Hostname: page-component-cd9895bd7-gxg78 Total loading time: 0 Render date: 2024-12-29T14:14:37.511Z Has data issue: false hasContentIssue false
  • English
  • Français

Conformational theory applied to polysaccharide structure

Published online by Cambridge University Press:  17 March 2009

David A. Brant
David A. Brant
Affiliation:
Department of Chemistry, University of California, Irvine, California 92717
Get access Rights & Permissions [Opens in a new window]

Extract

Theoretical methods of conformational analysis have been applied to the biopolymers with beneficial consequences for the elucidation of structure–function relationships in these molecules. The methodology of theoretical conformational analysis and the fruits of its application to the biopolymers, particularly the polypeptides, have been the subject of numerous reviews (Ramachandran & Sasisekharan, 1968; Scheraga, 1968; Venkatachalam & Ramachandran, 1969; Scheraga, 1971; Brant, 1972; Hopflnger, 1973). A critical evaluation of these techniques as applied to the polynucleotides has recently appeared (Olson, 1975 a, b).

Type
Research Article
Information
Quarterly Reviews of Biophysics , Volume 9 , Issue 4 , November 1976 , pp. 527 - 596
Copyright
Copyright © Cambridge University Press 1976

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

References

REFERENCES

Allen, L. C. (1975). A simple model of hydrogen bonding. J. Am. chem. Soc. 97, 6921–40.Google Scholar
Arnott, S. & Scott, W. E. (1972). Accurate X-ray diffraction analysis of fibrous polysaccharides containing pyranose rings. I. The linked atom approach. J. Chem. Soc. Perkin II, 324–35.CrossRefGoogle Scholar
Aspinall, G. O. (1970). Polysaccharides. New York: Pergamon Press.Google Scholar
Banks, W. & Greenwood, C. T. (1975). Starch and its Components. Edinburgh University Press.Google Scholar
Birshtein, T. M. & Ptitsyn, O. B. (1966). Conformation of Macromolecules. (English translation.) New York: Wiley-Interscience.Google Scholar
Bowen, H. J. M. & Sutton, L. E. (eds.) (1958). Tables of Interatomic Distances and Configuration in Molecules and Ions. The Chemical Society (London). Supplement, 1965.Google Scholar
Brant, D. A. (1968). Conformational energy estimates for helical polypeptide molecules. Macromolecules I, 295–300;Google Scholar
Ibid 2, 220.Google Scholar
Brant, D. A. (1972). Conformational analysis of biopolymers: Conformational energy calculations. A. Rev. Biophys. Bioeng. I, 369–408.CrossRefGoogle Scholar
Brant, D. A., Miller, W. G. & Flory, P. J. (1967). Conformational energy estimates for statistically coiling polypeptide chains. J. molec. Biol. 23, 47–65.Google Scholar
Brant, D. A. & Dimpfl, W. L. (1970). A theoretical interpretation of the aqueous solution properties of amylose and its derivatives. Macromolecules 3, 655–64.Google Scholar
Brant, D. A. & Goebel, K. D. (1975). A general treatment of the configurational statistics of polysaccharides. Macromolecules 8, 522–30.Google Scholar
Cael, J. J., Koenig, J. L. & Blackwell, J. (1974). Infrared and raman spectroscopy of carbohydrates. IV. Identification of configuration- and conformation-sensitive modes for D-glucose by normal coordinate analysis. Carbohydr. Res. 32, 79–91.Google Scholar
Cael, J. J., Gardner, K. H., Koenig, J. L. & Blackwell, J. (1975 a). Infrared and raman spectroscopy of carbohydrates. V. Normal coordinate analysis of cellulose I. J. chem. Phys. 62, 1145–53.Google Scholar
Cael, J. J., Koenig, J. L. & Blackwell, J. (1975 b). Infrared and raman spectroscopy of carbohydrates. VI. Normal coordinate analysis of Vamylose. Biopolymers 14, 1885–1903.Google Scholar
Cahn, R. S., Ingold, C. K. & Prelog, V. (1966). Specification of molecular chirality. Angew. Chem., int. Ed. Engi. 5, 385–415, 515.Google Scholar
Cleland, R. L. (1971). Ionic polysaccharides. V. Conformational studies of hyaluronic acid, cellulose, and laminarin. Biopolymers 10, 1925–48.Google Scholar
