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Bermejo GA, Tjandra N, Clore GM, Schwieters CD. Xplor-NIH: Better parameters and protocols for NMR protein structure determination. Protein Sci 2024; 33:e4922. [PMID: 38501482 PMCID: PMC10962493 DOI: 10.1002/pro.4922] [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: 10/28/2023] [Revised: 01/26/2024] [Accepted: 01/28/2024] [Indexed: 03/20/2024]
Abstract
The present work describes an update to the protein covalent geometry and atomic radii parameters in the Xplor-NIH biomolecular structure determination package. In combination with an improved treatment of selected non-bonded interactions between atoms three bonds apart, such as those involving methyl hydrogens, and a previously developed term that affects the system's gyration volume, the new parameters are tested using structure calculations on 30 proteins with restraints derived from nuclear magnetic resonance data. Using modern structure validation criteria, including several formally adopted by the Protein Data Bank, and a clear measure of structural accuracy, the results show superior performance relative to previous Xplor-NIH implementations. Additionally, the Xplor-NIH structures compare favorably against originally determined NMR models.
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Affiliation(s)
- Guillermo A. Bermejo
- Laboratory of Chemical PhysicsNational Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of HealthBethesdaMarylandUSA
| | - Nico Tjandra
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of HealthBethesdaMarylandUSA
| | - G. Marius Clore
- Laboratory of Chemical PhysicsNational Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of HealthBethesdaMarylandUSA
| | - Charles D. Schwieters
- Laboratory of Chemical PhysicsNational Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of HealthBethesdaMarylandUSA
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2
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Dhillon A, Persson BD, Volkov AN, Sülzen H, Kádek A, Pompach P, Kereïche S, Lepšík M, Danskog K, Uetrecht C, Arnberg N, Zoll S. Structural insights into the interaction between adenovirus C5 hexon and human lactoferrin. J Virol 2024; 98:e0157623. [PMID: 38323814 PMCID: PMC10949841 DOI: 10.1128/jvi.01576-23] [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: 10/10/2023] [Accepted: 01/13/2024] [Indexed: 02/08/2024] Open
Abstract
Adenovirus (AdV) infection of the respiratory epithelium is common but poorly understood. Human AdV species C types, such as HAdV-C5, utilize the Coxsackie-adenovirus receptor (CAR) for attachment and subsequently integrins for entry. CAR and integrins are however located deep within the tight junctions in the mucosa where they would not be easily accessible. Recently, a model for CAR-independent AdV entry was proposed. In this model, human lactoferrin (hLF), an innate immune protein, aids the viral uptake into epithelial cells by mediating interactions between the major capsid protein, hexon, and yet unknown host cellular receptor(s). However, a detailed understanding of the molecular interactions driving this mechanism is lacking. Here, we present a new cryo-EM structure of HAdV-5C hexon at high resolution alongside a hybrid structure of HAdV-5C hexon complexed with human lactoferrin (hLF). These structures reveal the molecular determinants of the interaction between hLF and HAdV-C5 hexon. hLF engages hexon primarily via its N-terminal lactoferricin (Lfcin) region, interacting with hexon's hypervariable region 1 (HVR-1). Mutational analyses pinpoint critical Lfcin contacts and also identify additional regions within hLF that critically contribute to hexon binding. Our study sheds more light on the intricate mechanism by which HAdV-C5 utilizes soluble hLF/Lfcin for cellular entry. These findings hold promise for advancing gene therapy applications and inform vaccine development. IMPORTANCE Our study delves into the structural aspects of adenovirus (AdV) infections, specifically HAdV-C5 in the respiratory epithelium. It uncovers the molecular details of a novel pathway where human lactoferrin (hLF) interacts with the major capsid protein, hexon, facilitating viral entry, and bypassing traditional receptors such as CAR and integrins. The study's cryo-EM structures reveal how hLF engages hexon, primarily through its N-terminal lactoferricin (Lfcin) region and hexon's hypervariable region 1 (HVR-1). Mutational analyses identify critical Lfcin contacts and other regions within hLF vital for hexon binding. This structural insight sheds light on HAdV-C5's mechanism of utilizing soluble hLF/Lfcin for cellular entry, holding promise for gene therapy and vaccine development advancements in adenovirus research.
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Affiliation(s)
- Arun Dhillon
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | | | - Alexander N. Volkov
- VIB-VUB Center for Structural Biology, Flemish Institute of Biotechnology (VIB), Brussels, Belgium
- Jean Jeener NMR Centre, Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Hagen Sülzen
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
- Faculty of Science, Charles University, Prague, Czech Republic
| | - Alan Kádek
- Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic
- Leibniz Institute of Virology (LIV), Hamburg, Germany
| | - Petr Pompach
- Biotechnology and Biomedical Center of the Academy of Sciences and Charles University in Vestec, Vestec, Czech Republic
| | - Sami Kereïche
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
- First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Martin Lepšík
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Katarina Danskog
- Department of Clinical Microbiology, Umeå University, Umeå, Sweden
| | - Charlotte Uetrecht
- Department of Health Sciences and Biomedicine, Faculty V: School of Life Sciences, CSSB Centre for Structural Systems Biology, Deutsches Elektronen Synchrotron DESY and Leibniz Institute of Virology, Hamburg, University of Siegen, Siegen, Germany
| | - Niklas Arnberg
- Department of Clinical Microbiology, Umeå University, Umeå, Sweden
| | - Sebastian Zoll
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
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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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Clore GM. NMR spectroscopy, excited states and relevance to problems in cell biology - transient pre-nucleation tetramerization of huntingtin and insights into Huntington's disease. J Cell Sci 2022; 135:jcs258695. [PMID: 35703323 PMCID: PMC9270955 DOI: 10.1242/jcs.258695] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Solution nuclear magnetic resonance (NMR) spectroscopy is a powerful technique for analyzing three-dimensional structure and dynamics of macromolecules at atomic resolution. Recent advances have exploited the unique properties of NMR in exchanging systems to detect, characterize and visualize excited sparsely populated states of biological macromolecules and their complexes, which are only transient. These states are invisible to conventional biophysical techniques, and play a key role in many processes, including molecular recognition, protein folding, enzyme catalysis, assembly and fibril formation. All the NMR techniques make use of exchange between sparsely populated NMR-invisible and highly populated NMR-visible states to transfer a magnetization property from the invisible state to the visible one where it can be easily detected and quantified. There are three classes of NMR experiments that rely on differences in distance, chemical shift or transverse relaxation (molecular mass) between the NMR-visible and -invisible species. Here, I illustrate the application of these methods to unravel the complex mechanism of sub-millisecond pre-nucleation oligomerization of the N-terminal region of huntingtin, encoded by exon-1 of the huntingtin gene, where CAG expansion leads to Huntington's disease, a fatal autosomal-dominant neurodegenerative condition. I also discuss how inhibition of tetramerization blocks the much slower (by many orders of magnitude) process of fibril formation.
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Affiliation(s)
- G. Marius Clore
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, USA
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