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Iqbal H, Fung KW, Gor J, Bishop AC, Makhatadze GI, Brodsky B, Perkins SJ. A solution structure analysis reveals a bent collagen triple helix in the complement activation recognition molecule mannan-binding lectin. J Biol Chem 2022; 299:102799. [PMID: 36528062 PMCID: PMC9898670 DOI: 10.1016/j.jbc.2022.102799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Revised: 12/05/2022] [Accepted: 12/09/2022] [Indexed: 12/23/2022] Open
Abstract
Collagen triple helices are critical in the function of mannan-binding lectin (MBL), an oligomeric recognition molecule in complement activation. The MBL collagen regions form complexes with the serine proteases MASP-1 and MASP-2 in order to activate complement, and mutations lead to common immunodeficiencies. To evaluate their structure-function properties, we studied the solution structures of four MBL-like collagen peptides. The thermal stability of the MBL collagen region was much reduced by the presence of a GQG interruption in the typical (X-Y-Gly)n repeat compared to controls. Experimental solution structural data were collected using analytical ultracentrifugation and small angle X-ray and neutron scattering. As controls, we included two standard Pro-Hyp-Gly collagen peptides (POG)10-13, as well as three more peptides with diverse (X-Y-Gly)n sequences that represented other collagen features. These data were quantitatively compared with atomistic linear collagen models derived from crystal structures and 12,000 conformations obtained from molecular dynamics simulations. All four MBL peptides were bent to varying degrees up to 85o in the best-fit molecular dynamics models. The best-fit benchmark peptides (POG)n were more linear but exhibited a degree of conformational flexibility. The remaining three peptides showed mostly linear solution structures. In conclusion, the collagen helix is not strictly linear, the degree of flexibility in the triple helix depends on its sequence, and the triple helix with the GQG interruption showed a pronounced bend. The bend in MBL GQG peptides resembles the bend in the collagen of complement C1q and may be key for lectin pathway activation.
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Affiliation(s)
- Hina Iqbal
- Department of Structural and Molecular Biology, University College London, London, United Kingdom
| | - Ka Wai Fung
- Department of Structural and Molecular Biology, University College London, London, United Kingdom
| | - Jayesh Gor
- Department of Structural and Molecular Biology, University College London, London, United Kingdom
| | - Anthony C. Bishop
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York, USA
| | - George I. Makhatadze
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York, USA
| | - Barbara Brodsky
- Department of Biomedical Engineering, Science and Technology Center, Tufts University, Medford, Massachusetts, USA
| | - Stephen J. Perkins
- Department of Structural and Molecular Biology, University College London, London, United Kingdom,For correspondence: Stephen J. Perkins
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2
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Wong H, Crowet JM, Dauchez M, Ricard-Blum S, Baud S, Belloy N. Multiscale modelling of the extracellular matrix. Matrix Biol Plus 2022; 13:100096. [PMID: 35072037 PMCID: PMC8763633 DOI: 10.1016/j.mbplus.2021.100096] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 12/06/2021] [Accepted: 12/07/2021] [Indexed: 12/29/2022] Open
Abstract
The extracellular matrix is a complex three-dimensional network of molecules that provides cells with a complex microenvironment. The major constituents of the extracellular matrix such as collagen, elastin and associated proteins form supramolecular assemblies contributing to its physicochemical properties and organization. The structure of proteins and their supramolecular assemblies such as fibrils have been studied at the atomic level (e.g., by X-ray crystallography, Nuclear Magnetic Resonance and cryo-Electron Microscopy) or at the microscopic scale. However, many protein complexes are too large to be studied at the atomic level and too small to be studied by microscopy. Most extracellular matrix components fall into this intermediate scale, so-called the mesoscopic scale, preventing their detailed characterization. Simulation and modelling are some of the few powerful and promising approaches that can deepen our understanding of mesoscale systems. We have developed a set of modelling tools to study the self-organization of the extracellular matrix and large motion of macromolecules at the mesoscale level by taking advantage of the dynamics of articulated rigid bodies as a mean to study a larger range of motions at the cost of atomic resolution.