Cook, G. M. W. & Stoddart, R. W. (1973). Surface Carbohydrates of the Eukaryotic Cell. London: Academic Press.Google Scholar
Cremer, D. & Pople, J. A. (1975). A general definition of ring puckering coordinates. J. Am. chem. Soc. 97, 1354–8.Google Scholar
Cross, R. J. Jr, Determination of intermolecular potentials using high-energy molecular beams. Accts. Chem. Res. 8, 225–30.CrossRefGoogle Scholar
De, Voe H. (1967). Theory of the conformations of biological macromolecules in solution. Structure and Stability of Biological Macromolecules (ed. Timasheff, S. N. and Fasman, G. D.), pp. 1–63. New York: Marcel Dekker.Google Scholar
Ditchfield, R., Hehre, W. J. & Pople, J. A. (1971). Self-consistentmolecularorbital methods. IX. An extended gaussian-type basis for molecular orbital studies of organic molecules. J. chem. Phys. 54, 724–8.Google Scholar
Donohue, J. (1968). Structural Chemistry and Molecular Biology (ed. Rich, A. and Davidson, N.), pp. 443–65. San Francisco: Freeman.Google Scholar
Dubin, P. L. & Brant, D. A. (1973). The aqueous solution configuration of amylose in the presence of helicogenic complexing agents. Polym. Prepr. Am. Chem. Soc. Div. Polym. Chem. 14, 169–74.Google Scholar
Dubin, P. L. & Brant, O. A. (1975). Charge induced conformational changes in carboxymethylamylose. Macromolecules 8, 831–42.CrossRefGoogle Scholar
Dunfield, L. G. & Whittington, S. G. (1974). Influence of the alternate chair conformation on the unperturbed dimensions of alginic acid. Macromolecules 7, 946–8.Google Scholar
Eliel, E. L., Allinger, N. L., Angyal, S. J. & Morrison, G. A. (1965). Conformational Analysis. New York: Wiley-Interscience.Google Scholar
Engler, E. M., Andose, J. O. & Schleyer, P.Von, R. (1973). Critical evaluation of molecular mechanics. J. Am. chem. Soc. 95, 8005–25.Google Scholar
Flory, P. J. (1953). Principles of Polymer Chemistry. Ithaca, New York: Cornell University Press.Google Scholar
Flory, P. J. (1969). Statistical Mechanics of Chain Molecules. New York: Wiley-Interscience.Google Scholar
Flory, P. J. (1971). Configuration dependent properties of polymer chains. Pure appl. Chem. 26, 309–26.Google Scholar
Flory, P. J. (1973). Molecular configuration in bulk polymers. Pure appl. Chem., Macromol. Chem. 8, 1–15.Google Scholar
Flory, P. J. (1974) Foundations of rotational isomeric state theory and general methods for generating configurational averages. Macromolecules 7, 381–92.CrossRefGoogle Scholar
French, A. D. & Murphy, V. G. (1973). The effects of changes in ring geometry on computer models of amylose. Carbohydr. Res. 27, 391–406.Google Scholar
Fu, Y.-C., McGuire, R. F. & Scheraga, H. A. (1974). Intermolecular potentials from crystal data. V. Crystal packing of poly [β(pchlorobenzyl)-L-aspartate]. Macromolecules 7, 468–80.Google Scholar
Gardner, K. H. & Blackwell, J. (1974). The structure of native cellulose. Biopolymers 13, 1975–2001.Google Scholar
Gibson, K. D. & Scheraga, H. A. (1967). Minimization of polypeptide energy. I. Preliminary structures of bovine pancreatic ribonuclease S-peptides. Proc. natn. Acad. Sci. U.S.A. 58, 420–7.Google Scholar
Gō, N. & Scheraga, H. A. (1969). Analysis of the contribution of internal vibrations to the statistical weights of equilibrium conformations of macromolecules. J. chem. Phys. 51, 4751–67.Google Scholar
Gō, N. & Scheraga, H. A. (1970). Ring closure and local conformational deformations of chain molecules. Macromolecules 3, 178–87.Google Scholar
Gō, N. & Scheraga, H. A. (1973). Ring closure in chain molecules with Cn, I or S2n, symmetry. Macromolecules 6, 273–81.Google Scholar
Goebel, C. V., Dimpfl, W. L. & Brant, D. A. (1970). The conformational energy of maltose and amylose. Macromolecules 3, 644–54.CrossRefGoogle Scholar
