Our overall objective is to solve the problem of how proteins fold into their native conformations and then (e.g. as enzymes) interact with substrates and other ligands. For this purpose, we are using the methodology of protein chemistry, and developing and applying experimental and theoretical techniques (to be used together) to provide an understanding of the internal interactions that stabilize native proteins in aqueous solution. The experimental work involves the use of immunochemistry, flash photolysis, fluorescence energy transfer, proteolytic digestion, Raman spectro- scopy, and recombinant DNA procedures to determine the pathways of folding of ribonuclease. When this work is finished, we will carry out similar studies of lysozyme and pancreatic trypsin inhibitor. The theoretical work involves the use of empirical potentials (including the effect of hydration), in various computational approaches to study the interactions involved in protein folding (bovine pancreatic trypsin inhibitor and leukocyte interferon). An understanding of the interactions in proteins is of potential applicability to the elucidation of the role of conformation in biological processes, e.g. the undesirable association of sickle- cell hemoglobin, or the induction of an oncogene product whose properties involve a conformational change when only one amino acid in the sequence is changed.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM014312-35
Application #
3268628
Study Section
Molecular and Cellular Biophysics Study Section (BBCA)
Project Start
1977-01-01
Project End
1993-06-30
Budget Start
1990-07-01
Budget End
1991-06-30
Support Year
35
Fiscal Year
1990
Total Cost
Indirect Cost
Name
Cornell University
Department
Type
Schools of Arts and Sciences
DUNS #
City
Ithaca
State
NY
Country
United States
Zip Code
14850
Cote, Yoann; Delarue, Patrice; Scheraga, Harold A et al. (2018) From a Highly Disordered to a Metastable State: Uncovering Insights of ?-Synuclein. ACS Chem Neurosci 9:1051-1065
Vorobjev, Yury N; Scheraga, Harold A; Vila, Jorge A (2018) A comprehensive analysis of the computed tautomer fractions of the imidazole ring of histidines in Loligo vulgaris. J Biomol Struct Dyn 36:3094-3105
Grassein, Paul; Delarue, Patrice; Scheraga, Harold A et al. (2018) Statistical Model To Decipher Protein Folding/Unfolding at a Local Scale. J Phys Chem B 122:3540-3549
Solé-Domènech, Santiago; Rojas, Ana V; Maisuradze, Gia G et al. (2018) Lysosomal enzyme tripeptidyl peptidase 1 destabilizes fibrillar A? by multiple endoproteolytic cleavages within the ?-sheet domain. Proc Natl Acad Sci U S A 115:1493-1498
Vorobjev, Yury N; Scheraga, Harold A; Vila, Jorge A (2018) Coupled molecular dynamics and continuum electrostatic method to compute the ionization pKa's of proteins as a function of pH. Test on a large set of proteins. J Biomol Struct Dyn 36:561-574
Keasar, Chen; McGuffin, Liam J; Wallner, Björn et al. (2018) An analysis and evaluation of the WeFold collaborative for protein structure prediction and its pipelines in CASP11 and CASP12. Sci Rep 8:9939
Rojas, Ana; Maisuradze, Nika; Kachlishvili, Khatuna et al. (2017) Elucidating Important Sites and the Mechanism for Amyloid Fibril Formation by Coarse-Grained Molecular Dynamics. ACS Chem Neurosci 8:201-209
He, Yi; Maisuradze, Gia G; Yin, Yanping et al. (2017) Sequence-, structure-, and dynamics-based comparisons of structurally homologous CheY-like proteins. Proc Natl Acad Sci U S A 114:1578-1583
Makowski, Mariusz; Liwo, Adam; Scheraga, Harold A (2017) Simple Physics-Based Analytical Formulas for the Potentials of Mean Force of the Interaction of Amino Acid Side Chains in Water. VII. Charged-Hydrophobic/Polar and Polar-Hydrophobic/Polar Side Chains. J Phys Chem B 121:379-390
Vila, Jorge A; Scheraga, Harold A (2017) Limiting Values of the one-bond C-H Spin-Spin Coupling Constants of the Imidazole Ring of Histidine at High-pH. J Mol Struct 1134:576-581

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