A large compressibility change of protein induced by a single amino acid substitution

Gekko, Kunihiko; Tamura, Youjiro; Ohmae, Eiji; Hayashi, Hideyuki; Kagamiyama, Hiroyuki; Ueno, Hiroshi

doi:10.1002/pro.5560050319

Cited by 33 publications

(25 citation statements)

References 12 publications

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“…The faster 'early responses', triggered as early as 400 femtoseconds, can be best described by the theory when impulse forces are used. Also, the sound speed estimated at 4-7 Å/ps in Mb is compared favorably with that in water (14 Å/ps) and concentration-dependent sound velocity in ~0.1 M protein solution (54,55). Furthermore, we identify several residues in Mb as 'disseminators' that propagate the signals faster than others and are found to be kinetically important to modulate gas molecule diffusion and rebinding (49,56).…”

Section: Introductionmentioning

confidence: 79%

Intramolecular Communication and Allosteric Sites in Enzymes Unraveled by Time-Dependent Linear Response Theory

Huang

Chang-Chein

Yang

2019

Preprint

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It has been an established idea in recent years that protein is a physiochemically connected network. Allostery, understood in this new context, is a manifestation of residue communicating to remote parts in a molecule, and hence a rising interest to identify communication pathways within such a network. Recently, we have developed the timedependent linear response theories (td-LRTs), which shown to well interpret the ligand photodissociation relaxation dynamics of myoglobin. In this article, we applied the td-LRT with impulse force to investigate the allostery on an enzyme system -the dihydrofolate reductase (DHFR), which catalyze the hydride transfer (HT) reaction -the reduction of dihydrofolate (DHF) to tetrahydrofolate (THF) using the cofactor nicotinamide adenine dinucleotide phosphate (NADPH). We developed a connection matrix to record the counts of mechanical signals propagating through donor-acceptor pairs launched from the active sites with the td-LRT. Through the connection matrix, the communication score (CS) of each residue is assigned, which quantify how often the signals propagate through a residue in its most accessible way. The sites with high CS are termed "intramolecular communication centers (ICCs)", which were shown to be highly conservative. Furthermore, we showed that the HT rate reduction by a single residue mutation is highly correlated with its CS. Especially, the mysterious 200-fold HT rate reduction of the distal mutation G121V from kinetic isotope effect experiment is well described by our model with its ultra-high CS which means the G121 participating on the signal propagation process most frequently. On the other hand, several mutants: G67V, S148A and W133F causing minor HT rate reduction were described by its low CS, which means fewer signals through those sites. We proposed that the fold of HT rate reduction for a given mutant is an exponential function of its CS, which suggests that the dynamics signal propagation in the wild type play a background role to facilitate the HT quantitatively.

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Section: Introductionmentioning

confidence: 79%

Intramolecular Communication and Allosteric Sites in Enzymes Unraveled by Time-Dependent Linear Response Theory

Huang

Chang-Chein

Yang

2019

Preprint

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“…A further clue to understanding both pressure and temperature stability was proposed by Gekko and co-workers. 43 On inspecting the effect of single amino acid substitutions on compressibility and thermodynamic stability of dihydrofolate reductase, they recently showed an inverse correlation between the two parameters. Because compressibility is also directly related to protein flexibility, 44 the creation of a void in the F31A mutant would result in increased flexibility, with concomitant decrease in both pressure and temperature stability of the mutant.…”

Section: Discussionmentioning

confidence: 99%

Extreme heat‐ and pressure‐resistant 7‐kDa protein P2 from the archaeon Sulfolobus solfataricus is dramatically destabilized by a single‐point amino acid substitution

