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Karabencheva-Christova TG, Christov CZ, Fields GB. Collagenolytic Matrix Metalloproteinase Structure–Function Relationships: Insights From Molecular Dynamics Studies. STRUCTURAL AND MECHANISTIC ENZYMOLOGY 2017; 109:1-24. [DOI: 10.1016/bs.apcsb.2017.04.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Saitô H, Ando I, Ramamoorthy A. Chemical shift tensor - the heart of NMR: Insights into biological aspects of proteins. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2010; 57:181-228. [PMID: 20633363 PMCID: PMC2905606 DOI: 10.1016/j.pnmrs.2010.04.005] [Citation(s) in RCA: 136] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2010] [Accepted: 04/26/2010] [Indexed: 05/19/2023]
Affiliation(s)
- Hazime Saitô
- Department of Life Science, Himeji Institute of Technology, University of Hyogo, Kamigori, Hyog, 678-1297, Japan
| | - Isao Ando
- Department of Chemistry and Materials Science, Tokyo Institute of Technology, Ookayama, Meguro-ku, Tokyo, 152-0033, Japan
| | - Ayyalusamy Ramamoorthy
- Biophysics and Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, MI 48109-1055, USA
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Torchia DA, Batchelder LS, Fleming WW, Jelinski LW, Sarkar SK, Sullivan CE. Mobility and Function in Elastin and Collagen. CIBA FOUNDATION SYMPOSIUM 93 - MOBILITY AND FUNCTION IN PROTEINS AND NUCLEIC ACIDS 2008; 93:98-115. [PMID: 6551234 DOI: 10.1002/9780470720752.ch6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
13C- and 2H-labelled amino acids have been incorporated into elastin and collagen and rotational correlation times of the labelled sites have been derived from an analysis of nuclear magnetic resonance relaxation parameters and line-shapes. The elastin experiments were designed to discriminate between the various models that have been proposed to account for the rubber-like elasticity of elastin. The correlation times of carbonyl carbons of the elastin backbone show that elastin chains are very flexible at the molecular level. In addition, the molecular dynamics and viscoelastic behaviour of elastin are well correlated over a wide range of temperatures and solvents. These results all support the rubber-like network model of elastin structure. The collagen experiments were designed to investigate the intermolecular interactions between molecules in collagen fibres. Correlation times of labelled sites in the collagen backbone and side-chains show that substantial flexibility, especially of the side-chains, takes place in reconstituted (non-cross-linked) collagen fibrils. Therefore, the interactions between side-chains that presumably direct and stabilize the fibrillar assembly take place in fluid domains. The molecular flexibility is not affected by the presence of cross-links but is absent when the collagen is mineralized.
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Saihi D, Vroman I, Giraud S, Bourbigot S. Microencapsulation of ammonium phosphate with a polyurethane shell. Part II. Interfacial polymerization technique. REACT FUNCT POLYM 2006. [DOI: 10.1016/j.reactfunctpolym.2006.02.001] [Citation(s) in RCA: 107] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Saihi D, Vroman I, Giraud S, Bourbigot S. Microencapsulation of ammonium phosphate with a polyurethane shell part I: Coacervation technique. REACT FUNCT POLYM 2005. [DOI: 10.1016/j.reactfunctpolym.2005.05.004] [Citation(s) in RCA: 87] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Abstract
The matrix metalloproteinase (MMP)/matrixin family has been implicated in both normal tissue remodeling and a variety of diseases associated with abnormal turnover of extracellular matrix components. The mechanism by which MMPs catabolize collagen (collagenolysis) is still largely unknown. Substrate flexibility, MMP active sites, and MMP exosites all contribute to collagen degradation. It has recently been demonstrated that the ability to cleave a triple helix (triple-helical peptidase activity) can be distinguished from the ability to cleave collagen (collagenolytic activity). This suggests that the ability to cleave a triple helix is not the limiting factor for collagenolytic activity-the ability to properly orient and potentially destabilize collagen is. For the MMP family, the catalytic domain can unwind and cleave a triple-helical structure, while the C-terminal hemopexin-like domain appears to be responsible for properly orienting collagen and destabilizing it to some degree. It is also possible that exosites within the catalytic and/or C-terminal hemopexin-like domain may exclude some MMPs from cleaving collagen. Overall, it appears that many proteases of distinct mechanisms possess triple-helical peptidase activity, and that convergent evolution led to a few proteases possessing collagenolytic activity. Proper orientation and distortion of the triple helix may be the key factor for collagenolysis.
