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Yu L, Wang R, Li S, Kara UI, Boerner EC, Chen B, Zhang F, Jian Z, Li S, Liu M, Wang Y, Liu S, Yang Y, Wang C, Zhang W, Yao Y, Wang X, Wang C. Experimental Insights into Conformational Ensembles of Assembled β-Sheet Peptides. ACS CENTRAL SCIENCE 2023; 9:1480-1487. [PMID: 37521785 PMCID: PMC10375872 DOI: 10.1021/acscentsci.3c00230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Indexed: 08/01/2023]
Abstract
Deciphering the conformations and interactions of peptides in their assemblies offers a basis for guiding the rational design of peptide-assembled materials. Here we report the use of scanning tunneling microscopy (STM), a single-molecule imaging method with a submolecular resolution, to distinguish 18 types of coexisting conformational substates of the β-strand of the 8-37 segment of human islet amyloid polypeptide (hIAPP 8-37). We analyzed the pairwise peptide-peptide interactions in the hIAPP 8-37 assembly and found 82 interconformation interactions within a free energy difference of 3.40 kBT. Besides hIAPP 8-37, this STM method validates the existence of multiple conformations of other β-sheet peptide assemblies, including mutated hIAPP 8-37 and amyloid-β 42. Overall, the results reported in this work provide single-molecule experimental insights into the conformational ensemble and interpeptide interactions in the β-sheet peptide assembly.
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Affiliation(s)
- Lanlan Yu
- State
Key Laboratory of Common Mechanism Research for Major Diseases, Haihe
Laboratory of Cell Ecosystem, Department of Biophysics and Structural
Biology, Institute of Basic Medical Sciences,
Chinese Academy of Medical Sciences, School of Basic Medicine Peking
Union Medical College, Beijing 100005, People’s
Republic of China
| | - Ruonan Wang
- State
Key Laboratory of Common Mechanism Research for Major Diseases, Haihe
Laboratory of Cell Ecosystem, Department of Biophysics and Structural
Biology, Institute of Basic Medical Sciences,
Chinese Academy of Medical Sciences, School of Basic Medicine Peking
Union Medical College, Beijing 100005, People’s
Republic of China
| | - Shucong Li
- Department
of Chemistry and Chemical Biology, Harvard
University, Cambridge, Massachusetts, 02138, United States
| | - Ufuoma I. Kara
- William
G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, Ohio 43210, United States
| | - Eric C. Boerner
- William
G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, Ohio 43210, United States
| | - Boyuan Chen
- William
G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, Ohio 43210, United States
| | - Feiyi Zhang
- State
Key Laboratory of Common Mechanism Research for Major Diseases, Haihe
Laboratory of Cell Ecosystem, Department of Biophysics and Structural
Biology, Institute of Basic Medical Sciences,
Chinese Academy of Medical Sciences, School of Basic Medicine Peking
Union Medical College, Beijing 100005, People’s
Republic of China
- Institute
for Advanced Materials, Jiangsu University, Zhenjiang, Jiangsu 212013, People’s
Republic of China
| | - Zhongyi Jian
- State
Key Laboratory of Common Mechanism Research for Major Diseases, Haihe
Laboratory of Cell Ecosystem, Department of Biophysics and Structural
Biology, Institute of Basic Medical Sciences,
Chinese Academy of Medical Sciences, School of Basic Medicine Peking
Union Medical College, Beijing 100005, People’s
Republic of China
| | - Shuyuan Li
- State
Key Laboratory of Common Mechanism Research for Major Diseases, Haihe
Laboratory of Cell Ecosystem, Department of Biophysics and Structural
Biology, Institute of Basic Medical Sciences,
Chinese Academy of Medical Sciences, School of Basic Medicine Peking
Union Medical College, Beijing 100005, People’s
Republic of China
| | - Mingwei Liu
- State
Key Laboratory of Common Mechanism Research for Major Diseases, Haihe
Laboratory of Cell Ecosystem, Department of Biophysics and Structural
Biology, Institute of Basic Medical Sciences,
Chinese Academy of Medical Sciences, School of Basic Medicine Peking
Union Medical College, Beijing 100005, People’s
Republic of China
| | - Yang Wang
- State
Key Laboratory of Common Mechanism Research for Major Diseases, Haihe
Laboratory of Cell Ecosystem, Department of Biophysics and Structural
