Thermodynamics, Chemical Reactions and Molecular Biology

Benzinger, T. H.

doi:10.1038/229100a0

Cited by 85 publications

(66 citation statements)

References 3 publications

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“…In the calculations, we set ⌬H ϭ 25 kJ mol Ϫ1 and ⌬S ϭ 100 J K Ϫ1 mol Ϫ1 , independent of temperature. [Note that the purely ''thermal'' contributions to ⌬H and ⌬S cancel out identically in the Gibbs energy and, hence, do not contribute to the temperature dependence of x A 0 (24,25).] For this choice of parameter values, x A 0 (T) goes from 1.000 at 77 K to 0.146 at 293 K (see Fig.…”

Section: Resultsmentioning

confidence: 99%

Biomolecular cryocrystallography: Structural changes during flash-cooling

Halle

2004

Proc. Natl. Acad. Sci. U.S.A.

194

143

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To minimize radiation damage, crystal structures of biological macromolecules are usually determined after rapid cooling to cryogenic temperatures, some 150 -200 K below the normal physiological range. The biological relevance of such structures relies on the assumption that flash-cooling is sufficiently fast to kinetically trap the macromolecule and associated solvent in a room-temperature equilibrium state. To test this assumption, we use a two-state model to calculate the structural changes expected during rapid cooling of a typical protein crystal. The analysis indicates that many degrees of freedom in a flash-cooled protein crystal are quenched at temperatures near 200 K, where local conformational and association equilibria may be strongly shifted toward low-enthalpy states. Such cryoartifacts should be most important for strongly solvent-coupled processes, such as hydration of nonpolar cavities and surface regions, conformational switching of solventexposed side chains, and weak ligand binding. The dynamic quenching that emerges from the model considered here can also rationalize the glass transition associated with the atomic fluctuations in the protein.protein structure ͉ protein hydration ͉ protein glass transition ͉ x-ray diffraction

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Section: Resultsmentioning

confidence: 99%

Biomolecular cryocrystallography: Structural changes during flash-cooling

Halle

2004

Proc. Natl. Acad. Sci. U.S.A.

194

143

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“…We have observed amide I line at 1638cm-1 in the FT-IR spectra of /3-PLV. Second derivative spectra showed splitting of (20) 2968 2967 2930 2935 2922 2920 2880 2876 2880 2879 2879 1471 1470 1470 1469 1467 1391 1394 1370 1372 1006 1006 970 981 918 907 845 852 199 200 Table III (19) ,(Cf3---Cy 1 )(3 l) + ,(C/3-Cy2)(63)…”

Section: Backbone Modesmentioning

confidence: 99%

“…H can be used to compute thermodynamic quantities such as free energy, entropy, specific heat, and enthalpy. The heat capacity, which can give information about the proportion of a protein which is in ahelical or /3 sheet structure and is necessary in evaluating the basic thermodynamics of enzyme reaction, 19 has been calculated using Debye's relation…”

Section: Calculation Of Heat Capacitymentioning

confidence: 99%

Normal Modes of Poly(L-valine) in Relation to Spectra of Oligovalines

Burman

Tandon

Gupta

et al. 1995

Polym J

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ABSTRACT:Poly(L-valine) (PLV) belongs to the class of polyamino acids having a bulky side chain. It preferably adopts fl-sheet conformation, although high molecular weight PL V may form an IX helix as well. In the present communication we report a detailed study of the phonons and their dispersion for f/-PLV and the spectra of oligovalines in relation to its polymeric form. The N-deuterated analog of f/-PLV has also been studied to confirm the correctness of assignments and force-field. Density-of-states and heat capacity have been obtained. The heat capacity is in very good agreement with the experimental measurements of Roles et al.

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“…42,48,122,123 Such functions are suggestive of entropydriven and hydrophobic effect mediated alterations in solvent organization. 117 Binding is associated with hydrophobic dehydration and aggregation.…”

Section: T à áSmentioning

confidence: 99%

Designing allosteric peptide ligands targeting a globular protein

et al. 2006

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Patented signal analytic algorithms applied to hydrophobically transformed, numerical amino acid sequences have previously been used to design short, protein‐targeted, L or D retro‐inverso peptides. These peptides have demonstrated allosteric and/or indirect agonist effects on a variety of G‐protein and tyrosine kinase coupled membrane receptors with 30% to over 80% hit rates. Here we extend these approaches to a globular protein target. We designed eight peptide ligands targeting an ELISA antibody responsive protein, β‐galactosidase, βGAL. Three of the eight 14mer peptides allosterically activated βGAL with ELISA methodology. Using Bayesian statistics, this 38% hit rate would have occurred 2 × 10−9 by chance. These peptides demonstrated binding site competitive or noncompetitive interactions, suggesting allosteric site multiplicity with respect to their βGAL binding‐mediated ELISA signal. Kinetic studies demonstrated the temperature dependence of the βGAL peptide binding functions. Using the van't Hoff relation, we found evidence for enthalpy–entropy compensation. This relation is often found for hydrophobic interactions in aqueous media, and is consistent with the postulated hydrophobic series encoding underlying our protein‐targeted, peptide design methods. It appears that our algorithmic, hydrophobic autocovariance eigenvector template approach to the design of allosteric peptides targeting membrane receptors may also be applicable to the design of peptide ligands targeting nonmembrane involved globular proteins. © 2006 Wiley Periodicals, Inc. Biopolymers 85: 38–59, 2007.This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com

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Thermodynamics, Chemical Reactions and Molecular Biology

Cited by 85 publications

References 3 publications

Biomolecular cryocrystallography: Structural changes during flash-cooling

Biomolecular cryocrystallography: Structural changes during flash-cooling

Normal Modes of Poly(L-valine) in Relation to Spectra of Oligovalines

Designing allosteric peptide ligands targeting a globular protein

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