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Affiliation(s)
- Janelle L Lauer-Fields
- Department of Chemistry and Biochemistry, Florida Atlantic University, 777 Glades Road, Boca Raton, FL 33431, USA
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Kurita JI, Shimahara H, Utsunomiya-Tate N, Tate SI. Measurement of 15N chemical shift anisotropy in a protein dissolved in a dilute liquid crystalline medium with the application of magic angle sample spinning. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2003; 163:163-173. [PMID: 12852920 DOI: 10.1016/s1090-7807(03)00080-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The chemical shifts of nuclei that have chemical shielding anisotropy, such as the 15N amide in a protein, show significant changes in their chemical shifts when the sample is altered from an isotropic state to an aligned state. Such orientation-dependent chemical shift changes provide information on the magnitudes and orientation of the chemical shielding tensors relative to the molecule's alignment frame. Because of the extremely high sensitivity of the chemical shifts to the sample conditions, the changes in chemical shifts induced by adding aligned bicelles do not arise only from the protein alignment but should also include the accumulated effects of environmental changes including protein-bicelle interactions. With the aim of determining accurate 15N chemical shielding tensor values for solution proteins, here we have used magic angle sample spinning (MAS) to observe discriminately the orientation-dependent changes in the 15N chemical shift. The application of MAS to an aligned bicelle solution removes the torque that aligns the bicelles against the magnetic field. Thus, the application of MAS to a protein in a bicelle solution eliminates only the molecular alignment effect, while keeping all other sample conditions the same. The observed chemical shift differences between experiments with and without MAS therefore provide accurate values of the orientation-dependent 15N chemical shifts. From the values for ubiquitin in a 7.5% (w/v) bicelle medium, we determined the 15N chemical shielding anisotropy (CSA) tensor. For this evaluation, we considered uncertainties in measuring the 1H-15N dipolar couplings and the 15N chemical shifts and also structural noise present in the reference X-ray structure, assuming a random distribution of each NH bond vector in a cone with 5 degrees deviation from the original orientation. Taking into account these types of noise, we determined the average 15N CSA tensor for the residues in ubiquitin as Delta sigma=-162.0+/-4.3 ppm, eta=0.18+/-0.02, and beta=18.6+/-0.5 degrees, assuming a 1H-15N bond length of 1.02 A. These tensor values are consistent with those obtained from solid-state NMR experiments.
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Affiliation(s)
- Jun-ichi Kurita
- Center for New Materials, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Tatsunokuchi, 923-1292 Ishikawa, Japan
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Huster D, Schiller J, Arnold K. Comparison of collagen dynamics in articular cartilage and isolated fibrils by solid-state NMR spectroscopy. Magn Reson Med 2002; 48:624-32. [PMID: 12353279 DOI: 10.1002/mrm.10272] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Native pig articular cartilage was investigated by (13)C cross polarization (CP) magic angle spinning (MAS) NMR at a magnetic field strength of 17.6 T. CP MAS spectra of cartilage are dominated by resonances from rigid collagen, while only low-intensity signals from the glycosaminoglycans are observed. The spectral resolution of collagen fibrils in native cartilage is somewhat higher than for isolated collagen fibrils from bovine achilles tendon investigated for comparison. This is confirmed qualitatively by (1)H-(1)H wideline separation spectra that show much lower line widths for cartilage collagen compared to isolated collagen. The strength of (1)H-(13)C dipolar couplings was measured in a 2D LG CP experiment providing a motionally averaged dipolar coupling value for each resolved signal. These scaled couplings were converted to molecular order parameters for the CH bond vector. Typical order parameters for isolated collagen were 0.91-0.96 for sidechains and 0.98-1.00 for the backbone. Somewhat lower order parameters were determined for cartilage collagen; 0.79-0.90 for the sidechain and 0.92-0.97 for the backbone. The only glycosaminoglycan signals that could be detected by CP MAS show order parameters of 0.48-0.92 and are assigned to relatively rigid hyaluronan and keratan sulfate. The higher mobility of collagen in cartilage is due to the high water content and collisions with the isotropically mobile glycosaminoglycans, such as chondroitin sulfate. Therefore, the mobility of cartilage macromolecules is broadly distributed from almost completely rigid to highly mobile, which lends cartilage its mechanical strength and shock-absorbing properties.
