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Rocha REO, Mariano DCB, Almeida TS, CorrêaCosta LS, Fischer PHC, Santos LH, Caffarena ER, da Silveira CH, Lamp LM, Fernandez-Quintero ML, Liedl KR, de Melo-Minardi RC, de Lima LHF. Thermostabilizing mechanisms of canonical single amino acid substitutions at a GH1 β-glucosidase probed by multiple MD and computational approaches. Proteins 2023; 91:218-236. [PMID: 36114781 DOI: 10.1002/prot.26424] [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: 05/26/2022] [Revised: 09/01/2022] [Accepted: 09/06/2022] [Indexed: 01/07/2023]
Abstract
β-glucosidases play a pivotal role in second-generation biofuel (2G-biofuel) production. For this application, thermostable enzymes are essential due to the denaturing conditions on the bioreactors. Random amino acid substitutions have originated new thermostable β-glucosidases, but without a clear understanding of their molecular mechanisms. Here, we probe by different molecular dynamics simulation approaches with distinct force fields and submitting the results to various computational analyses, the molecular bases of the thermostabilization of the Paenibacillus polymyxa GH1 β-glucosidase by two-point mutations E96K (TR1) and M416I (TR2). Equilibrium molecular dynamic simulations (eMD) at different temperatures, principal component analysis (PCA), virtual docking, metadynamics (MetaDy), accelerated molecular dynamics (aMD), Poisson-Boltzmann surface analysis, grid inhomogeneous solvation theory and colony method estimation of conformational entropy allow to converge to the idea that the stabilization carried by both substitutions depend on different contributions of three classic mechanisms: (i) electrostatic surface stabilization; (ii) efficient isolation of the hydrophobic core from the solvent, with energetic advantages at the solvation cap; (iii) higher distribution of the protein dynamics at the mobile active site loops than at the protein core, with functional and entropic advantages. Mechanisms i and ii predominate for TR1, while in TR2, mechanism iii is dominant. Loop A integrity and loops A, C, D, and E dynamics play critical roles in such mechanisms. Comparison of the dynamic and topological changes observed between the thermostable mutants and the wildtype protein with amino acid co-evolutive networks and thermostabilizing hotspots from the literature allow inferring that the mechanisms here recovered can be related to the thermostability obtained by different substitutions along the whole family GH1. We hope the results and insights discussed here can be helpful for future rational approaches to the engineering of optimized β-glucosidases for 2G-biofuel production for industry, biotechnology, and science.
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Affiliation(s)
- Rafael Eduardo Oliveira Rocha
- Laboratory of Molecular Modelling and Bioinformatics (LAMMB), Department of Physical and Biological Sciences, Campus Sete Lagoas, Universidade Federal de São João Del Rei, Sete Lagoas, Brazil.,Laboratory of Bioinformatics and Systems (LBS), Department of Computer Science, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil.,Laboratory of Molecular Modeling and Drug Design, Department of Biochemistry and Immunology, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Diego César Batista Mariano
- Laboratory of Bioinformatics and Systems (LBS), Department of Computer Science, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Tiago Silva Almeida
- Laboratory of Molecular Modelling and Bioinformatics (LAMMB), Department of Physical and Biological Sciences, Campus Sete Lagoas, Universidade Federal de São João Del Rei, Sete Lagoas, Brazil
| | - Leon Sulfierry CorrêaCosta