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Key Words
- Basement membrane
- CG, coarse-grained
- Cryo-EM, cryogenic electron microscopy
- DOF, degrees of freedom
- ECM, extracellular matrix
- EGF, epidermal growth factor
- Extracellular matrix
- FEM, finite element method
- MD, molecular dynamics
- Mesoscopic scale
- Modelling
- NC, non-collagenous
- NMR, nuclear magnetic resonance
- Rigid bodies
- SAXS, small-angle X-ray scattering
- Simulation
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Affiliation(s)
- Hua Wong
- Université de Reims Champagne Ardenne, CNRS, MEDyC UMR 7369, 51097 Reims, France
| | - Jean-Marc Crowet
- Université de Reims Champagne Ardenne, CNRS, MEDyC UMR 7369, 51097 Reims, France
| | - Manuel Dauchez
- Université de Reims Champagne Ardenne, CNRS, MEDyC UMR 7369, 51097 Reims, France
| | - Sylvie Ricard-Blum
- Univ. Lyon, University Claude Bernard Lyon 1, ICBMS, UMR 5246 CNRS, 69622 Villeurbanne Cedex, France
| | - Stéphanie Baud
- Université de Reims Champagne Ardenne, CNRS, MEDyC UMR 7369, 51097 Reims, France
- Université de Reims Champagne Ardenne, Plateau de Modélisation Moléculaire Multi-Echelle (P3M), Maison de la Simulation de Champagne-Ardenne (MaSCA), 51097 Reims, France
| | - Nicolas Belloy
- Université de Reims Champagne Ardenne, CNRS, MEDyC UMR 7369, 51097 Reims, France
- Université de Reims Champagne Ardenne, Plateau de Modélisation Moléculaire Multi-Echelle (P3M), Maison de la Simulation de Champagne-Ardenne (MaSCA), 51097 Reims, France
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3
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Al-Shaer A, Lyons A, Ishikawa Y, Hudson BG, Boudko SP, Forde NR. Sequence-dependent mechanics of collagen reflect its structural and functional organization. Biophys J 2021; 120:4013-4028. [PMID: 34390685 DOI: 10.1016/j.bpj.2021.08.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 05/25/2021] [Accepted: 08/06/2021] [Indexed: 01/06/2023] Open
Abstract
Extracellular matrix mechanics influence diverse cellular functions, yet surprisingly little is known about the mechanical properties of their constituent collagen proteins. In particular, network-forming collagen IV, an integral component of basement membranes, has been far less studied than fibril-forming collagens. A key feature of collagen IV is the presence of interruptions in the triple-helix-defining (Gly-X-Y) sequence along its collagenous domain. Here, we used atomic force microscopy to determine the impact of sequence heterogeneity on the local flexibility of collagen IV and of the fibril-forming collagen III. Our extracted flexibility profile of collagen IV reveals that it possesses highly heterogeneous mechanics, ranging from semiflexible regions as found for fibril-forming collagens to a lengthy region of high flexibility toward its N-terminus. A simple model in which flexibility is dictated only by the presence of interruptions fit the extracted profile reasonably well, providing insight into the alignment of chains and demonstrating that interruptions, particularly when coinciding in multiple chains, significantly enhance local flexibility. To a lesser extent, sequence variations within the triple helix lead to variable flexibility, as seen along the continuously triple-helical collagen III. We found this fibril-forming collagen to possess a high-flexibility region around its matrix-metalloprotease binding site, suggesting a unique mechanical fingerprint of this region that is key for matrix remodeling. Surprisingly, proline content did not correlate with local flexibility in either collagen type. We also found that physiologically relevant changes in pH and chloride concentration did not alter the flexibility of collagen IV, indicating such environmental changes are unlikely to control its compaction during secretion. Although extracellular chloride ions play a role in triggering collagen IV network formation, they do not appear to modulate the structure of its collagenous domain.
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Affiliation(s)
- Alaa Al-Shaer
- Department of Molecular Biology and Biochemistry, Burnaby, British Columbia, Canada
| | - Aaron Lyons
- Department of Physics, Burnaby, British Columbia, Canada
| | - Yoshihiro Ishikawa
- Department of Ophthalmology, University of California San Francisco, School of Medicine, San Francisco, California
| | - Billy G Hudson
- Department of Medicine, Division of Nephrology and Hypertension, Nashville, Tennessee; Vanderbilt Center for Matrix Biology, Vanderbilt University Medical Center, Nashville, Tennessee; Department of Biochemistry, Nashville, Tennessee; Department of Pathology, Microbiology, and Immunology, Nashville, Tennessee; Department of Cell and Developmental Biology, Nashville, Tennessee; Vanderbilt-Ingram Cancer Center, Nashville, Tennessee; Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee
| | - Sergei P Boudko
- Department of Medicine, Division of Nephrology and Hypertension, Nashville, Tennessee; Vanderbilt Center for Matrix Biology, Vanderbilt University Medical Center, Nashville, Tennessee; Department of Biochemistry, Nashville, Tennessee
| | - Nancy R Forde
- Department of Molecular Biology and Biochemistry, Burnaby, British Columbia, Canada; Department of Physics, Burnaby, British Columbia, Canada; Department of Chemistry, Burnaby, British Columbia, Canada; Centre for Cell Biology, Development and Disease, Simon Fraser University, Burnaby, British Columbia, Canada.