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Affiliation(s)
- Daniel Huster
- Junior Research Group Solid-state NMR studies of membrane-associated proteins, Biotechnological-Biomedical Center, University of Leipzig, Germany.
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Lauer-Fields JL, Fields GB. Triple-helical peptide analysis of collagenolytic protease activity. Biol Chem 2002; 383:1095-105. [PMID: 12437092 DOI: 10.1515/bc.2002.118] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Matrix metalloproteinase (MMP) family members are involved in the physiological remodeling of tissues and embryonic development as well as pathological destruction of extracellular matrix components. To study the mechanisms of MMP action on collagenous substrates, non-fluorogenic and fluorogenic triple-helical peptide models of MMP-1 cleavage sites in interstitial collagens have been constructed. Triple-helical peptides were assembled by either (a) covalent branching or (b) self-association driven by hydrophobic interactions. Fluorogenic triple-helical peptide (fTHP) substrates contained the fluorophore/quencher pair of (7-methoxycoumarin-4-yl)acetyl (Mca) and N-2,4-dinitrophenyl (Dnp) in the P5 and P5' positions, respectively. Investigation of MMP family hydrolysis of THPs showed kcat/Km values in the order of MMP-13 > MMP-1 approximately MMP-1(delta243-450) approximately MMP-2 >> MMP-3. Studies on the effect of temperature on fTHP and an analogous fluorogenic single-stranded peptide (fSSP) hydrolysis by MMP-1 showed that the activation energies between these two substrates differed by 3.4-fold, similar to the difference in activation energies for MMP-1 hydrolysis of type I collagen and gelatin. The general proteases trypsin and thermolysin were also studied for triple-helical peptidase activity. Both of these enzymes exhibited similar activation energies to MMP-1 for hydrolysis of fTHP versus fSSP. These results suggest that 'triple-helical peptidase' activity can be distinguished from 'collagenolytic' activity, and that mechanistically distinct enzymes convergently evolved to develop collagenolytic activity.
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Affiliation(s)
- Janelle L Lauer-Fields
- Department of Chemistry and Biochemistry, Florida Atlantic University, Boca Raton 33431-0991, USA
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Lauer-Fields JL, Tuzinski KA, Shimokawa KI, Nagase H, Fields GB. Hydrolysis of triple-helical collagen peptide models by matrix metalloproteinases. J Biol Chem 2000; 275:13282-90. [PMID: 10788434 DOI: 10.1074/jbc.275.18.13282] [Citation(s) in RCA: 104] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
The matrix metalloproteinase (MMP) family has been implicated in the process of a variety of diseases such as arthritis, atherosclerosis, and tumor cell metastasis. To study the mechanisms of MMP action on collagenous substrates, we have constructed homotrimeric triple-helical peptide (THP) models of the collagenase cleavage sites in types I and II collagen. The THPs incorporate either the alpha1(I)772-786 or the alpha1(II)772-783 sequence. The alpha1(I)772-786 and alpha1(II)772-783 THPs were hydrolyzed by MMP-1 at the Gly-Ile and Gly-Leu bonds, respectively, analogous to the bonds cleaved in corresponding native collagens. Thus, the THPs contained all necessary information to direct MMP-1 binding and proteolysis. Subsequent investigations using the alpha1(I)772-786 THP showed hydrolysis by MMP-2, MMP-13, and a COOH-terminal domain-deleted MMP-1 (MMP-1(Delta(243-450))) but not by MMP-3 or a COOH-terminal domain-deleted MMP-3 (MMP-3(Delta(248-460))). Kinetic analyses showed a k(cat)/K(m) value of 1,808 s(-1) m(-1) for MMP-1 hydrolysis of alpha1(I)772-786 THP, approximately 10-fold lower than for type I collagen. The effect is caused primarily by relative K(m) values. MMP-2 and MMP-13 cleaved the THP more rapidly than MMP-1, but MMP-2 cleavage occurred at distinct multiple sites. Comparison of MMP-1 and MMP-1(Delta(243-450)) hydrolysis of alpha1(I)772-786 THP showed that both can cleave a triple-helical substrate with a slightly higher K(m) value for MMP-1(Delta(243-450)). We propose that the COOH-terminal domain of MMPs is necessary for orienting whole, native collagen molecules but may not be necessary for binding to and cleaving a THP. This proposal is consistent with the large distance between the MMP-1 catalytic and COOH-terminal domains observed by three-dimensional structural analysis and supports previous suggestions that the features of the catalytic domain contribute significantly toward enzyme specificity.