Goebel, K. D. & Brant, D. A. (1970). The configuration of amylose and its derivatives in aqueous solution. Experimental results. Macromolecules 3, 634–43.Google Scholar
Goebel, K. D., Harvie, C. E. & Brant, D. A. (1976). The configurational statistics of cellulosic chains. Applied Polymer Symposium 28, 671–691.Google Scholar
Gorin, P. A. J. & Spencer, J. T. F. (1968). Structural chemistry of fungal polysaccharides. Advan. Carbohyd. Chem. 23, 367–417.Google ScholarPubMed
Hagler, A. T., Huler, E. & Lifson, S. (1974). Energy functions for peptides and proteins. I. Derivation of a consistent force field including the hydrogen bond from amide crystals. J. Am. chem. Soc. 96, 5319–27.Google Scholar
Hallman, G. M. & Whittington, S. G. (1973). Conformational statistics of some copolysaccharides. Macromolecules, 6, 386–89.Google Scholar
Hendrickson, J. B. (1961). Molecular geometry. I. Machine computation of the common rings. J. Am. chem. Soc. 83, 4537–47.Google Scholar
Herschbach, D. R., Johnston, H. S. & Rapp, D. (1959). Molecular partition functions in terms of local properties. J. chein. Phys. 31, 1652–61.Google Scholar
Hill, T. L. (1956). Statistical Mechanics. New York: McGraw-Hill.Google Scholar
Hill, T. L. (1960). Introduction to Statistical Thermodynamics. Reading, Massachusetts: Addison-Wesley.Google Scholar
Hirschfelder, J. O., Curtiss, C. F. & Byrd, R. B. (1964). Molecular Theory of Gases and Liquids. New York: John Wiley.Google Scholar
Hopfinger, A. J. (1973). Conformational Properties of Macromolecules. New York: Academic Press.Google Scholar
Hybl, A., Rundle, R. E. & Williams, D. E. (1965). The crystal and molecular structure of the cyclohexaamylose–potassium acetate complex. J. Am. chem. Soc. 87, 2779–88.Google Scholar
Jamieson, G. A. & Greenwalt, T. J. (eds.) (1969). The Red Cell Membrane: Structure and Function. Philadelphia: J. P. Lippincott.Google Scholar
Jeffrey, G. A., Pople, J. A. & Radom, L. (1972). The application of ab initio molecular orbital theory to the anomeric effect. A comparison of theoretical predictions and experimental data on conformations and bond lengths in some pyranoses and methyl pyranosides. Carbohydr. Res. 25, 117–31.Google Scholar
Jeffrey, G. A., Pople, J. A. & Radom, L. (1974). The application of abinitio molecular orbital theory to structural moieties of carbohydrates. Carbohydr. Res. 38, 81–95.CrossRefGoogle Scholar
Joesten, M. O. & Schaad, L. J. (1974). Hydrogen Bonding. New York: Marcel Dekker.Google Scholar
Kaloustian, M. K. (1974). The electrostatic dimension in conformational analysis. J. chem. Educ. 51, 777–80.CrossRefGoogle Scholar
Kilpatrick, J. E., Pitzer, K. S. & Spitzer, R. (1947). The thermodynamics and molecular structure of cyclopentane. J. Am. chem. Soc. 69, 2483–8.CrossRefGoogle Scholar
Kitaygorodski, A. I. (1965). The principle of close packing and the condition of thermodynamic stability of organic crystals. Acta Crystallogr. 18, 585–90.Google Scholar
Krimm, S. & Venkatachalam, C. M. (1971). Free-energy calculations of the interactions of helical poly (L-proline) with water. Proc. natn. Acad. Sci. U.S.A. 68, 2468–71.Google Scholar
Levitt, M. & Warshel, A. (1975). Computer simulation of protein folding. Nature, Lond. 253, 694–8.Google Scholar
Lifson, S. & Oppenheim, I. (1960). Neighbor interactions and internal rotations in polymer molecules. IV. Solvent effect on internal rotations. J. chem. Phys. 33, 109–15.Google Scholar
Lifson, S. & Warshel, A. (1968). Consistent force field calculations of conformations, vibrational spectra, and enthalpies of cycloalkane and n-alkane molecules. J. chem. Phys. 49, 5116–29.Google Scholar
Marchessault, R. H. (1975). Abbreviation and symbols for the description of conformation of polysaccharide chains. Draft SCBN/PS/7 of the IUPAC-IUB Subcommission on Biochemical Nomenclature (Chairman: R. H. Marchessault.).Google Scholar