Fusi¹,

Goossens²,

Consonni³

et al. 1997

Proteins

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This study reports the characterization of the recombinant 7-kDa protein P2 from Sulfolobus solfataricus and the mutants F31A and F31Y with respect to temperature and pressure stability. As observed in the NMR, FTIR, and CD spectra, wild-type protein and mutants showed substantially similar structures under ambient conditions. However, midpoint transition temperatures of the denaturation process were 361, 334, and 347 K for wild type, F31A, and F31Y mutants, respectively: thus, alanine substitution of phenylalanine destabilized the protein by as much as 27 K. Midpoint transition pressures for wild type and F31Y mutant could not be accurately determined because they lay either beyond (wild type) or close to (F31Y) 14 kbar, a pressure at which water undergoes a phase transition. However, a midpoint transition pressure of 4 kbar could be determined for the F31A mutant, implying a shift in transition of at least 10 kbar. The pressure-induced denaturation was fully reversible; in contrast, thermal denaturation of wild type and mutants was only partially reversible. To our knowledge, both the pressure resistance of protein P2 and the dramatic pressure and temperature destabilization of the F31A mutant are unprecedented. These properties may be largely accounted for by the role of an aromatic cluster where Phe31 is found at the core, because interactions among aromatics are believed to be almost pressure insensitive; furthermore, the alanine substitution of phenylalanine should create a cavity with increased compressibility and flexibility, which also involves an impaired pressure and temperature resistance.

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“…It is known that the adiabatic compressibility can reveal the structural characteristics of native proteins (27), conformational changes induced by ligand binding (29), reduction of disulfide bonds (30), and denaturation (31). Recent studies on various mutants of two E. coli proteins, dihydrofolate reductase (32) and aspartate aminotransferase (33), revealed that a perturbation as small as a single amino acid substitution induces large changes in adiabatic compressibility, demonstrating the sensitivity of this parameter that is comparable with the enzyme activity in response to structural perturbation.…”

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confidence: 99%

A Linear Correlation between the Energetics of Allosteric Communication and Protein Flexibility in the Escherichia coli Cyclic AMP Receptor Protein Revealed by Mutation-Induced Changes in Compressibility and Amide Hydrogen−Deuterium Exchange

Gekko

Obu

et al. 2004

Biochemistry

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Amino acid substitutions at distant sites in the Escherichia coli cyclic AMP receptor protein (CRP) have been shown to affect both the nature and magnitude of the energetics of cooperativity of cAMP binding, ranging from negative to positive. In addition, the binding to DNA is concomitantly affected. To correlate the effects of amino acid substitutions on the functional energetics and global structural properties in CRP, the partial specific volume (v(o)), the coefficient of adiabatic compressibility (beta(s)(o)), and the rate of amide proton exchange were determined for the wild-type and eight mutant CRPs (K52N, D53H, S62F, T127L, G141Q, L148R, H159L, and K52N/H159L) by using sound velocity, density measurements, and hydrogen-deuterium exchange as monitored by Fourier transform infrared spectroscopy at 25 degrees C. These mutations induced large changes in v(o) (0.747-0.756 mL/g) and beta(s)(o) (6.89-9.68 Mbar(-1)) compared to the corresponding values for wild-type CRP (v(o)= 0.750 mL/g and beta(s)(o)= 7.98 Mbar(-1)). These changes in global structural properties correlated with the rate of amide proton exchange. A linear correlation was established between beta(s)(o) and the energetics of cooperativity of binding of cAMP to the high-affinity sites, regardless of the nature of cooperativity, be it negative or positive. This linear correlation indicates that the nature and magnitude of cooperativity are a continuum. A similar linear correlation was established between compressibility and DNA binding affinity. In addition, linear correlations were also found among the dynamics of CRP and functional energetics. Double mutation (K52N/H159L) at positions 52 and 159, whose alpha-carbons are separated by 34.6 A, showed nonadditive effects on v(o) and beta(s)(o). These results demonstrate that a small alteration in the local structure due to amino acid substitution is dramatically magnified in the overall protein dynamics which plays an important role in modulating the allosteric behavior of CRP.

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A large compressibility change of protein induced by a single amino acid substitution

Cited by 33 publications

References 12 publications

Intramolecular Communication and Allosteric Sites in Enzymes Unraveled by Time-Dependent Linear Response Theory

Intramolecular Communication and Allosteric Sites in Enzymes Unraveled by Time-Dependent Linear Response Theory

Extreme heat‐ and pressure‐resistant 7‐kDa protein P2 from the archaeon Sulfolobus solfataricus is dramatically destabilized by a single‐point amino acid substitution

A Linear Correlation between the Energetics of Allosteric Communication and Protein Flexibility in the Escherichia coli Cyclic AMP Receptor Protein Revealed by Mutation-Induced Changes in Compressibility and Amide Hydrogen−Deuterium Exchange

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