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Modeling Biomolecules Using the WWW. Major Classes of Biomolecules. Peptides (Proteins) Carbohydrates Nucleic Acids Lipids. Modeling Peptides. Primary structure

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major classes of biomolecules
Major Classes of Biomolecules
  • Peptides (Proteins)
  • Carbohydrates
  • Nucleic Acids
  • Lipids
modeling peptides
Modeling Peptides
  • Primary structure
    • Most molecular modeling software allows construction of peptide models by appending pre-constructed amino acids in sequence, usually by selecting their 1- or 3-letter abbreviations.
  • Secondary structure
    • features such as a-helix, b (pleated) sheet, hairpin turns, etc. can be specified (examples on following panel).
hairpin turn secondary structure
Hairpin Turn Secondary Structure

Hairpin turn, alpha helix

Hairpin turn, Beta sheet

modeling peptides1
Modeling Peptides...
  • Tertiary structure
    • folding of chains…more difficult to model accurately, unless structure is known from X-ray or NMR.
  • Quaternary structure
    • Combination of several subunits...likewise difficult to model accurately, unless structure is known from X-ray or NMR.
modeling peptides2
Modeling Peptides...
  • Computations are usually limited to molecular mechanics, although semi-empirical MO calculations can be performed on small biopolymers.
  • MM Forcefields designed for biomolecules:
    • Amber (peptides and nucleic acids)/Kollman
    • OPLS (peptides and nucleic acids)/Jorgensen
    • BIO+ (biomacromolecules)/Karplus

(all of these are found in HyperChem)

  • Special database for Peptides
  • 20 Pre-optimized amino acids
  • Peptide menu choices
    • a helix
    • b (pleated) sheet
    • other
  • Termination modes:
    • NH2 or NH3+; CO2H or CO2-
  • Special database for Nucleotides
  • 4 Pre-optimized bases (A,T,C,G)
  • Nucleotide menu choices
    • DNA (double strand), DNA (single strand)
    • RNA (double strand), RNA (single strand)
    • DNA-RNA mixed
  • A, B or Z helical forms (differ in rise/base)
www pages dealing with modeling biomolecules
WWW pages dealing with Modeling Biomolecules
  • Georgia State University molecular modeling site: modeling problems, biomolecules:
  • Dr. Barry Honig’s web site (Columbia University… great images of biomolecules):
www pages dealing with modeling biomolecules1
WWW pages dealing with Modeling Biomolecules...
  • Molecular Graphics (rendering); University of Geneva, Switzerland (Dr. Jacques Weber)

  • NIH Center for Molecular Modeling
www pages dealing with modeling biomolecules2
WWW pages dealing with Modeling Biomolecules...
  • Molecular Modeling Research Group at the Dept. of Agricultural Environmental Sciences and Food Biotechnology, University of Sassari - ITALY:
  • The Research Collaboratory for Structural Bioinformatics (PDB database of structures of proteins and other biomolecules):