- Laboratory of Molecular Modelling and Bioinformatics (LAMMB), Department of Physical and Biological Sciences, Campus Sete Lagoas, Universidade Federal de São João Del Rei, Sete Lagoas, Brazil.,Computational Modeling Coordination (COMOD), Laboratório Nacional de Computação Científica (LNCC), Petrópolis, Brazil
| | - Pedro Henrique Camargo Fischer
- Laboratory of Molecular Modelling and Bioinformatics (LAMMB), Department of Physical and Biological Sciences, Campus Sete Lagoas, Universidade Federal de São João Del Rei, Sete Lagoas, Brazil
| | - Lucianna Helene Santos
- Laboratory of Bioinformatics and Systems (LBS), Department of Computer Science, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil.,Laboratory of Molecular Modeling and Drug Design, Department of Biochemistry and Immunology, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | | | | | - Leonida M Lamp
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Chemistry and Biomedicine Innsbruck (CCB), University of Innsbruck, Innsbruck, Austria
| | - Monica Lisa Fernandez-Quintero
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Chemistry and Biomedicine Innsbruck (CCB), University of Innsbruck, Innsbruck, Austria
| | - Klaus Roman Liedl
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Chemistry and Biomedicine Innsbruck (CCB), University of Innsbruck, Innsbruck, Austria
| | - Raquel Cardoso de Melo-Minardi
- Laboratory of Bioinformatics and Systems (LBS), Department of Computer Science, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Leonardo Henrique França de Lima
- Laboratory of Molecular Modelling and Bioinformatics (LAMMB), Department of Physical and Biological Sciences, Campus Sete Lagoas, Universidade Federal de São João Del Rei, Sete Lagoas, Brazil.,Institute of General, Inorganic and Theoretical Chemistry, and Center for Chemistry and Biomedicine Innsbruck (CCB), University of Innsbruck, Innsbruck, Austria
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Ho PS, Kao TY, Li CC, Lan YJ, Lai YC, Chiang YW. Nanodisc Lipids Exhibit Singular Behaviors Implying Critical Phenomena. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:15372-15383. [PMID: 36454955 DOI: 10.1021/acs.langmuir.2c02596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Nanodiscs are broadly used for characterization of membrane proteins as they are generally assumed to provide a near-native environment. In fact, it is an open question whether the physical properties of lipids in nanodiscs and membrane vesicles of the same lipid composition are identical. Here, we investigate the properties of lipids (1,2-dipalmitoyl-sn-glycero-3-phosphocholine, 1,2-dilauroyl-sn-glycero-3-phosphocholine, and their mixtures) in two different sample types, nanodiscs and multilamellar vesicles, by means of spin-label electron spin resonance techniques. Our results provide a quantitative description of lipid dynamics and ordering, elucidating the molecular details of how lipids in the two sample types behave differently in response to temperature and lipid composition. We show that the properties of lipids are altered in nanodiscs such that the dissimilarity of the fluid and gel lipid phases is reduced, and the first-order phase transitions are largely abolished in nanodiscs. We unveil that the ensemble of lipids in the middle of a nanodisc bilayer, as probed by the end-chain spin-label 16-PC, is promoted to a state close to a miscibility critical point, thereby rendering the phase transitions continuous. Critical phenomena have recently been proposed to explain features of the heterogeneity in native cell membranes. Our results lay the groundwork for how to establish a near-native environment in nanodiscs with simple organization of lipid components.
