1 / 17

Review of “Stability of Macromolecular Complexes”

Review of “Stability of Macromolecular Complexes”. Dan Kulp Brooijmans, Sharp, Kuntz. Purpose . Search for general principles governing macromolecular interactions Protein-Protein (Dimers) Nucleic Acid-Ligand (Aptamers) Nucleic Acid–Nucleic Acid (Duplexes)

kyran
Download Presentation

Review of “Stability of Macromolecular Complexes”

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript


  1. Review of “Stability of Macromolecular Complexes” Dan Kulp Brooijmans, Sharp, Kuntz

  2. Purpose • Search for general principles governing macromolecular interactions • Protein-Protein (Dimers) • Nucleic Acid-Ligand (Aptamers) • Nucleic Acid–Nucleic Acid (Duplexes) • Interactions/Contributions of specific forces to overall stability • Relationship between maximal affinity of macromolecular ligands and interface size • Subject of Study: Highest affinity complexes

  3. Background Research • Protein – Ligand interaction study • Look at strongest binding ligands • Two modes of free energy: • Linear increase w/ increasing molecular size • Plateau, no increase w/increasing mol. Size • Free Energy calculations of binding

  4. Differences in Interfaces… • Large macromolecular interfaces are flat • Small ligand binding sites are rough Pettit FK, Bowie JU. Protein surface roughness and small molecular binding sites. J Mol Biol 1999;285: 1377–1382.

  5. Other differences.. • Atomic composition • Small ligands • Diverse set, topology • Amino Acid side chains / Nucleic Acids • Evolutionary pressures • Small ligands = shorting binding period • Regulation • Protein-Protein binding = longer binding

  6. Selection of complexes • Protein – Protein Complexes • Homodimeric • 3 state denaturation (dissociation to monomers) • Resolution 3.1 Angstroms or better • Heterodimeric • Alanine mutants G > 5 kcal/mol • Nucleic Acid Complexes • DNA Duplex • Two state thermodynamics • Nucleic Acid aptamers • Bind small molecules/peptide ligands w/ high selectivity

  7. Calculations • Total binding energy • Attributed to ligand atoms only • Simplify calculation • Interface areas (IA) – dms/MidasPlus • Accessible Surface Area (ASA) • IA = ASA receptor + ASA ligand – ASA complex • Interface atoms • Non-hydrogen, “heavy” atoms • atoms that lose ASA during complex formation • DNA Duplex – non sugar/phosphate atoms Connolly ML. Analytical molecular surface calculation. J Appl Crystallogr 1983;16:548–558.

  8. Findings • Some Linear increase free energy w/ size • Maximal affinity plateau > 20 residues • 1.5 kcal/mol per interface atom • 120 cal/mol Angstrom^2 • Apparent differences in maximal affinity based on biological function • Protein-inhibitor complexes higher free energy compared to other interfaces of the same size

  9. Findings… • Homodimers vs Heterdimers • Expect Homodimers have higher max. affinity • NO! • Dissociation constants are more permanent and more difficult to measure correctly • Comparison inside biological classes • Max contribution per interface atom is less for larger complexes = plateau behavior

  10. Binding free energy vs # atoms

  11. Binding free energy per atom

  12. Exceptions • DNA Duplexes • Additive(Linear) Free Energy • Less per atom energy • Simple accounting scheme (2nd Structures) • Open Structure w/ size • NA aptamer • NA unstructured w/o ligand. • Ligand binding causes refolding • Hot spots • Contribute more per atom • K15A mutation in BPTI-trypsin complex • > 3 Kcal/mol

  13. Previous Study • Chothia et al. Nature, 1975 • Positive correlation between interaction surface size and stability. • More data available • Maximal useful affinity makes sense • Long dissociation times (years?)

  14. Better Interactions? • Atoms of low-molecular-weight ligands contribute more to energy than atoms of larger ligands. • More stable protein-protein complexes. Supported by finding that better than wild-type affinity achieved using phage display in vitro evolution. • Drug design – small molecule inhbitiors Dalby PA, Hoess RH, DeGrado WF. Evolution of binding affinity in a WWdomain probed by phage display. Protein Sci 2000;9:2366–2376.

  15. Free Energy per class..

More Related