McCullough, R. L. & Lindenmeyer, P. H. (1972). An analysis of limiting conditions on empirical non-bonded potential functions. Kolloid-Z. u. Z. Polymere 250, 440-52.Google Scholar
McGuire, R. F., Momany, F. A. & Scheraga, H. A. (1972). Energy parameters in polypeptides. V. An empirical hydrogen bond potential function based on molecular orbital calculations. J. Phys. Chem. 76, 375–93.Google Scholar
McGuire, R. F., Vanderkooi, G., Momany, F. A., Ingwall, R. T., Crippen, G. M., Lotan, N., Tuttle, R. W., Kashuba, K. L. & Scheraga, H. A. (1971). Determination of intermolecular potentials from crystal data. II. Crystal packing with applications to poly (amino acids). Macromolecules 4, 112–24.Google Scholar
Miller, W. G., Brant, O. A. & Flory, P. J. (1967). Random coil configurations of polypeptide copolymers. J. molec. Biol. 23, 67–80.CrossRefGoogle Scholar
Momany, F. A., Vanderkooi, G. & Scheraga, H. A. (1968). Determination of intermolecular potentials from crystal data. I. General theory and application to crystalline benzene at several temperatures. Proc. natn. Acad. Sd. U.S.A. 61, 429–36.Google Scholar
Murphy, V. G. & French, A. D. (1975). The structure of V-amylose dehydrate: A combined X-ray and stcreochemical approach. Biopolymers 14, 1487–1501.Google Scholar
Nelson, D. J. & Hermans, J. Jr, (1973). Non-bonded interatomic potential functions and crystal structure. Correction of the functions for use with macromolecules and application to polypeptide helixes. Biopolymers 12, 1269–84.CrossRefGoogle Scholar
Nicholson, G. L. (1974). The interactions of lectins with animal cell surfaces. int. Rev. Cytol. 39, 89–190.Google Scholar
Nigam, V. N. & Cantero, A. (1973). Polysaccharides in cancer: Glycoproteins and glycolipids. Adv. Cancer Res. 27, 1–80.Google Scholar
Olson, W. K. (1975 a). Configuration-dependent properties of randomly coiling polynucleotide chains. I. A comparison of theoretical energy estimates. Biopolymers 14, 1775–95.Google Scholar
Olson, W. K. (1975b). Configuration-dependent properties of randomly coiling polynucleotide chains. II. The role of the phosphodiester linkage. Biopolymers 14, 1797–1810.Google Scholar
Orville-Thomas, W. J. (1974). Internal Rotation in Molecules. New York: Wiley-Interscience.Google Scholar
Pickett, H. M. & Strauss, H. L. (1970). Conformational structure, energy, and inversion rates of cyclohexane and some related oxanes. J. Am. chem. Soc. 92, 7281–90.Google Scholar
Pitzer, K. S. (1959). Inter- and intramolecular forces and molecular polarizability. Adv. chem. Phys. 2, 59–83.Google Scholar
Poland, D. & Scheraga, H. A. (1967). Energy parameters in polypeptides. I. Charge distributions and the hydrogen bond. Biochemistry, 6, 3791–800.Google Scholar
Pople, J. A. & Beveridge, D. L. (1970). Approximate Molecular Orbital Theory. New York: McGraw-Hill.Google Scholar
Potenzone, R. Jr & Hopfinger, A. J. (1975). Conformational analysis of glycosaminoglycans. I. Charge distributions, torsional potentials, and steric maps. Carbohydr. Res. 40, 323–36.Google Scholar
Quintarelli, G. (ed.) (1968). The Chemical Physiology of Mucopolysaccharides. Boston: Little, Brown.Google Scholar
Ramachandran, G. N. & Sasiserharan, V. (1968). Conformations of polypeptides and proteins. Adv. Protein Chem. 23, 283–439.Google Scholar
Rao, V. S. R., Vijayalakshmi, K. S. & Sundararajan, P. R. (1971). Theoretical studies on the conformation of aldohexopyranoses. Carbohydr. Res. 17, 341–52.CrossRefGoogle ScholarPubMed
Rao, V. S. R., Yathindra, N. & Sundararajan, P. R. (1969). Configurational statistics of polysaccharide chains. I. Amylose. Biopolymers 8, 325–33.Google Scholar
Rees, D. A. (1972). Polysaccharide gels. A molecular view. Chemy ind. no. 16, pp. 630–6.Google Scholar
Rees, O. A. & Scott, W. E. (1971). Polysaccharide conformation. VI. Computer model-building for linear and branched pyranoglycans. Correlations with biological function. Preliminary assessment of inter-residue forces in aqueous solution. Further interpretation of optical rotation in terms of chain conformation. J. chem. Soc. B, pp. 469–79.Google Scholar
