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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

  • Peptides (Proteins)

  • Carbohydrates

  • Nucleic Acids

  • Lipids

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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).

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Hairpin Turn Secondary Structure

Hairpin turn, alpha helix

Hairpin turn, Beta sheet

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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.

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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)

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Modeling Biomolecules using HyperChem

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  • 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-

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  • 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)

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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):

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WWW pages dealing with Modeling Biomolecules...

  • Molecular Graphics (rendering); University of Geneva, Switzerland (Dr. Jacques Weber)

  • NIH Center for Molecular Modeling

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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):