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Affiliation(s)
- J L Lauer-Fields
- Department of Chemistry and Biochemistry, Florida Atlantic University, Boca Raton, Florida 33431-0991, USA.
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12
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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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Vinée P, Meurer B, Constantinesco A, Kohlberger B, Hauenstein KH, Laubenberger J. In vitro proton NMR study of collagen in human aortic wall. Magn Reson Med 1993; 29:292-5. [PMID: 8383787 DOI: 10.1002/mrm.1910290303] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The authors relate the findings in the 1H solid state line shape (at 60 MHz) of human aortic walls (n = 12) in native state and after histologically controlled selective lysis of collagen and elastin. An analysis of the line shape shows a composite free induction decay (FID) consisting of a low amplitude (3-7%) fast decaying component (T2 approximately 20 microseconds) and a slow decaying one (T2 > 1 ms). The fast component is identified as the protons of the collagen macromolecules. The second moment computed from the experimental fast component of the FID is in agreement with published studies examining the motional characteristics of collagen by multinuclear NMR employing spin labeling. A theoretical second moment is computed for the collagen macromolecular backbone from the atomic positions in the superhelix. Comparison with the observed experimental values allows determination of the step angle (29 degrees) of the fast rotational motion of the collagen strands along their long axis.
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Affiliation(s)
- P Vinée
- Laboratoire de Biomécanique, CHU Hautepierre, Strasbourg, France
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Holmes DF, Mould AP, Chapman JA. Morphology of sheet-like assemblies of pN-collagen, pC-collagen and procollagen studied by scanning transmission electron microscopy mass measurements. J Mol Biol 1991; 220:111-23. [PMID: 2067010 DOI: 10.1016/0022-2836(91)90385-j] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
At high concentrations, type I pN-collagen, pC-collagen and procollagen (the first 2 generated from procollagen by enzymic cleavage of C-propeptides and N-propeptides, respectively) can all be made to assemble in vitro into thin D-periodic sheets or tapes. Scanning transmission electron microscopy mass measurements show that the pN-collagen sheets and procollagen tapes have a mass per unit area corresponding to that of approximately 6.8 monolayers of close-packed molecules. pN-collagen sheets are extensive and remarkably uniform in mass thickness (fractional S.D. 0.035); procollagen tapes are neither as extensive nor as uniform in thickness. The mean thickness of pC-collagen tapes is less and the variability is greater. In pN-collagen sheets, the overlap: gap mass contrast in a D-period is increased from 5:4 (the ratio in a native collagen fibril) to 6:4, showing that the N-propeptides do not project into the gap but are folded back over the overlap zone. Assuming all N-propeptides to be constrained to the two surfaces of a sheet, their surface density can be found from the mass thickness of the sheet. In a lateral direction (i.e. normal to the axial direction where the spacing is D-periodic), the N-propeptide domains are calculated to be spaced, centre to centre, by 2.23 (+/- 0.1) nm on both surfaces. This value (approx. 1.5 x the triple-helix diameter) implies close-packing laterally with adjacent domains in contact. Sheet formation and the "surface-seeking" behaviour of propeptides can be understood in terms of the dual character of the molecules, evident from solubility data, with propeptides possessing interaction properties very different from those displayed by the rest of the molecule. The form and stability of sheets (and of first-formed fibrils assembling in vivo) could, it is suggested, depend on the partially fluid-like nature of lateral contacts between collagen molecules.
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Affiliation(s)
- D F Holmes
- Department of Medical Biophysics, University of Manchester, England
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Abstract
A possible mechanism for regulating the lateral growth of collagen fibrils in vivo is considered. A growth inhibitor associated with a particular part of the long semiflexible collagen molecule restricts that part of the molecule to the surface of the growing assembly. Lateral accretion ceases when these inhibitors form a complete circumferential layer around the fibril surface. Cell-mediated removal of the inhibitors allows lateral growth to proceed to a second limiting layer, and so on to subsequent limiting layers. In this way, cycles of inhibitor removal and limited lateral accretion permit growth to be synchronized over large populations of fibrils. Observed diameter distributions in bundles of embryonic and neonatal fibrils are those expected from a mechanism of this kind. The mechanism depends on the existence of axial order (D-periodicity) in fibrils, but not on any specific lateral packing of molecules. Rather, contacts between newly assembled molecules are presumed to be partly fluid-like in lateral directions (except where covalent cross-links have formed). Some initial fluidity in lateral packing prior to cross-linking does not preclude the subsequent emergence of quasi-crystalline packing as cross-links form. The cylindrical shape of fibrils in vivo may also be attributable in part to fluidity of intermolecular contacts at the growing surface.