Sarko, A. & Muggli, R. (1974). Packing analysis of carbohydrates and polysaccharides. III. Valonia cellulose and cellulose II. Macromolecules 7, 486–94.CrossRefGoogle Scholar
Scheraga, H. A. (1968). Calculations of conformations of polypeptides. Advan. Phys. Org. Chem. 6, 103–84.Google Scholar
Scheraga, H. A. (1971). Theoretical and experimental studies of conformations of polypeptides. Chem. Rev. 71, 195–217.Google Scholar
Schroeder, R. & Lippincott, E. R. (1957). Potential function model of hydrogen bonds: II. J. Phys. Chem., Ithaca 61, 921–28.CrossRefGoogle Scholar
Schwarz, J. C. P. (1973). Rules for conformation nomenclature for five- and six-membered rings in monosaccharides and their derivatives. J. chem. Soc. Chem. Comm. 505–508.Google Scholar
Stacy, M. & Barker, S. A. (1962). Carbohydrates in Living Tissues. London: Van Nostrand.Google Scholar
Stoddart, J. F. (1971). Stereochemistry of Carbohydrates. New York: John Wiley.Google Scholar
Suggett, A. (1975). Water. A Comprehensive Treatise, vol. 4 (ed. Franks, F.), pp. 519–67. New York: Plenum Press.Google Scholar
Tanner, D. W. & Berry, G. C. (1974) Properties of cellulose acetate in solution. I. Light scattering, osmometry, and viscometry on dilute solutions. J. Polym. Sci.: Polym. Phys. Ed. 12, 941–75.Google Scholar
Venkatachalam, C. M. & Ramachandran, G. N. (1969). Conformation of polypeptide chains. A. Rev. Biochem. 38, 45–82.Google Scholar
Vijayalakshmi, K. S. & Rao, V. S. R. (1973). Theoretical studies on the conformations of aldohexopyranose pentaacetates. Carbohydr. Res. 29, 427–37.Google Scholar
Volkenstein, M. V. (1963). Configuration Statistics of Polymeric Chains (English trans.). New York: Wiley-Interscience.Google Scholar
Warshel, A. & Lifson, S. (1970). Consistent force field calculations. II. Crystal structures, sublimation energies, molecular and lattice vibrations, molecular conformations, and enthalpies of alkanes. J. diem. Phys. 53, 582–94.Google Scholar
Whittington, S. G. (1971). Unperturbed dimensions of some I,4-linked homopolysaccharides. Macromolecules 4, 569–71.Google Scholar
Whittington, S. G. & Glover, R. M. (1972). Conformational statistics of I,3- and I,4-linked homopolysaccharides. Macromolecules 5, 55–8.Google Scholar
Williams, O. E. (1969). A method of calculating molecular crystal structures. Acta crystallogr. A 25, 464–70.Google Scholar
Wilson, E. B. JrDecius, J. C. & Cross, P. C.Molecular Vibrations. New York: McGraw-Hill.Google Scholar
Winter, W. T. & Sarko, A. (1974). Crystal and molecular structure of Vanhydrous amylose. Biopolymers 13, 1447–60.Google Scholar
Yathindra, N. & Rao, V. S. R. (1970). Configurational statistics of polysaccharide chains. II. Cellulose. Biopolymers 9, 783–90.Google Scholar
Yathindra, N. & Rao, V. S. R. (1971). Configurational statistics of polysaccharide chains. III. Linear β(I →4') xylan and mannan. Biopolymers 10, 1891–1900.Google Scholar
Zhdanov, Yu. A., Minkin, V. I., Minjaev, R. M. & Zacharov, I. I. (1973). Quantum chemistry of carbohydrates. III. Calculation of the electronic distribution in some carbohydrates by CNDO/2. Carbohydr. Res. 29, 405–411.Google Scholar
Zugenmaier, P. & Sarko, A. (1972 a). Non-bonded potential energy functions based on the dumb-bell model of diatomic molecules. Kolloid-Z. u. Z. Polymere 250, 434–9.Google Scholar
Zugenmaier, P. & Sarko, A. (1972 b). Packing analysis of carbohydrates and polysaccharides. I. Monosaccharides. Acta crystallogr. B 28, 3158–66.Google Scholar
Zugenmaier, P. & Sarko, A. (1976). Packing analysis of carbohydrates and polysaccharides. IV. A new method for detailed crystal structure refinement of polysaccharides and its application to V-amylose. (Submitted for publication.)Google Scholar