Microsecond kinetics in model single- and double-stranded amylose polymers† †Electronic supplementary information (ESI) available: Detailed structural definitions, methodological descriptions, analyses of the simulations and computed and experimental molecular properties are provided. See DOI: 10.10

Amylose, a component of starch with increasing biotechnological significance, is a linear glucose polysaccharide that self-organizes into single- and double-helical assemblies.

[1]  G. G. Stokes.  "J." , 1890, The New Yale Book of Quotations.

[2]  Albert,et al.  Food , 1917, Nature.

[3]  I. Mazin,et al.  Theory , 1934 .

[4]  R. E. Rundle,et al.  The Configuration of Starch in the Starch-Iodine Complex. IV. An X-Ray Diffraction Investigation of Butanol-Precipitated Amylose1 , 1943 .

[5]  C. Tanford.  Macromolecules , 1994, Nature.

[6]  W. Winter,et al.  Crystal and molecular structure of V‐anhydrous amylose , 1974 .

[7]  D. Cremer,et al.  General definition of ring puckering coordinates , 1975 .

[8]  F. D. Leeuw,et al.  The relationship between proton-proton NMR coupling constants and substituent electronegativities—I : An empirical generalization of the karplus equation , 1980 .

[9]  P. Zugenmaier,et al.  Detailed refinement of the crystal structure of Vh-amylose☆ , 1981 .

[10]  Shoji Harada,et al.  Interaction of Amylose with Iodine. II. Kinetic Studies of the Complex Formation by the Temperature-jump Method , 1982 .

[11]  W. L. Jorgensen,et al.  Comparison of simple potential functions for simulating liquid water , 1983 .

[12]  L. Napolitano.  Materials , 1984, Science.

[13]  C. Betzel,et al.  An Amylose Antiparallel Double Helix at Atomic Resolution , 1987, Science.

[14]  B. Pfannemüller.  Influence of chain length of short monodisperse amyloses on the formation of A- and B-type X-ray diffraction patterns , 1987 .

[15]  R. Dwek,et al.  Glycobiology , 2018, Biochimie.

[16]  A. Imberty,et al.  The double-helical nature of the crystalline part of A-starch. , 1988, Journal of molecular biology.

[17]  F. Eisenhaber,et al.  Monte carlo simulation of the hydration shell of double‐helical amylose: A left‐handed antiparallel double helix fits best into liquid water structure , 1992 .

[18]  K Schulten,et al.  VMD: visual molecular dynamics. , 1996, Journal of molecular graphics.

[19]  Wolfram Saenger,et al.  Strain-Induced "Band Flips" in Cyclodecaamylose and Higher Homologues. , 1998, Angewandte Chemie.

[20]  N. Cheetham,et al.  Amylose conformational transitions in binary DMSO/water mixtures , 1998 .

[21]  G. Sheldrick,et al.  V-Amylose at atomic resolution: X-ray structure of a cycloamylose with 26 glucose residues (cyclomaltohexaicosaose). , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[22]  Jiro Shimada,et al.  Conformation of Amylose in Aqueous Solution: Small-Angle X-ray Scattering Measurements and Simulations , 2000 .

[23]  R. Hancock,et al.  The Other Double Helix—The Fascinating Chemistry of Starch , 2000 .

[24]  R. Parker,et al.  Aspects of the Physical Chemistry of Starch , 2001 .

[25]  W. V. van Gunsteren,et al.  A fast SHAKE algorithm to solve distance constraint equations for small molecules in molecular dynamics simulations , 2001 .

[26]  Paramita Dasgupta,et al.  NMR and modelling studies of disaccharide conformation. , 2003, Carbohydrate research.

[27]  H. Breitinger.  Synthesis and characterization of 2,3-di-O-alkylated amyloses: hydrophobic substitution destabilizes helical conformation. , 2003, Biopolymers.

[28]  Wieslaw Nowak,et al.  Elastic properties of single amylose chains in water: a quantum mechanical and AFM study. , 2004, Journal of the American Chemical Society.

[29]  W. Goddard,et al.  M3B: A Coarse Grain Force Field for Molecular Simulations of Malto-Oligosaccharides and Their Water Mixtures , 2004 .

[30]  宁北芳,et al.  疟原虫var基因转换速率变化导致抗原变异[英]／Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A , 2005 .

[31]  Holger Gohlke,et al.  The Amber biomolecular simulation programs , 2005, J. Comput. Chem..

[32]  M. Kuttel,et al.  Free energy surfaces for the alpha(1 --> 4)-glycosidic linkage: implications for polysaccharide solution structure and dynamics. , 2005, The journal of physical chemistry. B.