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Cole HB, Sparks SW, Torchia DA. Comparison of the solution and crystal structures of staphylococcal nuclease with 13C and 15N chemical shifts used as structural fingerprints. Proc Natl Acad Sci U S A 1988; 85:6362-5. [PMID: 3413101 PMCID: PMC281971 DOI: 10.1073/pnas.85.17.6362] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
We report high-resolution 13C and 15N NMR spectra of crystalline staphylococcal nuclease (Nase) complexed to thymidine 3',5'-diphosphate and Ca2+. High sensitivity and resolution are obtained by applying solid-state NMR techniques--high power proton decoupling and cross-polarization magic angle sample spinning (CPMASS)--to protein samples that have been efficiently synthesized and labeled by an overproducing strain of Escherichia coli. A comparison of CPMASS and solution spectra of Nase labeled with either [methyl-13C]methionine or [15N]valine shows that the chemical shifts in the crystalline and solution states are virtually identical. This result is strong evidence that the protein conformations in the solution and crystalline states are nearly the same. Because of the close correspondence of the crystal and solution chemical shifts, sequential assignments obtained in solution apply to the crystal spectra. It should therefore be possible to study the molecular structure and dynamics of many sequentially assigned atomic sites in Nase crystals. Similar experiments are applicable to the growing number of proteins that can be obtained from efficient expression systems.
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Affiliation(s)
- H B Cole
- Bone Research Branch, National Institute of Dental Research, Bethesda, MD 20892
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Mack JW, Torchia DA, Steinert PM. Solid-state NMR studies of the dynamics and structure of mouse keratin intermediate filaments. Biochemistry 1988; 27:5418-26. [PMID: 2460129 DOI: 10.1021/bi00415a006] [Citation(s) in RCA: 56] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The molecular dynamics and structural organization of mouse epidermal keratin intermediate filaments (IF) have been studied via solid-state nuclear magnetic resonance (NMR) experiments performed on IF labeled both in vivo and in vitro with isotopically enriched amino acids. As a probe of the organization of the peripheral glycine-rich end domains of the IF, carbon-13 NMR experiments have been performed on subfilamentous forms (prekeratin) and on IF reassembled in vitro that had been labeled with either [1-13C]glycine or [2-13C]glycine, as more than 90% of the glycines of the keratins are located in the end domains. Although cross-labeling to seryl residues was observed, the proportion of serine located in the end domains is nearly the same as that for glycine. Measurements of carbon relaxation times, nuclear Overhauser enhancements, and signal intensities show that the motions of the peptide backbone in the end domains are effectively isotropic, with average correlation times distributed over the range of 0.2-20 ns. These results indicate that the end domains of IF are remarkably flexible and have little or no structural order. To probe the structural organization of the coiled-coil rod domains of the IF, separate samples of native keratin IF, raised in primary tissue culture, were labeled with L-[1-13C]leucine, L-[2H10]leucine, or L-[2,3,3-2H3]leucine, as greater than 90% of the leucyl residues of the keratin IF types studied are located in the coiled coils which form the central core of IF.(ABSTRACT TRUNCATED AT 250 WORDS)
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Affiliation(s)
- J W Mack
- Bone Research Branch, National Institute of Dental Research, Bethesda, Maryland 20892
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Freund I, Deutsch M, Sprecher A. Connective tissue polarity. Optical second-harmonic microscopy, crossed-beam summation, and small-angle scattering in rat-tail tendon. Biophys J 1986; 50:693-712. [PMID: 3779007 PMCID: PMC1329848 DOI: 10.1016/s0006-3495(86)83510-x] [Citation(s) in RCA: 345] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Connective tissue polarity has remained an intractable enigma for over two decades. We present new data on optical second harmonic generation in native, wet, rat-tail tendon. Scanning second-harmonic microscopy has revealed, for the first time, the existence of a discrete network of fine, polar, filamentous or columnar, structures, and, also, the presence of strongly polar surface, or near-surface patches. The thickness of these features was probed via crossed-beam optical frequency summation and the polar material is estimated to occupy a few percent of the tendon volume. The three-dimensional spatial distribution of filaments was studied with the aid of small-angle second-harmonic scattering, and the filaments were found to permeate the tendon cross-section in an apparently random fashion. These latter measurements also revealed that essentially all polar filaments had the same directionality. Concomitant studies of the polar collagen fibrils that comprise the bulk of tendon were in full accord with prior electron microscope results that had demonstrated that the directionality of these fibrils varies up/down in a purely random fashion, and thus cannot yield a net macroscopic polarity. Quantitative analysis of the second-harmonic data yields the conclusion that the observed polar structures cannot be simply local regions containing some accidental net excess of similarly oriented fibrils. The analytical expressions used in the analysis of the data obtained for this complex tissue were supported by extensive, realistic computer simulations. The discovery that the polarity of rat-tail tendon, and possibly other forms of connective tissue, resides in discrete structures, some of which are located near the tendon surface, should permit the ready isolation of polar-rich material for further study by a variety of techniques.
