Contributions to protein entropy and heat capacity from bond vector motions measured by NMR spin relaxation

Yang, Daiwen; Mok, Yu Keung; Forman-Kay, Julie D.; Farrow, Neil A.; Kay, Lewis E.

doi:10.1006/jmbi.1997.1285

Cited by 144 publications

(219 citation statements)

References 55 publications

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“…and characteristic temperatures~T *! for each backbone NH vector in the B1 domain~Mandel et al, 1996;Yang & Kay, 1996;Yang et al, 1997!. Plots of entropy~S B !…”

Section: Temperature Dependence Of Order Parametersmentioning

confidence: 99%

“…This may be a reflection of the high thermal stability of the B1 domain and the absence of significant slow timescale motions over the 0-50 8C temperature range. We know of three previous studies focusing on the variation of NH group order parameters with temperature~Man-del et al., 1996;Yang et al, 1997;Evenäs et al, 1999!. For RNase H~Mandel et al, 1996!, the variation was described in terms of a characteristic temperature~T *!…”

Section: Heat Capacities and Characteristic Temperaturesmentioning

confidence: 99%

“…Heat capacity and characteristic temperature statistics for b-sheet, a-helix, and other residues in the B1 domain are listed in Table 4, along with comparative data for other proteins~Mandel et al, 1996;Yang et al, 1997;Evenäs et al, 1999!. Within the B1 domain there is only a weak influence of secondary structure on the local heat capacity.…”

Section: Heat Capacities and Characteristic Temperaturesmentioning

confidence: 99%

“…These terms have been estimated to contribute ;82, ;3, and ;15%, respectively, to the total heat capacity of folded proteins, although DC p,NϪU is largely dominated by changes in the solvation term Gomez et al, 1995!. Although the total changes in thermodynamic parameters upon protein unfolding can be readily measured~e.g., by calorimetry!, a more thorough understanding of the factors contributing to protein stability requires the thermodynamic contributions of various physical effects to be separated. Recent advances in the collection and analysis of NMR relaxation data have made it possible to estimate the contributions of individual bond vector fluctuations to conformational entropy and heat capacity~Akke et al, 1993;Li et al, 1996;Yang & Kay, 1996;Yang et al, 1997!. The relaxation of protonated 15 N or 13 C nuclei in proteins is dominated by the angular fluctuations of the associated NH or CH bond vectors relative to the permanent magnetic field.…”

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confidence: 99%

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The role of backbone conformational heat capacity in protein stability: Temperature dependent dynamics of the B1 domain of Streptococcal protein G

et al. 2000

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The contributions of backbone NH group dynamics to the conformational heat capacity of the B1 domain of Streptococcal protein G have been estimated from the temperature dependence of 15 N NMR-derived order parameters. Longitudinal~R 1 ! and transverse~R 2 ! relaxation rates, transverse cross-relaxation rates~h xy !, and steady state $ 1 H%-15 N nuclear Overhauser effects were measured at temperatures of 0, 10, 20, 30, 40, and 50 8C for 89-100% of the backbone secondary amide nitrogen nuclei in the B1 domain. The ratio R 2 0h xy was used to identify nuclei for which conformational exchange makes a significant contribution to R 2 . Relaxation data were fit to the extended model-free dynamics formalism, incorporating an axially symmetric molecular rotational diffusion tensor. The temperature dependence of the order parameter~S 2 ! was used to calculate the contribution of each NH group to conformational heat capacity~C p ! and a characteristic temperature~T *!, representing the density of conformational energy states accessible to each NH group. The heat capacities of the secondary structure regions of the B1 domain are significantly higher than those of comparable regions of other proteins, whereas the heat capacities of less structured regions are similar to those in other proteins. The higher local heat capacities are estimated to contribute up to ;0.8 kJ0mol K to the total heat capacity of the B1 domain, without which the denaturation temperature would be ;9 8C lower~78 8C rather than 87 8C!. Thus, variation of backbone conformational heat capacity of native proteins may be a novel mechanism that contributes to high temperature stabilization of proteins.Keywords: B1 domain; entropy; heat capacity; NMR relaxation; order parameter; protein dynamics; protein stability Most globular proteins are marginally stable because the factors that favor formation of the native state, primarily desolvation of hydrophobic groups and formation of intramolecular hydrogen bonds and salt bridges, are almost equally balanced against those that favor denaturation, primarily the higher conformational entropy of the unfolded protein chain relative to that of the native state~Creigh-ton, 1993; Fersht, 1999!. At high temperatures, the balance between these factors is altered such that many proteins exhibit reversible thermal denaturation with a characteristic midpoint, the melting temperature~T m !. The free energy of unfolding of a proteiñ DG NϪU ! depends upon the changes in enthalpy, entropy, and heat capacity that occur upon unfolding and the temperature~T ! according to the equation~Creighton, 1993; Fersht, 1999!:in which DH 0 and DS 0 are the enthalpy and entropy changes, respectively, at a reference temperature T 0 and DC p,NϪU is the change in heat capacity at constant pressure, which is assumed to be invariant with temperature. Equation 1 indicates that native proteins may be stabilized by an increase in DH 0 or by a decrease in either DS 0 or DC p,NϪU . Thus, one possible strategy for a protein to achieve high thermal ...

