Conformational statistics of the nitrogen linkage in glycopeptides using umbrella sampling
- 1 December 1995
- journal article
- Published by Association for Computing Machinery (ACM) in ACM SIGBIO Newsletter
- Vol. 15 (3) , 2-10
- https://doi.org/10.1145/228243.228244
Abstract
The conformational statistics of the glycosylated dipeptide N - acetyl - δ - N - (2 - acetamido - β - D - glucopyranosyl) - L - asparaginyl - N' - methyl amide (glcNAc-Asn), a model of N-linked glycopeptides, was determined using umbrella sampling. The use of umbrella sampling allowed the importance sampling algorithm to accept new conformations with probabilities exceeding 40%. The satisfactory acceptance rate generated a chain of conformations and a set of properties suitable for comparison with available experimental results. Comparison of calculated structures for glcNAc-Asn with those determined experimentally by NMR, circular dichroism spectroscopy, and X-ray crystallography showed that the Momany-Scheraga conformation energy (ECEPP) over-emphasized non-bonded repulsions. Based on the experimentally determined structures, an effective two-fold potential barrier was imposed on the anomeric linkage. Predictions based on conformational statistics were sensitive to the choice of a three-fold or two-fold torsional barrier at the anomeric linkage.Keywords
This publication has 16 references indexed in Scilit:
- Crystal structure and solution conformation of 1-N-acetyl-β-D-glucopyranosyl amine: A model for the glycopeptide linkageBiopolymers, 1982
- Conformation of the glycopeptide linkage in asparagine-linked glycoproteinsBiochemistry, 1980
- Circular dichroism and the conformation of sugars having vicinal diacylamino substituentsJournal of the American Chemical Society, 1978
- Peptide chain conformation and the glycosylation of glycoproteinsBiochemical and Biophysical Research Communications, 1977
- Nonphysical sampling distributions in Monte Carlo free-energy estimation: Umbrella samplingJournal of Computational Physics, 1977
- Energy parameters in polypeptides. VII. Geometric parameters, partial atomic charges, nonbonded interactions, hydrogen bond interactions, and intrinsic torsional potentials for the naturally occurring amino acidsThe Journal of Physical Chemistry, 1975
- The application of ab initio molecular orbital theory to structural moieties of carbohydratesCarbohydrate Research, 1974
- Experimental Calibration of a Karplus Relationship in Order to Study the Conformations of Peptides by Nuclear Magnetic ResonanceMacromolecules, 1974
- Intermolecular potentials from crystal data. III. Determination of empirical potentials and application to the packing configurations and lattice energies in crystals of hydrocarbons, carboxylic acids, amines, and amidesThe Journal of Physical Chemistry, 1974
- IUPAC-IUB Commission on Biochemical Nomenclature. Abbreviations and symbols for the description of the conformation of polypeptide chains. Tentative rules (1969)Biochemistry, 1970