Biology, Institute of Basic Medical Sciences,
Chinese Academy of Medical Sciences, School of Basic Medicine Peking
Union Medical College, Beijing 100005, People’s
Republic of China
| | - Shuli Liu
- Department
of Clinical Laboratory, Peking University
Civil Aviation School of Clinical Medicine, Beijing 100123, People’s Republic of China
| | - Yanlian Yang
- CAS Key Laboratory
of Biological Effects of Nanomaterials and Nanosafety, CAS Key Laboratory
of Standardization and Measurement for Nanotechnology, Laboratory of Theoretical and Computational Nanoscience,
CAS Center for Excellence in Nanoscience, National Center for Nanoscience
and Technology, Beijing 100190, People’s Republic
of China
| | - Chen Wang
- CAS Key Laboratory
of Biological Effects of Nanomaterials and Nanosafety, CAS Key Laboratory
of Standardization and Measurement for Nanotechnology, Laboratory of Theoretical and Computational Nanoscience,
CAS Center for Excellence in Nanoscience, National Center for Nanoscience
and Technology, Beijing 100190, People’s Republic
of China
| | - Wenbo Zhang
- State
Key Laboratory of Common Mechanism Research for Major Diseases, Haihe
Laboratory of Cell Ecosystem, Department of Biophysics and Structural
Biology, Institute of Basic Medical Sciences,
Chinese Academy of Medical Sciences, School of Basic Medicine Peking
Union Medical College, Beijing 100005, People’s
Republic of China
| | - Yuxing Yao
- Division
of Chemistry and Chemical Engineering, California
Institute of Technology, Pasadena, California 91125, United States
| | - Xiaoguang Wang
- William
G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, Ohio 43210, United States
- Sustainability
Institute, The Ohio State University, Columbus, Ohio, 43210, United
States
| | - Chenxuan Wang
- State
Key Laboratory of Common Mechanism Research for Major Diseases, Haihe
Laboratory of Cell Ecosystem, Department of Biophysics and Structural
Biology, Institute of Basic Medical Sciences,
Chinese Academy of Medical Sciences, School of Basic Medicine Peking
Union Medical College, Beijing 100005, People’s
Republic of China
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Rosen MR, Leuthaeuser JB, Parish CA, Fetrow JS. Isofunctional Clustering and Conformational Analysis of the Arsenate Reductase Superfamily Reveals Nine Distinct Clusters. Biochemistry 2020; 59:4262-4284. [PMID: 33135415 DOI: 10.1021/acs.biochem.0c00651] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Arsenate reductase (ArsC) is a superfamily of enzymes that reduce arsenate. Due to active site similarities, some ArsC can function as low-molecular weight protein tyrosine phosphatases (LMW-PTPs). Broad superfamily classifications align with redox partners (Trx- or Grx-linked). To understand this superfamily's mechanistic diversity, the ArsC superfamily is classified on the basis of active site features utilizing the tools TuLIP (two-level iterative clustering process) and autoMISST (automated multilevel iterative sequence searching technique). This approach identified nine functionally relevant (perhaps isofunctional) protein groups. Five groups exhibit distinct ArsC mechanisms. Three are Grx-linked: group 4AA (classical ArsC), group 3AAA (YffB-like), and group 5BAA. Two are Trx-linked: groups 6AAAAA and 7AAAAAAAA. One is an Spx-like transcriptional regulatory group, group 5AAA. Three are potential LMW-PTP groups: groups 7BAAAA, and 7AAAABAA, which have not been previously identified, and the well-studied LMW-PTP family group 8AAA. Molecular dynamics simulations were utilized to explore functional site details. In several families, we confirm and add detail to literature-based mechanistic information. Mechanistic roles are hypothesized for conserved active site residues in several families. In three families, simulations of the unliganded structure sample specific conformational ensembles, which are proposed to represent either a more ligand-binding-competent conformation or a pathway toward a more binding-competent state; these active sites may be designed to traverse high-energy barriers to the lower-energy conformations necessary to more readily bind ligands. This more detailed biochemical understanding of ArsC and ArsC-like PTP mechanisms opens possibilities for further understanding of arsenate bioremediation and the LMW-PTP mechanism.
