Investigations on geometrical features in induced ordering of collagen by small molecules

Journal of Chemical Sciences (Impact Factor: 1.19). 10/2003; 115(5):751-766. DOI: 10.1007/BF02708265


Binding energies of the interaction of collagen like triple helical peptides with a series of polyphenols, viz. gallic acid,
catechin, epigallocatechingallate and pentagalloylglucose have been computed using molecular modelling approaches. A correlation
of calculated binding energies with the interfacial molecular volumes involved in the interaction is observed. Calculated
interface surface areas for the binding of polyphenols with collagen-like triple helical peptides vary in the range of 60–210
Å2 and hydrogen bond lengths vary in the range of 2.7–3.4 Å. Interfacial molecular volumes can be calculated from the solvent
inaccessible surface areas and hydrogen bond lengths involved in the binding of polyphenols to collagen. Molecular aggregation
of collagen in the presence of some polyphenols and chromium (III) salts has been probed experimentally in monolayer systems.
The monolayer arrangement of collagen seems to be influenced by the presence of small molecules like formaldehyde, gluteraldehyde,
tannic acid and chromium (III) salts. A fractal structure is observed on account of two-dimensional aggregation of collagen
induced by tanning species. Atomic force microscopy has been employed to probe the topographic images of two-dimensional aggregation
of collagen induced by chromium (III) salts. A case is made that long-range ordering of collagen by molecular species involved
in its stabilisation is influenced by molecular geometries involved in its interaction with small molecules.

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Available from: Balaraman Madhan
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    • "With regard to the bioinformatics on cross-linking chemistry of collagen, only very few reports are available collagen with polyphenols [12], and with alginic acid [13]. In order to select the suitable cross-linkers for the preparation of collagen based biomaterials, in the present study we made an attempt on bioinformatics in cross linking of selected cross linkers coenzyme Q10, dopaquinone, embelin, embelin complex-1 & 2, idebenone, 5-O-methyl embelin, potassium embelate (unless otherwise mentioned without potassium metal) and vilangin with collagen of both Type I and Type III. "
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    ABSTRACT: ABSTRACT: Identifying the molecular interactions using bioinformatics tools before venturing into wet lab studies saves the energy and time considerably. The present study summarizes, molecular interactions and binding energy calculations made for major structural protein, collagen of Type I and Type III with the chosen cross-linkers, namely, coenzyme Q10, dopaquinone, embelin, embelin complex-1 & 2, idebenone, 5-O-methyl embelin, potassium embelate and vilangin. Molecular descriptive analyses suggest, dopaquinone, embelin, idebenone, 5-O-methyl embelin, and potassium embelate display nil violations. And results of docking analyses revealed, best affinity for Type I (- 4.74 kcal/mol) and type III (-4.94 kcal/mol) collagen was with dopaquinone. Among the selected cross-linkers, dopaquinone, embelin, potassium embelate and 5-O-methyl embelin were the suitable cross-linkers for both Type I and Type III collagen and stabilizes the collagen at the expected level.
    Full-text · Article · Oct 2011 · BMC Research Notes
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    ABSTRACT: Collagen is an extremely important protein, which provides mechanical strength and structural integrity to various connective tissues. Ramachandran and his coworkers had proposed the triple helical structure for collagen employing fiber diffraction theory with stereochemical consideration. Due to its unique triple helical motif an understanding of the amino acid sequence-dependent stability of polypeptides is of renowned interest to the biophysicists and biochemists, in order to identify the nature of forces that stabilizes the three dimensional structure of proteins. Mutation in collagen genes COL1A1 and COL1A2 leads to Osteogenesis Imperfecta (OI), a brittle bone disease Often a point mutation in one of type I collagen genes can cause disease. Hence it is necessary to probe the stability of collagen upon mutation. In this study, the role of various collagen triplets influencing the stability of collagen has been addressed using various molecular modeling tools. In addition interaction of collagen like model peptides with polyphenol molecules have also been investigated to gain how various small molecules stabilizes the collagen matrix. The importance of geometrical features of polyphenol molecules has also been probed with the help of ab initio and molecular mechanics methods. Bioinformatic analysis has also been attempted on various types of collagen.
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    ABSTRACT: The change in the stability and conformational dynamics of a collagen-like microfibril segment (CMS), 23 amino acid residues long (around 5[3(GLY-X-Y) 8 ]), as a result of the interaction with water, formaldehyde, and gallic acid is studied by performing a series of nanosecond molecular dynamics simulations. Major changes in the conformation of CMS occur when interacting with water while in the other solutions: (1) pure formaldehyde, (2) 8.0% (v/v) formaldehyde/water, and (3) 1.4% (v/v) gallic acid/water; the variation is less evident. Possible CMS/modifying agents' binding sites are evidenced by the analysis of radial distribution functions, coordination number, and H-bonding network. In particular, in the case of formaldehyde a high preference for ARG, LYS, and GLN residues is found. Gallic acid molecules preferably bind to PRO and HPR residues. The examination of average interaction energies per residue and their van der Waals and electrostatic components confirms the results obtained with the structural analysis. Furthermore, both van der Waals and electrostatic terms are important for the stabilization of the CMS. This is especially noted when CMS interacts with gallic acid. A comparison between calculated and available experimental findings is proposed. The agreement is very satisfactory, thus validating the computational approach to these systems.
    Full-text · Article · Jul 2004 · The Journal of Physical Chemistry B
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