Nature's use of the protein-cofactor assembly provides molecules of extraordinary functional potency and diversity. With a combination of state of the art spectroscopy, bio-organic synthetic methods, protein design and synthesis, and macromolecular simulation methods we are now in a unique position to understand in detail how natural protein- cofactor assemblies function, to design synthetic versions to emulate them, and even to design combinations with radically new properties. The program project brings together a group of people who can make particular contributions to the project. Molecular dynamics simulations combined with continuum electrostatic calculations carried out by Sharp will be used to determine the contribution of the protein to the electric field and the effect of this field on the cofactor, on metal ligands, on particular residues within the protein and the surrounding water structure. These effects also will be evaluated by direct time and frequency dependent spectral probes of the dynamic spectral shifts of electron and vibrational inhomogeneities, including applications involving the detection of single molecules (Hochstrasser and Vanderkooi). Novel heme derivatives synthesized by Therien combined with proteins synthesized by the Dutton group allow for design of particular protein-cofactor assemblies with desired geometries and electric fields around the cofactor. Kinetics and stability of the polypeptide chain will be addressed by DeGrado and McCafferty, using computational and rapid kinetic techniques. Theoretical and experimental analysis of the protein-cofactor structure, stability, dynamics and the resultant functional properties will be used to guide the design and synthesis, while the facile ability to design and synthesize desired protein- cofactor assemblies will be used to refine our theoretical methods and interpretation of the experimental analyses. We propose that the interplay between these different approaches will dramatically advance our understanding and use of protein-cofactors assemblies.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Program Projects (P01)
Project #
5P01GM048130-09
Application #
6385768
Study Section
Special Emphasis Panel (ZRG3-BMT (01))
Program Officer
Wehrle, Janna P
Project Start
1993-08-01
Project End
2003-07-31
Budget Start
2001-08-01
Budget End
2002-07-31
Support Year
9
Fiscal Year
2001
Total Cost
$915,200
Indirect Cost
Name
University of Pennsylvania
Department
Biochemistry
Type
Schools of Medicine
DUNS #
042250712
City
Philadelphia
State
PA
Country
United States
Zip Code
19104
Fry, Bryan A; Solomon, Lee A; Leslie Dutton, P et al. (2016) Design and engineering of a man-made diffusive electron-transport protein. Biochim Biophys Acta 1857:513-521
Goparaju, Geetha; Fry, Bryan A; Chobot, Sarah E et al. (2016) First principles design of a core bioenergetic transmembrane electron-transfer protein. Biochim Biophys Acta 1857:503-512
Sharp, Kim A; Vanderkooi, Jane M (2010) Water in the half shell: structure of water, focusing on angular structure and solvation. Acc Chem Res 43:231-9
Zelent, Bogumil; Sharp, Kim A; Vanderkooi, Jane M (2010) Differential scanning calorimetry and fluorescence study of lactoperoxidase as a function of guanidinium-HCl, urea, and pH. Biochim Biophys Acta 1804:1508-15
Coleman, Ryan G; Sharp, Kim A (2010) Shape and evolution of thermostable protein structure. Proteins 78:420-33
Coleman, Ryan G; Sharp, Kim A (2010) Protein pockets: inventory, shape, and comparison. J Chem Inf Model 50:589-603
Zelent, B; Vanderkooi, J M (2009) Infrared spectroscopy used to study ice formation: the effect of trehalose, maltose, and glucose on melting. Anal Biochem 390:215-7
Coleman, Ryan G; Sharp, Kim A (2009) Finding and characterizing tunnels in macromolecules with application to ion channels and pores. Biophys J 96:632-45
Zelent, Bogumil; Vanderkooi, Jane M; Nucci, Nathaniel V et al. (2009) Phosphate assisted proton transfer in water and sugar glasses: a study using fluorescence of pyrene-1-carboxylate and IR spectroscopy. J Fluoresc 19:21-31
Nucci, Nathaniel V; Zelent, Bogumil; Vanderkooi, Jane M (2008) Pyrene-1-carboxylate in water and glycerol solutions: origin of the change of pK upon excitation. J Fluoresc 18:41-9

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