[33]  M. Akashi,et al.  Partially-methylated amyloses as effective hosts for inclusion complex formation with polymeric guests. , 2007, Chemical communications.

[34]  Mohsen Tafazzoli,et al.  New Karplus equations for 2JHH, 3JHH, 2JCH, 3JCH, 3JCOCH, 3JCSCH, and 3JCCCH in some aldohexopyranoside derivatives as determined using NMR spectroscopy and density functional theory calculations. , 2007, Carbohydrate research.

[35]  Karl Nicholas Kirschner,et al.  GLYCAM06: A generalizable biomolecular force field. Carbohydrates , 2008, J. Comput. Chem..

[36]  Carsten Kutzner,et al.  GROMACS 4:  Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation. , 2008, Journal of chemical theory and computation.

[37]  R. Sjöholm,et al.  Complete assignments of the (1)H and (13)C chemical shifts and J(H,H) coupling constants in NMR spectra of D-glucopyranose and all D-glucopyranosyl-D-glucopyranosides. , 2008, Carbohydrate research.

[38]  Tamar Schlick,et al.  Molecular dynamics-based approaches for enhanced sampling of long-time, large-scale conformational changes in biomolecules , 2009, F1000 biology reports.

[39]  M. Burghammer,et al.  Crystal Structure of A-amylose: A Revisit from Synchrotron Microdiffraction Analysis of Single Crystals , 2009 .

[40]  M J Harvey,et al.  ACEMD: Accelerating Biomolecular Dynamics in the Microsecond Time Scale. , 2009, Journal of chemical theory and computation.

[41]  W. V. Gunsteren,et al.  On the Conformational Properties of Amylose and Cellulose Oligomers in Solution , 2009 .

[42]  J. L. Willett,et al.  DFT conformation and energies of amylose fragments at atomic resolution. Part 2: 'Band-flip' and 'kink' forms of alpha-maltotetraose. , 2009, Carbohydrate research.

[43]  David P. Anderson,et al.  High-Throughput All-Atom Molecular Dynamics Simulations Using Distributed Computing , 2010, J. Chem. Inf. Model..

[44]  Benedict M. Sattelle,et al.  Free energy landscapes of iduronic acid and related monosaccharides. , 2010, Journal of the American Chemical Society.

[45]  Jens Krüger,et al.  Structural Stability of V-Amylose Helices in Water-DMSO Mixtures Analyzed by Molecular Dynamics. , 2011, Journal of chemical theory and computation.

[46]  M. B. Cardoso,et al.  Helical Conformation in Crystalline Inclusion Complexes of V-Amylose: A Historical Perspective , 2011 .

[47]  入江 正浩,et al.  Bull. Chem. Soc. Jpn. への投稿のすすめ , 2011 .

[48]  Benedict M. Sattelle,et al.  Is N-acetyl-d-glucosamine a rigid 4C1 chair? , 2011, Glycobiology.

[49]  T. Konishi,et al.  Gelation and Retrogradation Mechanism of Wheat Amylose , 2011, Materials.

[50]  Y. Kaneko,et al.  Preparation of inclusion complexes composed of amylose and biodegradable poly(glycolic acid- co -ɛ-caprolactone) by vine-twining polymerization and their lipase-catalyzed hydrolysis behavior , 2011 .

[51]  S. Marrink,et al.  Amylose folding under the influence of lipids. , 2012, Carbohydrate research.

[52]  Robert J Woods,et al.  Dependence of pyranose ring puckering on anomeric configuration: methyl idopyranosides. , 2012, The journal of physical chemistry. B.

[53]  Benedict M. Sattelle,et al.  Assigning kinetic 3D-signatures to glycocodes. , 2012, Physical chemistry chemical physics : PCCP.

[54]  Frank Noé,et al.  Kinetic characterization of the critical step in HIV-1 protease maturation , 2012, Proceedings of the National Academy of Sciences.

[55]  S. Sinha Ray,et al.  V-amylose Structural Characteristics, Methods of Preparation, Significance, and Potential Applications , 2012 .

[56]  Igor L. Medintz,et al.  Functionalizing nanoparticles with biological molecules: developing chemistries that facilitate nanotechnology. , 2013, Chemical reviews.

[57]  Kamlesh Kumar,et al.  Synthesis of amylose-polystyrene inclusion complexes by a facile preparation route. , 2013, Biomacromolecules.

[58]  B. Sattelle,et al.  Does microsecond sugar ring flexing encode 3D-shape and bioactivity in the heparanome? , 2013, Biomacromolecules.

[59]  B. Sattelle,et al.  Shaping up for structural glycomics: a predictive protocol for oligosaccharide conformational analysis applied to N-linked glycans , 2014, Carbohydrate research.