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4
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Qiu Y, Zhai C, Chen L, Liu X, Yeo J. Current Insights on the Diverse Structures and Functions in Bacterial Collagen-like Proteins. ACS Biomater Sci Eng 2021. [PMID: 33871954 DOI: 10.1021/acsbiomaterials.1c00018] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The dearth of knowledge on the diverse structures and functions in bacterial collagen-like proteins is in stark contrast to the deep grasp of structures and functions in mammalian collagen, the ubiquitous triple-helical scleroprotein that plays a central role in tissue architecture, extracellular matrix organization, and signal transduction. To fill and highlight existing gaps due to the general paucity of data on bacterial CLPs, we comprehensively reviewed the latest insight into their functional and structural diversity from multiple perspectives of biology, computational simulations, and materials engineering. The origins and discovery of bacterial CLPs were explored. Their genetic distribution and molecular architecture were analyzed, and their structural and functional diversity in various bacterial genera was examined. The principal roles of computational techniques in understanding bacterial CLPs' structural stability, mechanical properties, and biological functions were also considered. This review serves to drive further interest and development of bacterial CLPs, not only for addressing fundamental biological problems in collagen but also for engineering novel biomaterials. Hence, both biology and materials communities will greatly benefit from intensified research into the diverse structures and functions in bacterial collagen-like proteins.
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Affiliation(s)
- Yimin Qiu
- National Biopesticide Engineering Technology Research Center, Hubei Biopesticide Engineering Research Center, Hubei Academy of Agricultural Sciences, Biopesticide Branch of Hubei Innovation Centre of Agricultural Science and Technology, Wuhan 430064, PR China.,State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, PR China
| | - Chenxi Zhai
- J2 Lab for Engineering Living Materials, Sibley School of Mechanical and Aerospace Engineering, Cornell University, Ithaca, New York 14850, United States
| | - Ling Chen
- National Biopesticide Engineering Technology Research Center, Hubei Biopesticide Engineering Research Center, Hubei Academy of Agricultural Sciences, Biopesticide Branch of Hubei Innovation Centre of Agricultural Science and Technology, Wuhan 430064, PR China
| | - Xiaoyan Liu
- National Biopesticide Engineering Technology Research Center, Hubei Biopesticide Engineering Research Center, Hubei Academy of Agricultural Sciences, Biopesticide Branch of Hubei Innovation Centre of Agricultural Science and Technology, Wuhan 430064, PR China
| | - Jingjie Yeo
- J2 Lab for Engineering Living Materials, Sibley School of Mechanical and Aerospace Engineering, Cornell University, Ithaca, New York 14850, United States
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5
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Kananavičiūtė R, Kvederavičiūtė K, Dabkevičienė D, Mackevičius G, Kuisienė N. Collagen-like sequences encoded by extremophilic and extremotolerant bacteria. Genomics 2019; 112:2271-2281. [PMID: 31884159 DOI: 10.1016/j.ygeno.2019.12.023] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 12/17/2019] [Accepted: 12/25/2019] [Indexed: 12/14/2022]
Abstract
Collagens and collagen-like proteins are found in a wide range of organisms. The common feature of these proteins is a triple helix fold, requiring a characteristic pattern of amino acid sequences, composed of Gly-X-Y tripeptide repeats. Collagen-like proteins from bacteria are heterogeneous in terms of length and amino acid composition of their collagenous sequences. However, different bacteria live in different environments, some at extreme temperatures and conditions. This study explores the occurrence of collagen-like sequences in the genomes of different extreme condition-adapted bacteria, and investigates features that could be linked to conditions where they thrive. Our results show that proteins containing collagen-like sequences are encoded by genomes of various extremophiles. Some of these proteins contain conservative domains, characteristic of cell or endospore surface proteins, while most other proteins are unknown. The characteristics of collagenous sequences may depend on both, the phylogenetic relationship and the living conditions of the bacteria.
