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Moon J, Hu G, Hayashi T. Application of Machine Learning in the Quantitative Analysis of the Surface Characteristics of Highly Abundant Cytoplasmic Proteins: Toward AI-Based Biomimetics. Biomimetics (Basel) 2024; 9:162. [PMID: 38534847 DOI: 10.3390/biomimetics9030162] [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: 12/14/2023] [Revised: 02/12/2024] [Accepted: 02/29/2024] [Indexed: 03/28/2024] Open
Abstract
Proteins in the crowded environment of human cells have often been studied regarding nonspecific interactions, misfolding, and aggregation, which may cause cellular malfunction and disease. Specifically, proteins with high abundance are more susceptible to these issues due to the law of mass action. Therefore, the surfaces of highly abundant cytoplasmic (HAC) proteins directly exposed to the environment can exhibit specific physicochemical, structural, and geometrical characteristics that reduce nonspecific interactions and adapt to the environment. However, the quantitative relationships between the overall surface descriptors still need clarification. Here, we used machine learning to identify HAC proteins using hydrophobicity, charge, roughness, secondary structures, and B-factor from the protein surfaces and quantified the contribution of each descriptor. First, several supervised learning algorithms were compared to solve binary classification problems for the surfaces of HAC and extracellular proteins. Then, logistic regression was used for the feature importance analysis of descriptors considering model performance (80.2% accuracy and 87.6% AUC) and interpretability. The HAC proteins showed positive correlations with negatively and positively charged areas but negative correlations with hydrophobicity, the B-factor, the proportion of beta structures, roughness, and the proportion of disordered regions. Finally, the details of each descriptor could be explained concerning adaptative surface strategies of HAC proteins to regulate nonspecific interactions, protein folding, flexibility, stability, and adsorption. This study presented a novel approach using various surface descriptors to identify HAC proteins and provided quantitative design rules for the surfaces well-suited to human cellular crowded environments.
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Affiliation(s)
- Jooa Moon
- Department of Materials Science and Engineering, School of Materials and Chemical Technology, Tokyo Institute of Technology, Yokohama 226-8502, Japan
| | - Guanghao Hu
- Department of Materials Science and Engineering, School of Materials and Chemical Technology, Tokyo Institute of Technology, Yokohama 226-8502, Japan
| | - Tomohiro Hayashi
- Department of Materials Science and Engineering, School of Materials and Chemical Technology, Tokyo Institute of Technology, Yokohama 226-8502, Japan
- The Institute for Solid State Physics, The University of Tokyo, Kashiwa 277-0882, Japan
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2
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Roy C, Islam RNU, Banerjee S, Bandyopadhyay AK. Underlying features for the enhanced electrostatic strength of the extremophilic malate dehydrogenase interface salt-bridge compared to the mesophilic one. J Biomol Struct Dyn 2023:1-16. [PMID: 38147414 DOI: 10.1080/07391102.2023.2295972] [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: 07/13/2023] [Accepted: 10/20/2023] [Indexed: 12/28/2023]
Abstract
Malate dehydrogenase (MDH) exists in multimeric form in normal and extreme solvent conditions where residues of the interface are involved in specific interactions. The interface salt-bridge (ISB) and its microenvironment (ME) residues may have a crucial role in the stability and specificity of the interface. To gain insight into this, we have analyzed 218 ISBs from 42 interfaces of 15 crystal structures along with their sequences. Comparative analyses demonstrate that the ISB strength is ∼30 times greater in extremophilic cases than that of the normal one. To this end, the interface residue propensity, ISB design and pair selection, and ME-residue's types, i.e., type-I and type-II, are seen to be intrinsically involved. Although Type-I is a common type, Type-II appears to be extremophile-specific, where the net ME-residue count is much lower with an excessive net ME-energy contribution, which seems to be a novel interface compaction strategy. Furthermore, the interface strength can be enhanced by selecting the desired mutant from the net-energy profile of all possible mutations of an unfavorable ME-residue. The study that applies to other similar systems finds applications in protein-protein interaction and protein engineering.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Chittran Roy
- Department of Biotechnology, The University of Burdwan, Burdwan, West Bengal, India
- Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa, Israel
| | | | - Sahini Banerjee
- Department of Biological Sciences, Indian Statistical Institute, Kolkata, West Bengal, India
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Liu N, Xiao H, Zang Y, Zhou L, Mencius J, Yang Z, Quan S, Chen X. Simultaneous Improvement in the Thermostability and Catalytic Activity of Epoxidase Lsd18 for the Synthesis of Lasalocid A. Int J Mol Sci 2023; 24:16795. [PMID: 38069118 PMCID: PMC10706071 DOI: 10.3390/ijms242316795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 11/22/2023] [Accepted: 11/23/2023] [Indexed: 12/18/2023] Open
Abstract
Enzymes used in the synthesis of natural products are potent catalysts, capable of efficient and stereoselective chemical transformations. Lsd18 catalyzes two sequential epoxidations during the biosynthesis of lasalocid A, a polyether polyketide natural product. We performed protein engineering on Lsd18 to improve its thermostability and catalytic activity. Utilizing structure-guided methods of FoldX and Rosetta-ddG, we designed 15 mutants of Lsd18. Screening of these mutants using thermal shift assay identified stabilized variants Lsd18-T189M, Lsd18-S195M, and the double mutant Lsd18-T189M-S195M. Trypsin digestion, molecular dynamic simulation, circular dichroism (CD) spectroscopy, and X-ray crystallography provided insights into the molecular basis for the improved enzyme properties. Notably, enhanced hydrophobic interaction within the enzyme core and interaction of the protein with the FAD cofactor appear to be responsible for its better thermostability.