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Papatheofanis FJ. The contribution of acidic amino acids to biological calcification. Med Hypotheses 1985; 18:91-2. [PMID: 4069039 DOI: 10.1016/0306-9877(85)90123-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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Torchia DA, Hiyama Y, Sarkar SK, Sullivan CE, Young PE. Multinuclear magnetic resonance studies of collagen molecular structure and dynamics. Biopolymers 1985. [DOI: 10.1002/bip.360240107] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Saitô H, Tabeta R, Shoji A, Ozaki T, Ando I, Miyata T. A high-resolution 13C-NMR study of collagenlike polypeptides and collagen fibrils in solid state studied by the cross-polarization-magic angle-spinning method. Manifestation of conformation-dependent 13C chemical shifts and application to conformational characterization. Biopolymers 1984; 23:2279-97. [PMID: 6498301 DOI: 10.1002/bip.360231111] [Citation(s) in RCA: 88] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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26
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Eads TM, Mandelkern L. Backbone and side-chain motion in myosin, subfragment 1, and rod determined by natural abundance carbon-13 NMR. J Biol Chem 1984. [DOI: 10.1016/s0021-9258(18)90566-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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27
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Sarkar SK, Young PE, Sullivan CE, Torchia DA. Detection of cis and trans X-Pro peptide bonds in proteins by 13C NMR: application to collagen. Proc Natl Acad Sci U S A 1984; 81:4800-3. [PMID: 6589627 PMCID: PMC391578 DOI: 10.1073/pnas.81.15.4800] [Citation(s) in RCA: 57] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Heretofore the complexity of natural abundance spectra has precluded the use of 13C NMR to detect cis peptide bonds in proteins. We have incorporated [4-13C]proline into chicken calvaria collagen and report here well-resolved C gamma signals, arising from cis and trans X-Pro and X-Hyp peptide bonds (where X is any amino acid residue) in the 13C NMR spectrum of the thermally unfolded protein. Measurement of 13C signal areas shows that 16% of the X-Pro and 8% of X-Hyp bonds are cis in the unfolded collagen. These results strongly support the conclusion drawn from kinetic studies that cis-trans isomerization of peptide bonds is the rate-limiting step in helix propagation after nucleation. Our method can be applied to other proteins as well and should aid in testing the generality of the hypothesis of Brandts, Halvorson, and Brennan that cis-trans isomerization is the rate-limiting step in protein folding when proline is present.