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Affiliation(s)
- Rūta Kananavičiūtė
- Institute of Biosciences, Life Sciences Center, Vilnius University, Saulėtekio av. 7, LT- 10257 Vilnius, Lithuania.
| | - Kotryna Kvederavičiūtė
- Institute of Biotechnology Life Sciences Center, Vilnius University, Saulėtekio av. 7, LT- 10257 Vilnius, Lithuania
| | - Daiva Dabkevičienė
- Institute of Biosciences, Life Sciences Center, Vilnius University, Saulėtekio av. 7, LT- 10257 Vilnius, Lithuania
| | - Gytis Mackevičius
- Faculty of Mathematics and Informatics, Vilnius University, Naugarduko g. 24, LT-03225 Vilnius, Lithuania
| | - Nomeda Kuisienė
- Institute of Biosciences, Life Sciences Center, Vilnius University, Saulėtekio av. 7, LT- 10257 Vilnius, Lithuania
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6
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Xu T, Zhou CZ, Xiao J, Liu J. Unique Conformation in a Natural Interruption Sequence of Type XIX Collagen Revealed by Its High-Resolution Crystal Structure. Biochemistry 2018; 57:1087-1095. [PMID: 29376320 DOI: 10.1021/acs.biochem.7b01010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Naturally occurring interruptions in nonfibrillar collagen play key roles in molecular flexibility, collagen degradation, and ligand binding. The structural feature of the interruption sequences and the molecular basis for their functions have not been well studied. Here, we focused on a G5G type natural interruption sequence G-POALO-G from human type XIX collagen, a homotrimer collagen, as this sequence possesses distinct properties compared with those of a pathological similar Gly mutation sequence in collagen mimic peptides. We determined the crystal structures of the host-guest peptide (GPO)3-GPOALO-(GPO)4 to 1.03 Å resolution in two crystal forms. In these structures, the interruption zone brings localized disruptions to the triple helix and introduces a light 6-8° bend with the same directional preference to the whole molecule, which may correspond structurally to the first physiological kink site in type XIX collagen. Furthermore, at the G5G interruption site, the presence of Ala and Leu residues, both with free N-H groups, allows the formation of more direct and water-mediated interchain hydrogen bonds than in the related Gly → Ala structure. These could partly explain the difference in thermal stability between the different interruptions. In addition, our structures provide a detailed view of the dynamic property of such an interrupted zone with respect to hydrogen bonding topology, torsion angles, and helical parameters. Our results, for the first time, also identified the binding of zinc to the end of the triple helix. These findings will shed light on how the interruption sequence influences the conformation of the collagen molecule and provide a structural basis for further functional studies.
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Affiliation(s)
- Tingting Xu
- School of Life Sciences, University of Science and Technology of China , Hefei 230026, China.,State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences , Guangzhou 510530, China
| | - Cong-Zhao Zhou
- School of Life Sciences, University of Science and Technology of China , Hefei 230026, China
| | - Jianxi Xiao
- State Key Laboratory of Applied Organic Chemistry, Key Laboratory of Nonferrous Metal Chemistry and Resources Utilization of Gansu Province, College of Chemistry and Chemical Engineering, Lanzhou University , Lanzhou 730000, China
| | - Jinsong Liu
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences , Guangzhou 510530, China.,Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences , Guangzhou 510530, China
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7
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Sutherland TD, Huson MG, Rapson TD. Rational design of new materials using recombinant structural proteins: Current state and future challenges. J Struct Biol 2017; 201:76-83. [PMID: 29097186 DOI: 10.1016/j.jsb.2017.10.012] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 10/26/2017] [Accepted: 10/28/2017] [Indexed: 11/27/2022]
Abstract
Sequence-definable polymers are seen as a prerequisite for design of future materials, with many polymer scientists regarding such polymers as the holy grail of polymer science. Recombinant proteins are sequence-defined polymers. Proteins are dictated by DNA templates and therefore the sequence of amino acids in a protein is defined, and molecular biology provides tools that allow redesign of the DNA as required. Despite this advantage, proteins are underrepresented in materials science. In this publication we investigate the advantages and limitations of using proteins as templates for rational design of new materials.