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Affiliation(s)
- Ning Liu
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi’an 710127, China; (N.L.); (H.X.)
| | - Hongli Xiao
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi’an 710127, China; (N.L.); (H.X.)
| | - Yongjian Zang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi’an Jiaotong University, Xi’an 710049, China; (Y.Z.); (Z.Y.)
- Institute of Physics and Electronic Information, Yunnan Normal University, Kunming 650504, China
| | - Longji Zhou
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China; (L.Z.); (J.M.)
| | - Jun Mencius
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China; (L.Z.); (J.M.)
| | - Zhiwei Yang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi’an Jiaotong University, Xi’an 710049, China; (Y.Z.); (Z.Y.)
| | - Shu Quan
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China; (L.Z.); (J.M.)
| | - Xi Chen
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi’an 710127, China; (N.L.); (H.X.)
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Mendoza J, Purchal M, Yamada K, Koutmos M. Structure of full-length cobalamin-dependent methionine synthase and cofactor loading captured in crystallo. Nat Commun 2023; 14:6365. [PMID: 37821448 PMCID: PMC10567725 DOI: 10.1038/s41467-023-42037-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 09/28/2023] [Indexed: 10/13/2023] Open
Abstract
Cobalamin-dependent methionine synthase (MS) is a key enzyme in methionine and folate one-carbon metabolism. MS is a large multi-domain protein capable of binding and activating three substrates: homocysteine, folate, and S-adenosylmethionine for methylation. Achieving three chemically distinct methylations necessitates significant domain rearrangements to facilitate substrate access to the cobalamin cofactor at the right time. The distinct conformations required for each reaction have eluded structural characterization as its inherently dynamic nature renders structural studies difficult. Here, we use a thermophilic MS homolog (tMS) as a functional MS model. Its exceptional stability enabled characterization of MS in the absence of cobalamin, marking the only studies of a cobalamin-binding protein in its apoenzyme state. More importantly, we report the high-resolution full-length MS structure, ending a multi-decade quest. We also capture cobalamin loading in crystallo, providing structural insights into holoenzyme formation. Our work paves the way for unraveling how MS orchestrates large-scale domain rearrangements crucial for achieving challenging chemistries.
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Affiliation(s)
- Johnny Mendoza
- Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Meredith Purchal
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI, 48109, USA
- New England Biolabs, Inc., Ipswich, MA, 01938, England
| | - Kazuhiro Yamada
- Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA.
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA.
| | - Markos Koutmos
- Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA.
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI, 48109, USA.
- Program in Biophysics, University of Michigan, Ann Arbor, MI, 48109, USA.
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Rivera M, Burgos‐Bravo F, Engelberger F, Asor R, Lagos‐Espinoza MIA, Figueroa M, Kukura P, Ramírez‐Sarmiento CA, Baez M, Smith SB, Wilson CAM. Effect of temperature and nucleotide on the binding of BiP chaperone to a protein substrate. Protein Sci 2023; 32:e4706. [PMID: 37323096 PMCID: PMC10303699 DOI: 10.1002/pro.4706] [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: 12/18/2022] [Revised: 06/01/2023] [Accepted: 06/12/2023] [Indexed: 06/17/2023]
Abstract
BiP (immunoglobulin heavy-chain binding protein) is a Hsp70 monomeric ATPase motor that plays broad and crucial roles in maintaining proteostasis inside the cell. Structurally, BiP is formed by two domains, a nucleotide-binding domain (NBD) with ATPase activity connected by a flexible hydrophobic linker to the substrate-binding domain. While the ATPase and substrate binding activities of BiP are allosterically coupled, the latter is also dependent on nucleotide binding. Recent structural studies have provided new insights into BiP's allostery; however, the influence of temperature on the coupling between substrate and nucleotide binding to BiP remains unexplored. Here, we study BiP's binding to its substrate at the single molecule level using thermo-regulated optical tweezers which allows us to mechanically unfold the client protein and explore the effect of temperature and different nucleotides on BiP binding. Our results confirm that the affinity of BiP for its protein substrate relies on nucleotide binding, by mainly regulating the binding kinetics between BiP and its substrate. Interestingly, our findings also showed that the apparent affinity of BiP for its protein substrate in the presence of nucleotides remains invariable over a wide range of temperatures, suggesting that BiP may interact with its client proteins with similar affinities even when the temperature is not optimal. Thus, BiP could play a role as a "thermal buffer" in proteostasis.
