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Goldberga I, Li R, Duer MJ. Collagen Structure-Function Relationships from Solid-State NMR Spectroscopy. Acc Chem Res 2018; 51:1621-1629. [PMID: 29931970 DOI: 10.1021/acs.accounts.8b00092] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The extracellular matrix of a tissue is as important to life as the cells within it. Its detailed molecular structure defines the environment of a tissue's cells and thus their properties, including differentiation and metabolic status. Collagen proteins are the major component of extracellular matrices. Self-assembled collagen fibrils provide both specific mechanical properties to handle external stresses on tissues and, at the molecular level, well-defined protein binding sites to interact with cells. How the cell-matrix interactions are maintained against the stresses on the tissue is an important and as yet unanswered question. Similarly, how collagen molecular and fibrillar structures change in aging and disease is a crucial open question. Solid-state NMR spectroscopy offers insight into collagen molecular conformation in intact in vivo and in vitro tissues, and in this Account we review how NMR spectroscopy is beginning to provide answers to these questions. In vivo 13C,15N labeling of the extracellular matrix has given insight into collagen molecular dynamics and generated multidimensional NMR "fingerprints" of collagen molecular structure that allow comparison of local collagen conformation between tissues. NMR studies have shown that charged collagen residues (Lys, Arg) adopt extended-side-chain conformations in the fibrillar structure to facilitate charge-charge interactions between neighboring collagen molecules, while hydrophobic residues (Leu, Ile) fold along the collagen molecular axis to minimize the hydrophobic area exposed to surrounding water. Detailed NMR and molecular modeling work has shown that the abundant Gly-Pro-Hyp (Hyp = hydroxyproline) triplets in collagen triple helices confer well-defined flexibility because the proline is conformationally metastable, in contrast to the expectation that these triplets confer structural rigidity. The alignment of the Gly-Pro-Hyp triplets within the fibril structure means that the Gly-Pro-Hyp molecular flexibility generates fibril flexibility. The fibrillar bands of Gly-Pro-Hyp are highly correlated with collagen ligand binding sites, leading to the hypothesis that the fibril alignment of Gly-Pro-Hyp triplets is essential to protect collagen-ligand binding against external stresses on the tissue. Non-enzymatic chemistry between collagen side-chain amine groups (Lys, Arg) and reducing sugars-glycation-is an important source of matrix structural change in aging and disease. Glycation leads to stiffening of collagen fibrils, which is widely speculated to be the result of intermolecular cross-linking. The chemistry of non-enzymatic glycation has been extensively detailed through NMR studies and has been shown to lead to side-chain modifications as the majority reaction products, rather than intermolecular cross-links, with resultant molecular misalignment in the fibrils. Thus, a picture is beginning to emerge in which collagen glycation causes stiffening through misalignment of collagen molecular flexible regions rather than intermolecular cross-linking, meaning that new thinking is needed on how to alleviate collagen structural changes in aging and disease.
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Affiliation(s)
- Ieva Goldberga
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Rui Li
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Melinda J. Duer
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
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Wong VWC, Reid DG, Chow WY, Rajan R, Green M, Brooks RA, Duer MJ. Preparation of highly and generally enriched mammalian tissues for solid state NMR. JOURNAL OF BIOMOLECULAR NMR 2015; 63:119-123. [PMID: 26407607 DOI: 10.1007/s10858-015-9977-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Accepted: 08/08/2015] [Indexed: 06/05/2023]
Abstract
An appreciable level of isotope labelling is essential for future NMR structure elucidation of mammalian biomaterials, which are either poorly expressed, or unexpressable, using micro-organisms. We present a detailed protocol for high level (13)C enrichment even in slow turnover murine biomaterials (fur keratin), using a customized diet supplemented with commercial labelled algal hydrolysate and formulated as a gel to minimize wastage, which female mice consumed during pregnancy and lactation. This procedure produced approximately eightfold higher fur keratin labelling in pups, exposed in utero and throughout life to label, than in adults exposed for the same period, showing both the effectiveness, and necessity, of this approach.
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Affiliation(s)
| | - David G Reid
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Wing Ying Chow
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Rakesh Rajan
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Maggie Green
- Central Biomedical Resources, School of Clinical Medicine, University of Cambridge, West Forvie Building, Forvie Site, Robinson Way, Cambridge, CB2 0SZ, UK
| | - Roger A Brooks
- Department of Trauma and Orthopaedic Surgery, Addenbrooke's Hospital, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Melinda J Duer
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.