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Affiliation(s)
| | - Mickey G Huson
- CSIRO, Black Mountain, GPO Box 1700, Acton, ACT 2601, Australia
| | - Trevor D Rapson
- CSIRO, Black Mountain, GPO Box 1700, Acton, ACT 2601, Australia
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8
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Abstract
Fibrillar collagens (types I, II, III, V, XI, XXIV and XXVII) constitute a sub-group within the collagen family (of which there are 28 types in humans) whose functions are to provide three-dimensional frameworks for tissues and organs. These networks confer mechanical strength as well as signalling and organizing functions through binding to cellular receptors and other components of the extracellular matrix (ECM). Here we describe the structure and assembly of fibrillar collagens, and their procollagen precursors, from the molecular to the tissue level. We show how the structure of the collagen triple-helix is influenced by the amino acid sequence, hydrogen bonding and post-translational modifications, such as prolyl 4-hydroxylation. The numerous steps in the biosynthesis of the fibrillar collagens are reviewed with particular attention to the role of prolyl 3-hydroxylation, collagen chaperones, trimerization of procollagen chains and proteolytic maturation. The multiple steps controlling fibril assembly are then discussed with a focus on the cellular control of this process in vivo. Our current understanding of the molecular packing in collagen fibrils, from different tissues, is then summarized on the basis of data from X-ray diffraction and electron microscopy. These results provide structural insights into how collagen fibrils interact with cell receptors, other fibrillar and non-fibrillar collagens and other ECM components, as well as enzymes involved in cross-linking and degradation.
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Affiliation(s)
- Jordi Bella
- Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester, M13 9PT, UK.
| | - David J S Hulmes
- Tissue Biology and Therapeutic Engineering Unit (UMR5305), CNRS/Université Claude Bernard Lyon 1, Lyon, France
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9
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Collagen structure: new tricks from a very old dog. Biochem J 2016; 473:1001-25. [PMID: 27060106 DOI: 10.1042/bj20151169] [Citation(s) in RCA: 154] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Accepted: 02/01/2016] [Indexed: 12/22/2022]
Abstract
The main features of the triple helical structure of collagen were deduced in the mid-1950s from fibre X-ray diffraction of tendons. Yet, the resulting models only could offer an average description of the molecular conformation. A critical advance came about 20 years later with the chemical synthesis of sufficiently long and homogeneous peptides with collagen-like sequences. The availability of these collagen model peptides resulted in a large number of biochemical, crystallographic and NMR studies that have revolutionized our understanding of collagen structure. High-resolution crystal structures from collagen model peptides have provided a wealth of data on collagen conformational variability, interaction with water, collagen stability or the effects of interruptions. Furthermore, a large increase in the number of structures of collagen model peptides in complex with domains from receptors or collagen-binding proteins has shed light on the mechanisms of collagen recognition. In recent years, collagen biochemistry has escaped the boundaries of natural collagen sequences. Detailed knowledge of collagen structure has opened the field for protein engineers who have used chemical biology approaches to produce hyperstable collagens with unnatural residues, rationally designed collagen heterotrimers, self-assembling collagen peptides, etc. This review summarizes our current understanding of the structure of the collagen triple helical domain (COL×3) and gives an overview of some of the new developments in collagen molecular engineering aiming to produce novel collagen-based materials with superior properties.
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10
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Fu I, Case DA, Baum J. Dynamic Water-Mediated Hydrogen Bonding in a Collagen Model Peptide. Biochemistry 2016; 54:6029-37. [PMID: 26339765 DOI: 10.1021/acs.biochem.5b00622] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
In the canonical (G-X-Y)(n) sequence of the fibrillar collagen triple helix, stabilizing direct interchain hydrogen bonding connects neighboring chains. Mutations of G can disrupt these interactions and are linked to connective tissue diseases. Here we integrate computational approaches with nuclear magnetic resonance (NMR) to obtain a dynamic view of hydrogen bonding distributions in the (POG)(4)(-)(POA)-(POG)(5) peptide, showing that the solution conformation, dynamics, and hydrogen bonding deviate from the reported X-ray crystal structure in many aspects. The simulations and NMR data provide clear evidence of inequivalent environments in the three chains. Molecular dynamics (MD) simulations indicate direct interchain hydrogen bonds in the leading chain, water bridges in the middle chain, and nonbridging waters in the trailing chain at the G → A substitution site. Theoretical calculations of NMR chemical shifts using a quantum fragmentation procedure can account for the unusual downfield NMR chemical shifts at the substitution sites and are used to assign the resonances to the individual chains. The NMR and MD data highlight the sensitivity of amide shifts to changes in the acceptor group from peptide carbonyls to water. The results are used to interpret solution NMR data for a variety of glycine substitutions and other sequence triplet interruptions to provide new connections between collagen sequences, their associated structures, dynamical behavior, and their ability to recognize collagen receptors.
