Thermodynamics and kinetics of protein

Mittal, J., Best, R.B. Thermodynamics and kinetics of protein folding under confinement. Proc. Natl. Acad. Sci. U.S.A. 2008,105, 20233-8. 

Fligh-spin iron in a nonheme environment exhibits a significant change in the thermodynamics and kinetics of protein binding on reduction from Fe " to Fe ". This is illustrated by the mammalian serum iron-transport protein, transferrin. The thermodynamic affinity for Fe " is 10 in the presence of carbonate as a synergistic anion, and is reduced to 10 on reduction to Pg2-i- 21,22 jj-on-ligand turnover is also enhanced upon reduction. The net result is a non-Nernstian spectroelectrochemical response because of an elec-trochemically driven reduction followed by a coupled equilibrium dissociation of Fe " as illustrated in eqns (2.4) and (2.5) ... 

We focus on four interrelated aspects of protein-protein and protein-nucleic acid interactions. Section 2 deals with building structural models for protein complexes. In Section 3 we present an overview of the various methods for computing contributions to the stability of protein complexes. In Section 4 the focus shifts to the rates of forming protein complexes. Finally in Section 5 we discuss the impacts of protein dynamics on the structures, thermodynamics, and kinetics of protein complexes. 

A. R. Dinner and M. Karplus, The thermodynamics and kinetics of protein folding A lattice model analysis of multiple pathways with intermediates. J. Phys. Chem. B 103, 7976-7994 (1999). 

A. Sali, E. Shaknovich, and M. Karplus, Thermodynamics and kinetics of protein folding, in DIMACS Series in Discrete Mathematics and Theoretical Computer Science, Vol. 23, American Mathematical Society, 1996, pp. 199-213. 

Second, these proteins are particularly stable and because of the particularly rich spectroscopy of their heme porphyrin active sites, a wide variety of physical methods are available to monitor the thermodynamics and kinetics of binding, and subsequent electron transfer reactions, ranging from 2D NMR to laser flash techniques. 

H. P. Bachinger J. Engel, The Thermodynamics and Kinetics of Collagen Folding. In Protein Folding Handbook J. Buchner,... 

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V. Petri, M. Hsieh, E. Jamison and M. Brenowitz. DNA sequence-specific recognition by the Saccharomyces cerevisiae "TATA" binding protein promoter-dependent differences in the thermodynamics and kinetics of binding. Biochemistry 37 (1998) 15842-9. 

Multidomain proteins may be viewed as conjugated proteins in which each domain may affect the folding dynamics and thermodynamic properties of its counterpart domain. Experimentally, the thermodynamics and kinetics of both isolated domains and conjugated constructs from several multidomain proteins were studied (a very detailed and fairly current report can be found in Reference [29]). A computational characterization of the mechanistic principles of the folding of multidomain proteins [33], utilizing native structure-based models, provides a reduced microscopic description of their folding, which in turn may enable the formulation of the forces involved in the interplay between neighboring domains. 

The studies discussed above gives an idea of conformational stability of proteins in ILs as inferred from the t measurement and melting temperature determination followed by various spectroscopic methods. However, stability of a protein/enzyme has contributions from both thermodynamic and kinetic parameters [55]. While thermal unfolding studies help to extract important thermodynamic parameters, stability of the proteins could also arise from the kinetic barrier to the conformational changes in the protein scaffold [55]. However, except for monellin [48], the thermodynamic stability in other cases has not been examined. Thus, in context of stability of proteins/enzymes in ILs, it is important and imperative to study and probe thermal unfolding as well as the thermodynamics and kinetics of the conformational change of the proteins in ILs. 

Friedel, M., Sheeler, D.J., Shea, J.-E. Effects of confinement and crowding on the thermodynamics and kinetics of folding of a minimalist, 6-barrel protein. J. Chem. Phys. 2003,118, 8106-13. 

Over the past 5 years, the combination of metallopor-phyrin with dendrimer chemistry led to a faseinating new class of Hb and Mb models," . with the dendritie superstrueture mimicking the encapsulation of the heme in the natural protein environment. Modification of the dendritic shell around the ironfll) porphyrin core modulates the shape, density, and polarity of these model systems, thereby profoundly affecting the thermodynamics and kinetics of the complexes formed with O2 and CO. 

These semisynthetic approaches resolve inherent problems in the analysis of posttranslationally modified proteins, where recombinant production of normative structures is either difficult or impossible. The constructed prenylated Rab protein probes were then further used to study the thermodynamics and kinetics of their interaction with regulatory proteins (see Section 6.4.1). 

Confinement and Crowding on the Thermodynamics and Kinetics of Folding of a Minimalist Beta-barrel Protein. 

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