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13C chemical shift and 13C-15N dipolar tensors for the peptide bond: [1-13C]glycyl[15N]glycine·HCl·H2O. ACTA ACUST UNITED AC 1983. [DOI: 10.1016/0022-2364(83)90238-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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29
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Sarkar SK, Sullivan CE, Torchia DA. Solid state 13C NMR study of collagen molecular dynamics in hard and soft tissues. J Biol Chem 1983. [DOI: 10.1016/s0021-9258(17)44563-7] [Citation(s) in RCA: 52] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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30
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31
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Cross TA, Opella SJ. Protein dynamics by solid-state nuclear magnetic resonance spectroscopy. Peptide backbone of the coat protein in fd bacteriophage. J Mol Biol 1982; 159:543-9. [PMID: 7166755 DOI: 10.1016/0022-2836(82)90301-1] [Citation(s) in RCA: 35] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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32
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Batchelder LS, Sullivan CE, Jelinski LW, Torchia DA. Characterization of leucine side-chain reorientation in collagen-fibrils by solid-state 2H NMR. Proc Natl Acad Sci U S A 1982; 79:386-9. [PMID: 6952191 PMCID: PMC345746 DOI: 10.1073/pnas.79.2.386] [Citation(s) in RCA: 79] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
We have used 2H quadrupole-echo NMR spectroscopy to study the molecular dynamics of the leucine side chain in collagen fibrils labeled with [2H10]leucine. X-ray crystallographic studies of leucine and small leucyl-containing peptides and proteins [Benedetti, C. (1977) in Proceedings of the Fifth American Peptides Symposium, eds, Goodman, M. & Meienhofer, J. (Wiley, New York), pp. 257--274; Janin, J., Wodak, S., Levitt, M. & Maigret, B. (1978) J. Mol. Biol. 125, 357--386] show that the amino acid side chain exists predominantly in only two of the nine possible conformations. 2H NMR spectra of polycrystalline D,L [2H10]leucine obtained from -45 degrees C to +100 degrees C showed that interconversion of the two conformations did not take place on the 2H NMR timescale in this temperature range. In contrast, experimental lineshapes observed for [2H10]leucine-labeled collagen fibrils from -85 degrees C to +30 degrees C were simulated by using a model in which the side chain hops at various rates between the two predominant conformations found by the x-ray studies. A small difference between calculated and observed linewidths above the freezing point of water can be accounted for by backbone reorientation or by the presence of a small percentage of other side-chain conformations. Thus, these results provide strong evidence that the two predominant x-ray conformations not only exist in the fibrils as the preferred orientations but interconvert at rates that are proportional to temperature over the range - 85 degrees C to +30 degrees C. These observations concur with previous NNR studies of collagen fibrils that demonstrated a mobile contact region between collagen molecules.
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Silver FH. A molecular model for linear and lateral growth of type I collagen fibrils. COLLAGEN AND RELATED RESEARCH 1982; 2:219-29. [PMID: 7151387 DOI: 10.1016/s0174-173x(82)80016-2] [Citation(s) in RCA: 35] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
A model is proposed for Type I collagen fibrillogenesis in which linear and lateral growth are directed by attractive charged pair interactions. It is suggested that linear growth decreases the rate of rotational motion resulting in an increased rate of lateral collisions. The mechanism of linear aggregation involves interactions between sets of unusual charged pairs located at positions 53, 54 and 56 and positions 990 and 992 as well as in the non-helical ends. These charged pairs attract each other electrostatically as well as form a hydrophobic pocket between the molecules. Lateral growth occurs by attractions between D-staggered, charged pairs which alternate between intra- and interchain states. Interchain interactions lead to lateral association of neighboring molecules and formation of a D-staggered unit containing five trimers. Rotational motion of the triple-helical backbone as well as the ability of charged pairs in their interchain state to interact by several different possible combinations between alpha-chains suggest that lateral packing of collagen molecules into fibrils at least in vitro may not need to be specific.