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Affiliation(s)
- Mikaela R Rosen
- Department of Chemistry, Gottwald Center for the Sciences, University of Richmond, Richmond, Virginia 23713, United States
| | - Janelle B Leuthaeuser
- Department of Chemistry, Gottwald Center for the Sciences, University of Richmond, Richmond, Virginia 23713, United States
| | - Carol A Parish
- Department of Chemistry, Gottwald Center for the Sciences, University of Richmond, Richmond, Virginia 23713, United States
| | - Jacquelyn S Fetrow
- Department of Chemistry, Gottwald Center for the Sciences, University of Richmond, Richmond, Virginia 23713, United States
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Zhang W, Mo S, Liu M, Liu L, Yu L, Wang C. Rationally Designed Protein Building Blocks for Programmable Hierarchical Architectures. Front Chem 2020; 8:587975. [PMID: 33195088 PMCID: PMC7658299 DOI: 10.3389/fchem.2020.587975] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 10/05/2020] [Indexed: 01/23/2023] Open
Abstract
Diverse natural/artificial proteins have been used as building blocks to construct a variety of well-ordered nanoscale structures over the past couple of decades. Sophisticated protein self-assemblies have attracted great scientific interests due to their potential applications in disease diagnosis, illness treatment, biomechanics, bio-optics and bio-electronics, etc. This review outlines recent efforts directed to the creation of structurally defined protein assemblies including one-dimensional (1D) strings/rings/tubules, two-dimensional (2D) planar sheets and three-dimensional (3D) polyhedral scaffolds. We elucidate various innovative strategies for manipulating proteins to self-assemble into desired architectures. The emergent applications of protein assemblies as versatile platforms in medicine and material science with improved performances have also been discussed.
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Affiliation(s)
- Wenbo Zhang
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Department of Biophysics and Structural Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Shanshan Mo
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Department of Biophysics and Structural Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Mingwei Liu
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Department of Biophysics and Structural Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Lei Liu
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, United States
| | - Lanlan Yu
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Department of Biophysics and Structural Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Chenxuan Wang
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Department of Biophysics and Structural Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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Agarwal PK, Bernard DN, Bafna K, Doucet N. Enzyme dynamics: Looking beyond a single structure. ChemCatChem 2020; 12:4704-4720. [PMID: 33897908 PMCID: PMC8064270 DOI: 10.1002/cctc.202000665] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Indexed: 12/23/2022]
Abstract
Conventional understanding of how enzymes function strongly emphasizes the role of structure. However, increasing evidence clearly indicates that enzymes do not remain fixed or operate exclusively in or close to their native structure. Different parts of the enzyme (from individual residues to full domains) undergo concerted motions on a wide range of time-scales, including that of the catalyzed reaction. Information obtained on these internal motions and conformational fluctuations has so far uncovered and explained many aspects of enzyme mechanisms, which could not have been understood from a single structure alone. Although there is wide interest in understanding enzyme dynamics and its role in catalysis, several challenges remain. In addition to technical difficulties, the vast majority of investigations are performed in dilute aqueous solutions, where conditions are significantly different than the cellular milieu where a large number of enzymes operate. In this review, we discuss recent developments, several challenges as well as opportunities related to this topic. The benefits of considering dynamics as an integral part of the enzyme function can also enable new means of biocatalysis, engineering enzymes for industrial and medicinal applications.
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Affiliation(s)
- Pratul K. Agarwal
- Department of Physiological Sciences and High-Performance Computing Center, Oklahoma State University, Stillwater, Oklahoma 74078
- Arium BioLabs, 2519 Caspian Drive, Knoxville, Tennessee 37932
| | - David N. Bernard
- Centre Armand-Frappier Santé Biotechnologie, Institut national de la recherche scientifique (INRS), Université du Québec, 531 Boulevard des Prairies, Laval, Quebec, H7V 1B7, Canada
| | - Khushboo Bafna
- Department of Chemistry and Chemical Biology, and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180
| | - Nicolas Doucet
- Centre Armand-Frappier Santé Biotechnologie, Institut national de la recherche scientifique (INRS), Université du Québec, 531 Boulevard des Prairies, Laval, Quebec, H7V 1B7, Canada
- PROTEO, the Quebec Network for Research on Protein Function, Structure, and Engineering, 1045 Avenue de la Médecine, Université Laval, Québec, QC, G1V 0A6, Canada
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