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“…and characteristic temperatures~T *! for each backbone NH vector in the B1 domain~Mandel et al, 1996;Yang & Kay, 1996;Yang et al, 1997!. Plots of entropy~S B !…”

Section: Temperature Dependence Of Order Parametersmentioning

confidence: 99%

Section: Heat Capacities and Characteristic Temperaturesmentioning

confidence: 99%

Section: Heat Capacities and Characteristic Temperaturesmentioning

confidence: 99%

mentioning

confidence: 99%

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The role of backbone conformational heat capacity in protein stability: Temperature dependent dynamics of the B1 domain of Streptococcal protein G

et al. 2000

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“…The entropy change between the folded and unfolded forms of SNase was calculated [275] in the frame of a model relating the amplitude of bond vector motions to conformational entropy. A spectral density model based on a truncated Lorentzian distribution of correlation times was used [276] to characterize the internal dynamics of protein unfolded states.…”

Section: Describing the Relaxation Measurements In Terms Of Internal mentioning

confidence: 99%

Quantitative Analysis of Biomolecular NMR Spectra: A Prerequisite for the Determination of the Structure and Dynamics of Biomolecules

Malliavin

2006

COC

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Nuclear Magnetic Resonance (NMR) became during the two last decades an important method for biomolecular structure determination. NMR permits to study biomolecules in solution and gives access to the molecular flexibility at atomic level on a complete structure: in that respect, it is occupying a unique place i n structural biology. During the first years of its development, NMR was trying to meet the requirements previously defined in X-ray crystallography. But, NMR then started to determine its own criteria for the definition of a structure. Indeed, the atomic coordinates of an NMR structure are calculated using restraints on geometrical parameters (angles and distances) of the structure, which are only indirectly related to atom positions: in that respect, NMR and X-ray crystallography are very different. The indirect relation between the NMR measurements and the molecular structure and dynamics makes critical the precision and the interpretation of the NMR parameters and the development of quantitative analysis methods. The methods published since 1997 for liquid-NMR of proteins are reviewed here. First, methods for structure determination are presented, as well as methods for spectral assignment and for structure quality assessment. Second, the quantitative analysis of structure mobility i s reviewed.

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Correlation between changes in nuclear magnetic resonance order parameters and conformational entropy: Molecular dynamics simulations of native and denatured staphylococcal nuclease

2000

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Recent work has suggested that changes in NMR order parameters may quantitatively reflect changes in the conformational entropy of a protein ensemble. The extent of the mathematical relationship between local entropy changes as seen by NMR order parameters and the full protein entropy change is a complex issue. As a step towards a fuller understanding of this problem, molecular dynamics calculations of both native and denatured staphylococcal nuclease were performed. The N-H bond vector motion, in both explicit and implicit solvent, was analyzed to estimate local and global entropy changes. The calculated N-H bond vector order parameters from simulation agreed on average with experimental values for both native and denatured structures. However, the inverted-U profile of order parameters versus residue number observed experimentally for denatured nuclease was only partially reproduced by simulation of compact denatured structures. Comparisons made across the full set of simulations revealed a correlation between the N-H order parameter-based conformational entropy change and the total quasiharmonic-based conformational entropy change between the native and denatured structures. The calculations showed that about 25% of the total entropy change was reflected by changes in simulated S2 values. This result suggests that NMR-derived order parameters may be used to provide a reasonable estimate of the total conformational entropy change on protein folding.

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Contributions to protein entropy and heat capacity from bond vector motions measured by NMR spin relaxation

Cited by 144 publications

References 55 publications

The role of backbone conformational heat capacity in protein stability: Temperature dependent dynamics of the B1 domain of Streptococcal protein G

The role of backbone conformational heat capacity in protein stability: Temperature dependent dynamics of the B1 domain of Streptococcal protein G

Quantitative Analysis of Biomolecular NMR Spectra: A Prerequisite for the Determination of the Structure and Dynamics of Biomolecules

Correlation between changes in nuclear magnetic resonance order parameters and conformational entropy: Molecular dynamics simulations of native and denatured staphylococcal nuclease

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