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Martins IBS, Viegas RG, Sanches MN, de Araujo AS, Leite VBP. Probing Mastoparan-like Antimicrobial Peptides Interaction with Model Membrane Through Energy Landscape Analysis. J Phys Chem B 2024; 128:163-171. [PMID: 38159056 DOI: 10.1021/acs.jpcb.3c05852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Abstract
Antimicrobial Peptides (AMPs) have emerged as promising alternatives to conventional antibiotics due to their capacity to disrupt the lipid packing of bacterial cell membranes. This mechanism of action may prevent the development of resistance by bacteria. Understanding their role in lipid packing disruption and their structural properties upon interaction with bacterial membranes is highly desirable. In this study, we employed Molecular Dynamics simulations and the Energy Landscape Visualization Method (ELViM) to characterize and compare the conformational ensembles of mastoparan-like Polybia-MP1 and its analogous H-MP1, in which histidines replace lysine residues. Two situations were analyzed: (i) the peptides in their free state in an aqueous solution containing water and ions and (ii) the peptides spontaneously adsorbing onto an anionic lipid bilayer, used as a bacteria membrane mimetic. ELViM was used to project a single effective conformational phase space for both peptides, providing a comparative analysis. This projection enabled us to map the conformational ensembles of each peptide in an aqueous solution and assess the structural effects of substituting lysines with histidines in H-MP1. Furthermore, a single conformational phase space analysis was employed to describe structural changes during the adsorption process using the same framework. We show that ELViM provides a comprehensive analysis, able to identify discrepancies in the conformational ensembles of these peptides that may affect their affinity to the membrane and adsorption kinetics.
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Affiliation(s)
- Ingrid B S Martins
- Department of Physics, Institute of Biosciences, Humanities and Exact Sciences, São Paulo State University (UNESP), São José do Rio Preto, SP 15054-000, Brazil
- Biophysics Institute Carlos Chagas Filho, Federal University of Rio de Janeiro, Rio de Janeiro, RJ 21941-902, Brazil
| | - Rafael G Viegas
- Department of Physics, Institute of Biosciences, Humanities and Exact Sciences, São Paulo State University (UNESP), São José do Rio Preto, SP 15054-000, Brazil
- Federal Institute of Education, Science and Technology of São Paulo (IFSP), Catanduva, SP 15.808-305, Brazil
| | - Murilo N Sanches
- Department of Physics, Institute of Biosciences, Humanities and Exact Sciences, São Paulo State University (UNESP), São José do Rio Preto, SP 15054-000, Brazil
| | - Alexandre S de Araujo
- Department of Physics, Institute of Biosciences, Humanities and Exact Sciences, São Paulo State University (UNESP), São José do Rio Preto, SP 15054-000, Brazil
| | - Vitor B P Leite
- Department of Physics, Institute of Biosciences, Humanities and Exact Sciences, São Paulo State University (UNESP), São José do Rio Preto, SP 15054-000, Brazil
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Dias RVR, Pedro RP, Sanches MN, Moreira GC, Leite VBP, Caruso IP, de Melo FA, de Oliveira LC. Unveiling Metastable Ensembles of GRB2 and the Relevance of Interdomain Communication during Folding. J Chem Inf Model 2023; 63:6344-6353. [PMID: 37824286 DOI: 10.1021/acs.jcim.3c00955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2023]
Abstract
The folding process of multidomain proteins is a highly intricate phenomenon involving the assembly of distinct domains into a functional three-dimensional structure. During this process, each domain may fold independently while interacting with others. The folding of multidomain proteins can be influenced by various factors, including their composition, the structure of each domain, or the presence of disordered regions, as well as the surrounding environment. Misfolding of multidomain proteins can lead to the formation of nonfunctional structures associated with a range of diseases, including cancers or neurodegenerative disorders. Understanding this process is an important step for many biophysical analyses such as stability, interaction, malfunctioning, and rational drug design. One such multidomain protein is growth factor receptor-bound protein 2 (GRB2), an adaptor protein that is essential in regulating cell survival. GRB2 consists of one central Src homology 2 (SH2) domain flanked by two Src homology 3 (SH3) domains. The SH2 domain interacts with phosphotyrosine regions in other proteins, while the SH3 domains recognize proline-rich regions on protein partners during cell signaling. Here, we combined computational and experimental techniques to investigate the folding process of GRB2. Through computational simulations, we sampled the conformational space and mapped the mechanisms involved by the free energy profiles, which may indicate possible intermediate states. From the molecular dynamics trajectories, we used the energy landscape visualization method (ELViM), which allowed us to visualize a three-dimensional (3D) representation of the overall energy surface. We identified two possible parallel folding routes that cannot be seen in a one-dimensional analysis, with one occurring more frequently during folding. Supporting these results, we used differential scanning calorimetry (DSC) and fluorescence spectroscopy techniques to confirm these intermediate states in vitro. Finally, we analyzed the deletion of domains to compare our model outputs to previously published results, supporting the presence of interdomain modulation. Overall, our study highlights the significance of interdomain communication within the GRB2 protein and its impact on the formation, stability, and structural plasticity of the protein, which are crucial for its interaction with other proteins in key signaling pathways.