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35
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36
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Torchia D, Hasson M, Hascall V. 13C nuclear magnetic resonance suggests a flexible proteoglycan core protein. J Biol Chem 1981. [DOI: 10.1016/s0021-9258(19)68935-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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37
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Silver FH, Trelstad RL. Physical properties of type I collagen in solution: structure of alpha-chains and beta- and gamma-components and two-component mixtures. Biopolymers 1981; 20:359-371. [PMID: 7459424 DOI: 10.1002/bip.1981.360200208] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- F H Silver
- Department of Pathology, Shriners Burns Institute and Massachusetts General Hospital, and Harvard Medical School, Boston, Massachusetts 02114
| | - R L Trelstad
- Department of Pathology, Shriners Burns Institute and Massachusetts General Hospital, and Harvard Medical School, Boston, Massachusetts 02114
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Jelinski LW, Sullivan CE, Batchelder LS, Torchia DA. Deuterium nuclear magnetic resonance of specifically labeled native collagen. Investigation of protein molecular dynamics using the quadrupolar echo technique. Biophys J 1980; 32:515-29. [PMID: 7248459 PMCID: PMC1327347 DOI: 10.1016/s0006-3495(80)84987-3] [Citation(s) in RCA: 33] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Collagen was labeled with [3,3,3-d3]alanine and with [d10]leucine via tissue culture. 2H nuclear magnetic resonance (NMR) spectra were obtained of collagen in solution and as fibrils using the quadrupolar echo technique. The 2H NMR data for [3,3,3-d3]alanine-labeled collagen fibrils were analyzed in terms of a model for motion in which the molecule is considered to jump between two sites, separated azimuthally by an angle 2 delta, in a time which is rapid compared with the residence time in both sites. The data suggest that the molecule undergoes reorientation over an angle, 2 delta, of approximately 30 degrees in the fibrils, and that the average angle between the alanine C alpha--C beta bond axis and the long axis of the helix is approximately 75 degrees. Reorientation is possibly segmental. The T2 for [3,3,3-d3]alanine-labeled collagen fibrils was estimated to be 105 mus. The 2H NMR data for the methyl groups of [d10]leucine-labeled collagen were analyzed qualitatively. These data established that for collagen in solution and as fibrils, rotation occurs about the leucine side-chain bonds, in addition to threefold methyl rotation and reorientation of the peptide backbone. The T2 for the methyl groups of leucine-labeled collagen is estimated to be approximately 130 mus. Taken together, these data provide strong evidence that both polypeptide backbone reorientation and amino acid side-chain motion occur in collagen molecules in the fibrils. Stabilizing interactions that determine fibril structure must therefore depend upon at least two sets of contacts in any given local region.
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Gelman R, Piez K. Collagen fibril formation in vitro. A quasielastic light-scattering study of early stages. J Biol Chem 1980. [DOI: 10.1016/s0021-9258(19)70613-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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41
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Abstract
A three-dimensional crystal model for packing of collagen molecules (type I) in the native fibril has recently been proposed by Hulmes and Miller. It provides a straightforward explanation of the major features of the X-ray diffraction pattern, and is consistent with measurements of fibril density. However, there is independent evidence for a well defined microfibrillar substructure, which is absent from their model. This evidence, which is derived from electron microscopy and studies of in vitro assembly, the pattern of covalent crosslinks and sequence analysis, is convincing. Therefore, we have searched for a means to reconcile this conflict. We now propose two models which contain five-stranded microfibrils compressed to place molecules (in cross-section) on a pseudohexagonal lattice. The unit cells are equivalent or related to the cell proposed by Hulmes and Miller. In the simplest case, molecules, and thus microfibrils, are straight-tilted. However, it is not ruled out that molecules are supercoiled and microfibrils are straight. Noncrystallographic considerations favour supercoiling.
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Abstract
Collagen was labelled through tissue culture with [3,3,3-d3]alanine. 2HNMR spectra were obtained of the labelled collagen as fibrils and in solution using the quadrupolar echo technique for solids. The 2H NMR data were analysed in terms of a model for reorientation in which the molecule is considered to jump between two orientations in a time which is short compared to the residence time in each site, and short compared to (delta vq)-1. The best fit of the data indicates that the collagen molecule in the fibrils experiences reorientation about its long axis over an angular range of approximately 30--40 degrees. The T2 for [3,3,3-d3]alanine-labelled collagen fibrils is estimated to be approximately 110 mus.
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43
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Jelinski LW, Torchia DA. Investigation of labeled amino acid side-chain motion in collagen using 13C nuclear magnetic resonance. J Mol Biol 1980; 138:255-72. [PMID: 7411609 DOI: 10.1016/0022-2836(80)90286-7] [Citation(s) in RCA: 38] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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44
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Termine JD, Torchia DA. 13C-1H magnetic double-resonance study of fetal enamel matrix proteins. Biopolymers 1980. [DOI: 10.1002/bip.1980.360190403] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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45
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Fleming WW, Sullivan CE, Torchia DA. Characterization of molecular motions in 13C-labeled aortic elastin by 13C-1H magnetic double resonance. Biopolymers 1980; 19:597-617. [PMID: 7357071 DOI: 10.1002/bip.1980.360190311] [Citation(s) in RCA: 37] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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46
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47
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Hilton BD, Woodward CK. On the mechanism of isotope exchange kinetics of single protons in bovine pancreatic trypsin inhibitor. Biochemistry 1979; 18:5834-41. [PMID: 42434 DOI: 10.1021/bi00593a013] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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