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Affiliation(s)
- Pei-Shan Ho
- Department of Chemistry, National Tsing Hua University, Hsinchu 300-044, Taiwan
| | - Te-Yu Kao
- Department of Chemistry, National Tsing Hua University, Hsinchu 300-044, Taiwan
| | - Chieh-Chin Li
- Department of Chemistry, National Tsing Hua University, Hsinchu 300-044, Taiwan
| | - Yu-Jing Lan
- Department of Chemistry, National Tsing Hua University, Hsinchu 300-044, Taiwan
| | - Yei-Chen Lai
- Department of Chemistry, National Chung Hsing University, Taichung 402-002, Taiwan
| | - Yun-Wei Chiang
- Department of Chemistry, National Tsing Hua University, Hsinchu 300-044, Taiwan
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3
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Qing R, Hao S, Smorodina E, Jin D, Zalevsky A, Zhang S. Protein Design: From the Aspect of Water Solubility and Stability. Chem Rev 2022; 122:14085-14179. [PMID: 35921495 PMCID: PMC9523718 DOI: 10.1021/acs.chemrev.1c00757] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Indexed: 12/13/2022]
Abstract
Water solubility and structural stability are key merits for proteins defined by the primary sequence and 3D-conformation. Their manipulation represents important aspects of the protein design field that relies on the accurate placement of amino acids and molecular interactions, guided by underlying physiochemical principles. Emulated designer proteins with well-defined properties both fuel the knowledge-base for more precise computational design models and are used in various biomedical and nanotechnological applications. The continuous developments in protein science, increasing computing power, new algorithms, and characterization techniques provide sophisticated toolkits for solubility design beyond guess work. In this review, we summarize recent advances in the protein design field with respect to water solubility and structural stability. After introducing fundamental design rules, we discuss the transmembrane protein solubilization and de novo transmembrane protein design. Traditional strategies to enhance protein solubility and structural stability are introduced. The designs of stable protein complexes and high-order assemblies are covered. Computational methodologies behind these endeavors, including structure prediction programs, machine learning algorithms, and specialty software dedicated to the evaluation of protein solubility and aggregation, are discussed. The findings and opportunities for Cryo-EM are presented. This review provides an overview of significant progress and prospects in accurate protein design for solubility and stability.
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Affiliation(s)
- Rui Qing
- State
Key Laboratory of Microbial Metabolism, School of Life Sciences and
Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
- Media
Lab, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
- The
David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Shilei Hao
- Media
Lab, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
- Key
Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400030, China
| | - Eva Smorodina
- Department
of Immunology, University of Oslo and Oslo
University Hospital, Oslo 0424, Norway
| | - David Jin
- Avalon GloboCare
Corp., Freehold, New Jersey 07728, United States
| | - Arthur Zalevsky
- Laboratory
of Bioinformatics Approaches in Combinatorial Chemistry and Biology, Shemyakin−Ovchinnikov Institute of Bioorganic
Chemistry RAS, Moscow 117997, Russia
| | - Shuguang Zhang
- Media
Lab, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
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Kao TY, Hung CL, Lan YJ, Lee SW, Chiang YW. Simple Cryoprotectant-Free Method to Advance Pulsed Dipolar ESR Spectroscopy for Capturing Protein Conformational Ensembles. J Phys Chem B 2022; 126:423-429. [PMID: 35005966 DOI: 10.1021/acs.jpcb.1c08190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Double electron-electron resonance (DEER) is a powerful technique for studying protein conformations. To preserve the room-temperature ensemble, proteins are usually shock-frozen in liquid nitrogen prior to DEER measurements. The use of cryoprotectant additives is, therefore, necessary to ensure the formation of a vitrified state. Here, we present a simple modification of the freezing process using a flexible fused silica microcapillary, which increases the freezing rates and thus enables DEER measurement without the use of cryoprotectants. The Bid protein, which is highly sensitive to cryoprotectant additives, is used as a model. We show that DEER with the simple modification can successfully reveal the cold denaturation of Bid, which was not possible with the conventional DEER preparations. The DEER result reveals the nature of Bid folding. Our method advances DEER for capturing the chemically and thermally induced conformational changes of a protein in a cryoprotectant-free medium.
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Affiliation(s)
- Te-Yu Kao
- Department of Chemistry, National Tsing Hua University, Hsinchu 300-044, Taiwan
| | - Chien-Lun Hung
- Department of Chemistry, National Tsing Hua University, Hsinchu 300-044, Taiwan
| | - Yu-Jing Lan
- Department of Chemistry, National Tsing Hua University, Hsinchu 300-044, Taiwan
| | - Su Wei Lee
- Department of Chemistry, National Tsing Hua University, Hsinchu 300-044, Taiwan
| | - Yun-Wei Chiang
- Department of Chemistry, National Tsing Hua University, Hsinchu 300-044, Taiwan
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