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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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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-


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Spartan

  • 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: http://heme.gsu.edu/glactone/

  • Dr. Barry Honig’s web site (Columbia University… great images of biomolecules):http://wiki.c2b2.columbia.edu/honiglab_public/index.php/Main_Page


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WWW pages dealing with Modeling Biomolecules...

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

    http://scsg9.unige.ch/fln/eng/toc.html

  • NIH Center for Molecular Modelinghttp://cmm.info.nih.gov/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:http://antas.agraria.uniss.it

  • The Research Collaboratory for Structural Bioinformatics (PDB database of structures of proteins and other biomolecules):http://www.rcsb.org


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