Gerald D. Fasman

Prediction of protein structure and the principles of protein conformation

1. Principles and Patterns of Protein Conformation.- 2. The Structure of the Photochemical Reaction Center of Rhodopseudomonas viridis and Its Implications for Function.- 3. Virus Structure.- 4. Protein Stability and Function: Theoretical Studies.- 5. Stabilization Energies of Protein Conformation.- 6. The Development of the Prediction of Protein Structure.- 7. The Role of Energy Minimization in Simulation Strategies of Biomolecular Systems.- 8. The Role of Electrostatic Interactions in the Structure of Globular Proteins.- 9. Chou-Fasman Prediction of the Secondary Structure of Proteins: The Chou-Fasman-Prevelige Algorithm.- 10. The GOR Method for Predicting Secondary Structures in Proteins.- 11. Prediction of Packing of Secondary Structure.- 12. Prediction of Protein Structural Classes from Amino Acid Compositions.- 13. Use of Class Prediction to Improve Protein Secondary Structure Prediction: Joint Prediction with Methods Based on Sequence Homology.- 14. Redundancies in Protein Sequences.- 15. The Hydrophobicity Profile.- 16. Hydrophobic Moments as Tools for Analyzing Protein Sequences and Structures.- 17. Tertiary Structure Prediction.- 18. Structure Prediction for Membrane Proteins.- 19. Identification of Membrane Proteins and Soluble Protein Secondary Structural Elements, Domain Structure, and Packing Arrangements by Fourier-Transform Amphipathic Analysis.- 20. Guide for Studies on Structure and Function Employing Synthetic Polypeptides.- Appendixes (included in Chapter 6).- Appendix 1: List of Reviews on Protein Folding and Prediction of Secondary and Tertiary Structure.- Appendix 2: Programs Available through This Publication for Protein Secondary Structure Prediction.- Appendix 3: Commercially Available Programs.- Appendix 4: Relevant Programs Described in the Literature.- Appendix 5: National Resource Data Bases.

[27] Circular dichroism and optical rotatory dispersion of proteins and polypeptides

Publisher Summary This chapter discusses the methodology of circular dichroism (CD) and optical rotatory dispersion (ORD) data gathering and analysis in the rapidly changing field of protein structure, making use of synthetic polypeptide studies when necessary. ORD is the measurement, as a function of wavelength, of a molecules ability to rotate the plane of linearly polarized light. CD is similar data evaluating the molecules unequal absorption of right- and left-handed circularly polarized light. CD and ORD can yield useful estimates of protein secondary structure. Although all the amino acids except glycine contain at least one asymmetric carbon atom, most amino acids display only small ORD and CD bands. It is the conformation of the protein—that is, the asymmetric and periodic arrangement of peptide units in space, which gives rise to their characteristic ORD and CD spectra. In recent years, X-ray diffraction analysis has lead to the complete mapping of the peptide backbone and side-chain positions of lysozyme, several other enzymes, and quite a few other proteins in the solid state.

[32] Differential spectrofluorometry

Publisher Summary A technique for studying changes in protein conformation, which is related to absorption, is fluorescence. This technique allows the use of much smaller samples because of the greater sensitivity of the method. Changes in the environment (e.g., solvent perturbation, substrate binding, conformational changes) about a tyrosine or tryptophan residue, incorporated either in a protein molecule or free in solution, have been shown to lead to changes in the fluorescence emission spectrum of these amino acids. In addition to these causes of fluorescence alteration, specific quenching effects induced by environmental factors can cause large fluorescent changes. The correlation of the fluorescence spectrum with the absolute immediate medium surrounding these moieties is difficult. In analogy with difference absorption spectroscopy, difference fluorescence spectroscopy offers a highly sensitive method to measure conformational changes in proteins or to probe the surface to locate aromatic residues. Any system, which possesses a fluorescent moiety, is amenable to study.