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Duer MJ. The contribution of solid-state NMR spectroscopy to understanding biomineralization: atomic and molecular structure of bone. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2015; 253:98-110. [PMID: 25797009 DOI: 10.1016/j.jmr.2014.12.011] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Revised: 12/15/2014] [Accepted: 12/23/2014] [Indexed: 05/06/2023]
Abstract
Solid-state NMR spectroscopy has had a major impact on our understanding of the structure of mineralized tissues, in particular bone. Bone exemplifies the organic-inorganic composite structure inherent in mineralized tissues. The organic component of the extracellular matrix in bone is primarily composed of ordered fibrils of collagen triple-helical molecules, in which the inorganic component, calcium phosphate particles, composed of stacks of mineral platelets, are arranged around the fibrils. This perspective argues that key factors in our current structural model of bone mineral have come about through NMR spectroscopy and have yielded the primary information on how the mineral particles interface and bind with the underlying organic matrix. The structure of collagen within the organic matrix of bone or any other structural tissue has yet to be determined, but here too, this perspective shows there has been real progress made through application of solid-state NMR spectroscopy in conjunction with other techniques. In particular, NMR spectroscopy has highlighted the fact that even within these structural proteins, there is considerable dynamics, which suggests that one should be cautious when using inherently static structural models, such as those arising from X-ray diffraction analyses, to gain insight into molecular roles. It is clear that the NMR approach is still in its infancy in this area, and that we can expect many more developments in the future, particularly in understanding the molecular mechanisms of bone diseases and ageing.
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Affiliation(s)
- Melinda J Duer
- Dept. of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.
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Chow WY, Rajan R, Muller KH, Reid DG, Skepper JN, Wong WC, Brooks RA, Green M, Bihan D, Farndale RW, Slatter DA, Shanahan CM, Duer MJ. NMR spectroscopy of native and in vitro tissues implicates polyADP ribose in biomineralization. Science 2014; 344:742-6. [PMID: 24833391 DOI: 10.1126/science.1248167] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Nuclear magnetic resonance (NMR) spectroscopy is useful to determine molecular structure in tissues grown in vitro only if their fidelity, relative to native tissue, can be established. Here, we use multidimensional NMR spectra of animal and in vitro model tissues as fingerprints of their respective molecular structures, allowing us to compare the intact tissues at atomic length scales. To obtain spectra from animal tissues, we developed a heavy mouse enriched by about 20% in the NMR-active isotopes carbon-13 and nitrogen-15. The resulting spectra allowed us to refine an in vitro model of developing bone and to probe its detailed structure. The identification of an unexpected molecule, poly(adenosine diphosphate ribose), that may be implicated in calcification of the bone matrix, illustrates the analytical power of this approach.
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Affiliation(s)
- W Ying Chow
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Rakesh Rajan
- Orthopaedic Research Unit, University of Cambridge, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK
| | - Karin H Muller
- Department of Physiology, Development, and Neuroscience, University of Cambridge, Downing Site, Cambridge CB2 3DY, UK
| | - David G Reid
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Jeremy N Skepper
- Department of Physiology, Development, and Neuroscience, University of Cambridge, Downing Site, Cambridge CB2 3DY, UK
| | - Wai Ching Wong
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Roger A Brooks
- Orthopaedic Research Unit, University of Cambridge, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK
| | - Maggie Green
- Central Biomedical Resources, University of Cambridge, School of Clinical Medicine, West Forvie Building, Forvie Site, Robinson Way, Cambridge CB2 0SZ, UK
| | - Dominique Bihan
- Department of Biochemistry, University of Cambridge, Downing Site, Cambridge CB2 1QW, UK
| | - Richard W Farndale
- Department of Biochemistry, University of Cambridge, Downing Site, Cambridge CB2 1QW, UK
| | - David A Slatter
- Department of Biochemistry, University of Cambridge, Downing Site, Cambridge CB2 1QW, UK
| | - Catherine M Shanahan
- British Heart Foundation Centre of Research Excellence, Cardiovascular Division, James Black Centre, King's College London, 125 Coldharbour Lane, London SE5 9NU, UK
| | - Melinda J Duer
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.
