uncovered by characterizing the position-dependent drift-velocity (v(Q)) and the diffusion (D(Q)) coefficients. These coordinate-dependent coefficients were taken into account to obtain the folding and transition path times over the free energy transition states containing the intermediate kinetic traps. This analysis may be useful to predict the aggregated kinetic traps of scaffold-epitope proteins that might compose novel diagnostic and therapeutic platforms.
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Affiliation(s)
- Ronaldo Junio de Oliveira
- Laboratório de Biofísica Teórica, Departamento de Física, Instituto de Ciências Exatas, Naturais e Educação, Universidade Federal do Triângulo Mineiro, Uberaba, MG38064-200, Brazil
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7
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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.
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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.
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8
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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.
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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
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9
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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.
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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
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10
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de Godoi Contessoto V, Ramos FC, de Melo RR, de Oliveira VM, Scarpassa JA, de Sousa AS, Zanphorlin LM, Slade GG, Leite VBP, Ruller R. Electrostatic interaction optimization improves catalytic rates and thermotolerance on xylanases. Biophys J 2021; 120:2172-2180. [PMID: 33831390 DOI: 10.1016/j.bpj.2021.03.036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 02/08/2021] [Accepted: 03/23/2021] [Indexed: 10/21/2022] Open
Abstract
Understanding the aspects that contribute to improving proteins' biochemical properties is of high relevance for protein engineering. Properties such as the catalytic rate, thermal stability, and thermal resistance are crucial for applying enzymes in the industry. Different interactions can influence those biochemical properties of an enzyme. Among them, the surface charge-charge interactions have been a target of particular attention. In this study, we employ the Tanford-Kirkwood solvent accessibility model using the Monte Carlo algorithm (TKSA-MC) to predict possible interactions that could improve stability and catalytic rate of a WT xylanase (XynAWT) and its M6 xylanase (XynAM6) mutant. The modeling prediction indicates that mutating from a lysine in position 99 to a glutamic acid (K99E) favors the native state stabilization in both xylanases. Our lab results showed that mutated xylanases had their thermotolerance and catalytic rate increased, which conferred higher processivity of delignified sugarcane bagasse. The TKSA-MC approach employed here is presented as an efficient computational-based design strategy that can be applied to improve the thermal resistance of enzymes with industrial and biotechnological applications.
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Affiliation(s)
- Vinícius de Godoi Contessoto
- Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, São Paulo, Brazil; Center for Theoretical Biological Physics, Rice University, Houston, Texas; Department of Physics, Institute of Biosciences, Letters and Exact Sciences, São Paulo State University, São José do Rio Preto, São Paulo, Brazil
| | - Felipe Cardoso Ramos
- Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, São Paulo, Brazil
| | - Ricardo Rodrigues de Melo
- Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, São Paulo, Brazil
| | - Vinícius Martins de Oliveira
- Brazilian Biosciences National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, São Paulo, Brazil
| | - Josiane Aniele Scarpassa
- Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, São Paulo, Brazil
| | - Amanda Silva de Sousa
- Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, São Paulo, Brazil
| | - Letıcia Maria Zanphorlin
- Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, São Paulo, Brazil
| | - Gabriel Gouvea Slade
- Theoretical Biophysics Laboratory, Institute of Exact Sciences, Natural and Education, Federal University of Triângulo Mineiro, Uberaba, Minas Gerais, Brazil
| | - Vitor Barbanti Pereira Leite
- Department of Physics, Institute of Biosciences, Letters and Exact Sciences, São Paulo State University, São José do Rio Preto, São Paulo, Brazil.
| | - Roberto Ruller
- Microorganisms and General Biochemistry Laboratory, Institute of Bioscience, Federal University of Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul, Brazil
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11
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Xia C, Kang W, Wang J, Wang W. Temperature Dependence of Internal Friction of Peptides. J Phys Chem B 2021; 125:2821-2832. [PMID: 33689339 DOI: 10.1021/acs.jpcb.0c09056] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Internal friction is a valuable concept to describe the kinetics of proteins. As is well known, internal friction can be modulated by solvent features (such as viscosity). How can internal friction be affected by environmental temperature? The answer to this question is not evident. In the present work, we approach this problem with simulations on two model peptides. The thermodynamics and relaxation kinetics are characterized through long molecular dynamics simulations, with the viscosity modulated by varying the mass of solvent molecules. Based on the extrapolation to zero viscosity together with scaling of the relaxation time scales, we discover that internal friction is almost invariant at various temperatures. Controlled simulations further support the idea that internal friction is independent of environmental temperature. Comparisons between the two model peptides help us to understand the diverse phenomena in experiments.