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Affiliation(s)
- Maira Rivera
- 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
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y FarmacéuticasUniversidad de ChileSantiagoChile
| | - Francesca Burgos‐Bravo
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y FarmacéuticasUniversidad de ChileSantiagoChile
- Institute for Quantitative BiosciencesUniversity of CaliforniaBerkeleyCaliforniaUSA
| | - Felipe Engelberger
- 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
| | - Roi Asor
- Physical and Theoretical Chemistry Laboratory, Department of ChemistryUniversity of OxfordOxfordUK
- The Kavli Institute for Nanoscience DiscoveryOxfordUK
| | - Miguel I. A. Lagos‐Espinoza
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y FarmacéuticasUniversidad de ChileSantiagoChile
| | - Maximiliano Figueroa
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias BiológicasUniversidad de ConcepciónConcepciónChile
| | - Philipp Kukura
- Physical and Theoretical Chemistry Laboratory, Department of ChemistryUniversity of OxfordOxfordUK
- The Kavli Institute for Nanoscience DiscoveryOxfordUK
| | - 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
| | - Mauricio Baez
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y FarmacéuticasUniversidad de ChileSantiagoChile
| | | | - Christian A. M. Wilson
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y FarmacéuticasUniversidad de ChileSantiagoChile
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A novel EDAR variant identified in non-syndromic tooth agenesis: Insights from molecular dynamics. Arch Oral Biol 2023; 146:105600. [PMID: 36470092 DOI: 10.1016/j.archoralbio.2022.105600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 11/20/2022] [Accepted: 11/30/2022] [Indexed: 12/03/2022]
Abstract
OBJECTIVE This study aims to investigate a novel pathogenic variant in a Chinese family of non-syndromic tooth agenesis (NSTA) and study the impact of the variant on related protein and pathway. DESIGN One NSTA family was collected. Whole exome sequencing and Sanger sequencing were performed on the proband with NSTA and his 5 family members. The pathogenic influence of the mutant is evaluated by bioinformatics analyses including evolutionary conservation analysis and secondary structure prediction. Molecular dynamics (MD) simulations and binding free energy calculations were then performed to explore changes in the tertiary structure and binding ability of the protein. RESULTS We found a novel missense ectodysplasin A receptor (EDAR) variant (c .1292 T > G; p.Ile431Arg) in all affected family members. The results of bioinformatics analyses revealed that the EDAR had harmful changes after mutation. MD simulations and the binding free energy calculations results showed that the mutant EDAR protein and EDAR/ectodysplasin-A receptor-associated adapter (EDARADD) complex displayed tertiary structural change, and EDAR possessed a lower affinity to EDARADD after mutation. CONCLUSIONS We found a novel EDAR variant (c.1292 T > G; p.Ile431Arg) in one NSTA family, which affects the binding of EDAR and EDARADD.
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Wang A, Yue K, Wei Y, Zhong W, Zhang G. Temperature‐induced structural change of integrin αvβ3 receptor and its interaction with the
RGD
peptide ligand. Pept Sci (Hoboken) 2022. [DOI: 10.1002/pep2.24302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Anqi Wang
- School of Energy and Environmental Engineering University of Science and Technology Beijing Beijing China
- Shunde Graduate School of University of Science and Technology Beijing Shunde Guangdong Province China
| | - Kai Yue
- School of Energy and Environmental Engineering University of Science and Technology Beijing Beijing China
- Shunde Graduate School of University of Science and Technology Beijing Shunde Guangdong Province China
| | - Yiang Wei
- School of Energy and Environmental Engineering University of Science and Technology Beijing Beijing China
| | - Weishen Zhong
- School of Energy and Environmental Engineering University of Science and Technology Beijing Beijing China
- Shunde Graduate School of University of Science and Technology Beijing Shunde Guangdong Province China
| | - Genpei Zhang
- School of Energy and Environmental Engineering University of Science and Technology Beijing Beijing China
- Shunde Graduate School of University of Science and Technology Beijing Shunde Guangdong Province China
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Sunny JS, Mukund N, Natarajan A, Saleena LM. Identifying heat shock response systems from the genomic assembly of Ureibacillus thermophilus LM102 using protein-protein interaction networks. Gene X 2020; 737:144449. [DOI: 10.1016/j.gene.2020.144449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 01/28/2020] [Accepted: 02/04/2020] [Indexed: 11/30/2022] Open
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Physical and molecular bases of protein thermal stability and cold adaptation. Curr Opin Struct Biol 2016; 42:117-128. [PMID: 28040640 DOI: 10.1016/j.sbi.2016.12.007] [Citation(s) in RCA: 107] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2016] [Revised: 11/15/2016] [Accepted: 12/11/2016] [Indexed: 11/20/2022]
Abstract
The molecular bases of thermal and cold stability and adaptation, which allow proteins to remain folded and functional in the temperature ranges in which their host organisms live and grow, are still only partially elucidated. Indeed, both experimental and computational studies fail to yield a fully precise and global physical picture, essentially because all effects are context-dependent and thus quite intricate to unravel. We present a snapshot of the current state of knowledge of this highly complex and challenging issue, whose resolution would enable large-scale rational protein design.
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