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Affiliation(s)
- Raphael V R Dias
- Department of Physics, São Paulo State University (UNESP), Institute of Biosciences, Humanities, and Exact Sciences, São José do Rio Preto, SP 15054-000, Brazil
- Multiuser Center for Biomolecular Innovation (CMIB), São Paulo State University (UNESP), São José do Rio Preto, SP 15054-000, Brazil
| | - Renan P Pedro
- Department of Physics, São Paulo State University (UNESP), Institute of Biosciences, Humanities, and Exact Sciences, São José do Rio Preto, SP 15054-000, Brazil
- Multiuser Center for Biomolecular Innovation (CMIB), São Paulo State University (UNESP), São José do Rio Preto, SP 15054-000, Brazil
| | - Murilo N Sanches
- Department of Physics, São Paulo State University (UNESP), Institute of Biosciences, Humanities, and Exact Sciences, São José do Rio Preto, SP 15054-000, Brazil
| | - Giovana C Moreira
- Department of Physics, São Paulo State University (UNESP), Institute of Biosciences, Humanities, and Exact Sciences, São José do Rio Preto, SP 15054-000, Brazil
- Multiuser Center for Biomolecular Innovation (CMIB), São Paulo State University (UNESP), São José do Rio Preto, SP 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, SP 15054-000, Brazil
| | - Icaro P Caruso
- Department of Physics, São Paulo State University (UNESP), Institute of Biosciences, Humanities, and Exact Sciences, São José do Rio Preto, SP 15054-000, Brazil
- Multiuser Center for Biomolecular Innovation (CMIB), São Paulo State University (UNESP), São José do Rio Preto, SP 15054-000, Brazil
| | - Fernando A de Melo
- Department of Physics, São Paulo State University (UNESP), Institute of Biosciences, Humanities, and Exact Sciences, São José do Rio Preto, SP 15054-000, Brazil
- Multiuser Center for Biomolecular Innovation (CMIB), São Paulo State University (UNESP), São José do Rio Preto, SP 15054-000, Brazil
| | - Leandro C de Oliveira
- Department of Physics, São Paulo State University (UNESP), Institute of Biosciences, Humanities, and Exact Sciences, São José do Rio Preto, SP 15054-000, Brazil
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Viegas RG, Sanches MN, Chen AA, Paulovich FV, Garcia AE, Leite VBP. Characterizing the Folding Transition-State Ensembles in the Energy Landscape of an RNA Tetraloop. J Chem Inf Model 2023; 63:5641-5649. [PMID: 37606640 DOI: 10.1021/acs.jcim.3c00426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/23/2023]
Abstract
Molecular dynamics (MD) simulations have become increasingly powerful and can now describe the folding/unfolding of small biomolecules in atomic detail. However, a major challenge in MD simulations is to represent the complex energy landscape of biomolecules using a small number of reaction coordinates. In this study, we investigate the folding pathways of an RNA tetraloop, gcGCAAgc, using five classical MD simulations with a combined simulation time of approximately 120 μs. Our approach involves analyzing the tetraloop dynamics, including the folding transition state ensembles, using the energy landscape visualization method (ELViM). The ELViM is an approach that uses internal distances to compare any two conformations, allowing for a detailed description of the folding process without requiring root mean square alignment of structures. This method has previously been applied to describe the energy landscape of disordered β-amyloid peptides and other proteins. The ELViM results in a non-linear projection of the multidimensional space, providing a comprehensive representation of the tetraloop's energy landscape. Our results reveal four distinct transition-state regions and establish the paths that lead to the folded tetraloop structure. This detailed analysis of the tetraloop's folding process has important implications for understanding RNA folding, and the ELViM approach can be used to study other biomolecules.
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Affiliation(s)
- Rafael G Viegas
- Federal Institute of Education, Science and Technology of São Paulo (IFSP), Catanduva, São Paulo 15.808-305, Brazil
- 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
| | - 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
| | - Alan A Chen
- Department of Chemistry and the RNA Institute, University at Albany, Albany, New York 12222, United States
| | - Fernando V Paulovich
- Department of Mathematics and Computer Science, Eindhoven University of Technology, P.O. Box 513, Eindhoven 5600 MB, the Netherlands
| | - Angel E Garcia
- Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
- Physics Division, National Science Foundation, 2415 Eisenhower Ave, Alexandria, Virginia 22314, 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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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Sanches MN, Knapp K, Oliveira AB, Wolynes PG, Onuchic JN, Leite VBP. Examining the Ensembles of Amyloid-β Monomer Variants and Their Propensities to Form Fibers Using an Energy Landscape Visualization Method. J Phys Chem B 2021; 126:93-99. [PMID: 34968059 DOI: 10.1021/acs.jpcb.1c08525] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The amyloid-β (Aβ) monomer, an intrinsically disordered peptide, is produced by the cleavage of the amyloid precursor protein, leading to Aβ-40 and Aβ-42 as major products. These two isoforms generate pathological aggregates, whose accumulation correlates with Alzheimer's disease (AD). Experiments have shown that even though the natural abundance of Aβ-42 is smaller than that for Aβ-40, the Aβ-42 is more aggregation-prone compared to Aβ-40. Moreover, several single-point mutations are associated with early onset forms of AD. This work analyzes coarse-grained associative-memory, water-mediated, structure and energy model (AWSEM) simulations of normal Aβ-40 and Aβ-42 monomers, along with six single-point mutations associated with early onset disease. We analyzed the simulations using the energy landscape visualization method (ELViM), a reaction-coordinate-free approach suited to explore the frustrated energy landscapes of intrinsically disordered proteins. ELViM is shown to distinguish the monomer ensembles of variants that rapidly form fibers from those that do not form fibers as readily. It also delineates the amino acid contacts characterizing each ensemble. The results shed light on the potential of ELViM to probe intrinsically disordered proteins.
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Affiliation(s)
- 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
| | - Kaitlin Knapp
- Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, United States
| | - Antonio B Oliveira
- Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, United States
| | - Peter G Wolynes
- Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, United States
| | - José N Onuchic
- Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, United States.,Departments of Physics and Astronomy, Chemistry, and Biosciences, 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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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] [What about the content of this article? (0)] [Affiliation(s)] [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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