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Affiliation(s)
- Iwen Fu
- Department of Chemistry and Chemical Biology and BioMaPS Institute, Rutgers University , Piscataway, New Jersey 08854, United States
| | - David A Case
- Department of Chemistry and Chemical Biology and BioMaPS Institute, Rutgers University , Piscataway, New Jersey 08854, United States
| | - Jean Baum
- Department of Chemistry and Chemical Biology and BioMaPS Institute, Rutgers University , Piscataway, New Jersey 08854, United States
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11
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Sun X, Liu S, Yu W, Wang S, Xiao J. CD and NMR investigation of collagen peptides mimicking a pathological Gly-Ser mutation and a natural interruption in a similar highly charged sequence context. Protein Sci 2015; 25:383-92. [PMID: 26457583 DOI: 10.1002/pro.2828] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2015] [Revised: 10/06/2015] [Accepted: 10/07/2015] [Indexed: 12/29/2022]
Abstract
Even a single Gly substitution in the triple helix domain of collagen leads to pathological conditions while natural interruptions are suggested to play important functional roles. Two peptides-one mimicking a pathological Gly-Ser substitution (ERSEQ) and the other one modeling a similar natural interruption sequence (DRSER)-are designed to facilitate the comparison for elucidating the molecular basis of their different biological roles. CD and NMR investigation of peptide ERSEQ indicates a reduction of the thermal stability and disruption of hydrogen bonding at the Ser mutation site, providing a structural basis of the OI disease resulting from the Gly-Ser mutation in the highly charged RGE environment. Both CD and NMR real-time folding results indicate that peptide ERSEQ displays a comparatively slower folding rate than peptide DRSER, suggesting that the Gly-Ser mutation may lead to a larger interference in folding than the natural interruption in a similar RSE context. Our studies suggest that unlike the rigid GPO environment, the abundant R(K)GE(D) motif may provide a more flexible sequence environment that better accommodates mutations as well as interruptions, while the electrostatic interactions contribute to its stability. These results shed insight into the molecular features of the highly charged motif and may aid the design of collagen biomimetic peptides containing important biological sites.
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Affiliation(s)
- Xiuxia Sun
- Key Laboratory of Nonferrous Metal Chemistry and Resources Utilization of Gansu Province, State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, 730000, People's Republic of China
| | - Songqing Liu
- Key Laboratory of Nonferrous Metal Chemistry and Resources Utilization of Gansu Province, State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, 730000, People's Republic of China
| | - Wenyuan Yu
- Key Laboratory of Nonferrous Metal Chemistry and Resources Utilization of Gansu Province, State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, 730000, People's Republic of China
| | - Shaoru Wang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, People's Republic of China
| | - Jianxi Xiao
- Key Laboratory of Nonferrous Metal Chemistry and Resources Utilization of Gansu Province, State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, 730000, People's Republic of China
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12
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Xiao J, Sun X, Madhan B, Brodsky B, Baum J. NMR studies demonstrate a unique AAB composition and chain register for a heterotrimeric type IV collagen model peptide containing a natural interruption site. J Biol Chem 2015. [PMID: 26209635 DOI: 10.1074/jbc.m115.654871] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
All non-fibrillar collagens contain interruptions in the (Gly-X-Y)n repeating sequence, such as the more than 20 interruptions found in chains of basement membrane type IV collagen. Two selectively doubly labeled peptides are designed to model a site in type IV collagen with a GVG interruption in the α1(IV) and a corresponding GISLK sequence within the α2(IV) chain. CD and NMR studies on a 2:1 mixture of these two peptides support the formation of a single-component heterotrimer that maintains the one-residue staggering in the triple-helix, has a unique chain register, and contains hydrogen bonds at the interruption site. Formation of hydrogen bonds at interruption sites may provide a driving force for self-assembly and chain register in type IV and other non-fibrillar collagens. This study illustrates the potential role of interruptions in the structure, dynamics, and folding of natural collagen heterotrimers and forms a basis for understanding their biological role.
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Affiliation(s)
- Jianxi Xiao
- the Key Laboratory of Nonferrous Metal Chemistry and Resources Utilization of Gansu Province, State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, China, From the Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854
| | - Xiuxia Sun
- the Key Laboratory of Nonferrous Metal Chemistry and Resources Utilization of Gansu Province, State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, China
| | - Balaraman Madhan
- the Central Leather Research Institute, Council of Scientific and Industrial Research, Adyar, Chennai-600020, India
| | - Barbara Brodsky
- the Department of Biomedical Engineering, Tufts University, Medford, Massachusetts 02446, and
| | - Jean Baum
- From the Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854,
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