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Lee DK, Wittebort RJ, Ramamoorthy A. Characterization of 15N Chemical Shift and 1H−15N Dipolar Coupling Interactions in a Peptide Bond of Uniaxially Oriented and Polycrystalline Samples by One-Dimensional Dipolar Chemical Shift Solid-State NMR Spectroscopy. J Am Chem Soc 1998. [DOI: 10.1021/ja981599u] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- D. K. Lee
- Contribution from the Biophysics Research Division and Department of Chemistry, The University of Michigan, Ann Arbor, Michigan 48109-1055, and Department of Chemistry, University of Louisville, Louisville, Kentucky 40292
| | - R. J. Wittebort
- Contribution from the Biophysics Research Division and Department of Chemistry, The University of Michigan, Ann Arbor, Michigan 48109-1055, and Department of Chemistry, University of Louisville, Louisville, Kentucky 40292
| | - A. Ramamoorthy
- Contribution from the Biophysics Research Division and Department of Chemistry, The University of Michigan, Ann Arbor, Michigan 48109-1055, and Department of Chemistry, University of Louisville, Louisville, Kentucky 40292
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Li MH, Fan P, Brodsky B, Baum J. Two-dimensional NMR assignments and conformation of (Pro-Hyp-Gly)10 and a designed collagen triple-helical peptide. Biochemistry 1993; 32:7377-87. [PMID: 8338835 DOI: 10.1021/bi00080a007] [Citation(s) in RCA: 101] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Homonuclear and heteronuclear 2D NMR methods are used to study two triple-helical peptides. One peptide, (POG)10, is considered to be the most stable prototype of a triple helix. The second peptide, (POG)3ITGARGLAGPOG(POG)3 (denoted T3-785), was designed to model an imino acid poor region of collagen and contains 12 residues from near the unique collagenase cleavage site in type III collagen. Both peptides associated as trimers, with melting temperatures of 60 degrees C for (POG)10 and 25 degrees C for the T3-785 peptide. Sequence-specific assignments were made for a tripeptide unit POG in (POG)10, and 80% of the POG triplets are found to be in an equivalent environment. In T3-785, with nonrepeating X-Y-Gly units incorporated in the sequence, the three chains of the homotrimer can be distinguished from one another by NMR. The solution conformation of (POG)10 is very similar to the model derived from X-ray fiber diffraction data, although the peptide contains less ordered regions at the peptide ends. In the trimer from of T3-785, the central residues of the three chains are closely packed, and the data are consistent with a triple-helical model with a one-residue stagger of three parallel chains. For T3-785, in contrast to (POG)10, there are also resonances from a less ordered form, which are probably due to the presence of a small amount of monomer. The similarity of the backbone conformations of T3-785 and (POG)10 suggests that an alternative conformation is not present in the imino acid poor region.
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Affiliation(s)
- M H Li
- Department of Chemistry, Rutgers University, Piscataway, New Jersey 08855-0939
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Chen JM, Kung CE, Feairheller SH, Brown EM. An energetic evaluation of a "Smith" collagen microfibril model. JOURNAL OF PROTEIN CHEMISTRY 1991; 10:535-52. [PMID: 1799411 DOI: 10.1007/bf01025482] [Citation(s) in RCA: 57] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
An energy minimized three-dimensional structure of a collagen microfibril template was constructed based on the five-stranded model of Smith (1968), using molecular modeling methods and Kollman force fields (Weiner and Kollman, 1981). For this model, individual molecules were constructed with three identical polypeptide chains [Gly-Pro-Pro)n, (Gly-Prop-Hyp)n, or (Gly-Ala-Ala)n, where n = 4, 12, and 16) coiled into a right-handed triple-helical structure. The axial distance between adjacent amino acid residues is about 0.29 nm per polypeptide chain, and the pitch of each chain is approximately 3.3 residues. The microfibril model consists of five parallel triple helices packed so that a left-handed superhelical twist exists. The structural characteristics of the computed microfibril are consistent with those obtained for collagen by X-ray diffraction and electron microscopy. The energy minimized Smith microfibril model for (Gly-Pro-Pro)12 has an axial length of about 10.2 nm (for a 36 amino acid residue chain), which gives an estimated D-spacing (234 amino acids per chain) of approximately 66.2 nm. Studies of the microfibril models (Gly-Pro-Pro)12, (Gly-Pro-Hyp)12, and (Gly-Ala-Ala)12 show that nonbonded van der Waals interactions are important for microfibril formation, while electrostatic interactions contribute to the stability of the microfibril structure and determine the specificity by which collagen molecules pack within the microfibril.
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Affiliation(s)
- J M Chen
- U.S. Department of Agriculture, ARS, Eastern Regional Research Center, Philadelphia, Pennsylvania 19118
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Hiyama Y, Torchia DA. Heterogeneity of intact collagen by solid state multinuclear magnetic resonance. BASIC LIFE SCIENCES 1990; 56:273-85. [PMID: 2078174 DOI: 10.1007/978-1-4684-5868-8_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Y Hiyama
- Bone Research Branch, National Institute of Dental Research, National Institutes of Health, Bethesda, MD 20892
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