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Affiliation(s)
- Chenliang Xia
- School of Physics, Nanjing University, Nanjing 210093, P.R.China.,National Laboratory of Solid State Microstructure, Collaborative Innovation Center of Advanced Microstructures, Nanjing 210093, P.R.China
| | - Wenbin Kang
- School of Public Health and Management, Hubei University of Medicine, Shiyan 442000, P.R. China
| | - Jun Wang
- School of Physics, Nanjing University, Nanjing 210093, P.R.China.,National Laboratory of Solid State Microstructure, Collaborative Innovation Center of Advanced Microstructures, Nanjing 210093, P.R.China
| | - Wei Wang
- School of Physics, Nanjing University, Nanjing 210093, P.R.China.,National Laboratory of Solid State Microstructure, Collaborative Innovation Center of Advanced Microstructures, Nanjing 210093, P.R.China
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12
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The road less traveled in protein folding: evidence for multiple pathways. Curr Opin Struct Biol 2020; 66:83-88. [PMID: 33220553 DOI: 10.1016/j.sbi.2020.10.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 10/11/2020] [Indexed: 11/23/2022]
Abstract
Free Energy Landscape theory of Protein Folding, introduced over 20 years ago, implies that a protein has many paths to the folded conformation with the lowest free energy. Despite the knowledge in principle, it has been remarkably hard to detect such pathways. The lack of such observations is primarily due to the fact that no one experimental technique can detect many parts of the protein simultaneously with the time resolution necessary to see such differences in paths. However, recent technical developments and employment of multiple experimental probes and folding prompts have illuminated multiple folding pathways in a number of proteins that had all previously been described with a single path.
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13
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de Oliveira VM, Caetano DLZ, da Silva FB, Mouro PR, de Oliveira AB, de Carvalho SJ, Leite VBP. pH and Charged Mutations Modulate Cold Shock Protein Folding and Stability: A Constant pH Monte Carlo Study. J Chem Theory Comput 2020; 16:765-772. [PMID: 31756296 DOI: 10.1021/acs.jctc.9b00894] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The folding and stability of proteins is a fundamental problem in several research fields. In the present paper, we have used different computational approaches to study the effects caused by changes in pH and for charged mutations in cold shock proteins from Bacillus subtilis (Bs-CspB). First, we have investigated the contribution of each ionizable residue for these proteins to their thermal stability using the TKSA-MC, a Web server for rational mutation via optimizing the protein charge interactions. Based on these results, we have proposed a new mutation in an already optimized Bs-CspB variant. We have evaluated the effects of this new mutation in the folding energy landscape using structure-based models in Monte Carlo simulation at constant pH, SBM-CpHMC. Our results using this approach have indicated that the charge rearrangements already in the unfolded state are critical to the thermal stability of Bs-CspB. Furthermore, the conjunction of these simplified methods was able not only to predict stabilizing mutations in different pHs but also to provide essential information about their effects in each stage of protein folding.
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Affiliation(s)
- Vinícius M de Oliveira
- Brazilian Biosciences National Laboratory, National Center for Research in Energy and Materials, LNBio/CNPEM , Campinas , São Paulo , 13083-970 , Brazil
| | - Daniel L Z Caetano
- Department of Physics , São Paulo State University (UNESP), Institute of Biosciences, Humanities and Exact Sciences , São José do Rio Preto , São Paulo , 15054-000 , Brazil
| | - Fernando B da Silva
- Department of Physics , São Paulo State University (UNESP), Institute of Biosciences, Humanities and Exact Sciences , São José do Rio Preto , São Paulo , 15054-000 , Brazil
| | - Paulo R Mouro
- Department of Physics , São Paulo State University (UNESP), Institute of Biosciences, Humanities and Exact Sciences , São José do Rio Preto , São Paulo , 15054-000 , Brazil
| | - Antonio B de Oliveira
- Department of Physics , São Paulo State University (UNESP), Institute of Biosciences, Humanities and Exact Sciences , São José do Rio Preto , São Paulo , 15054-000 , Brazil
| | - Sidney J de Carvalho
- Department of Physics , São Paulo State University (UNESP), Institute of Biosciences, Humanities and Exact Sciences , São José do Rio Preto , São Paulo , 15054-000 , Brazil
| | - 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 Paulo , 15054-000 , Brazil.,Center for Theoretical Biological Physics , Rice University , Houston , Texas 77005 , United States
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14
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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.
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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
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15
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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
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16
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Observation of Continuous Contraction and a Metastable Misfolded State during the Collapse and Folding of a Small Protein. J Mol Biol 2019; 431:3814-3826. [DOI: 10.1016/j.jmb.2019.07.024] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 07/12/2019] [Accepted: 07/12/2019] [Indexed: 01/22/2023]
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17
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Fang J. A critical review of five machine learning-based algorithms for predicting protein stability changes upon mutation. Brief Bioinform 2019; 21:1285-1292. [PMID: 31273374 DOI: 10.1093/bib/bbz071] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 05/14/2019] [Accepted: 05/16/2019] [Indexed: 01/02/2023] Open
Abstract
A number of machine learning (ML)-based algorithms have been proposed for predicting mutation-induced stability changes in proteins. In this critical review, we used hypothetical reverse mutations to evaluate the performance of five representative algorithms and found all of them suffer from the problem of overfitting. This approach is based on the fact that if a wild-type protein is more stable than a mutant protein, then the same mutant is less stable than the wild-type protein. We analyzed the underlying issues and suggest that the main causes of the overfitting problem include that the numbers of training cases were too small, and the features used in the models were not sufficiently informative for the task. We make recommendations on how to avoid overfitting in this important research area and improve the reliability and robustness of ML-based algorithms in general.
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Affiliation(s)
- Jianwen Fang
- Computational & Systems Biology Branch, Biometric Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, 9609 Medical Center Drive, Rockville, MD 20850, USA
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