Compressibility-structure relationship of globular proteins

Gekko, Kunihiko; Hasegawa, Yasunobu

doi:10.1021/bi00369a034

Cited by 441 publications

(425 citation statements)

References 58 publications

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“…Six mutant enzymes having Gly, Ala, Cys, Leu, Phe, or Tyr at position 39 were used for the compressibility study. The & value for wild-type AspAT, 4.3 x cm2 dyn" (Table l), is comparable with that of lysozyme and a-chymotrypsin, 4.67 and 4.15 X cm2 dyn", respectively (Gekko & Hasegawa, 1986, 1989 (Fig. 1) and between p, and 1 7 '…”

Section: K Gekko Et Alsupporting

confidence: 56%

“…Also listed are their partial specific volume at infinite dilution, V0, protein concentration dependence of sound velocity, du/dc, steady-state kinetic parameter for enzyme reaction, k,,,/K,,, and free energy of urea denaturation, AG,". The &value for wild-type DHFR (8.2 X cm2 dyn-I) is comparable with that for 0-lactoglobulin, myoglobin, and dactalbumin (8.45, 8.98, and 8.27 X IO-'2 cm2 dyn-l, respectively, at 25 "C) (Gekko & Hasegawa, 1986), indicating that a Activity of DHFR was measured in 1 0 0 mM imidazole-HCI buffer, pH 7.0, containing 12 mM 2-mercaptoethanol at 25 "C (Gekko et al, 1994). Activity of AspAT was measured with a substrate, aspartate, in 50 mM HEPES buffer, pH 8.0, containing 0.1 M KC1 at 25 "C (Hayashi et al, 1991).…”

supporting

confidence: 58%

“…(The contributions of both the cavity and hydration to the compressibility have been analyzed quantitatively for some globular proteins [Gekko & Noguchi, 1979;Gekko & Hasegawa, 19861). Observed p, and E" values for wild-type and mutant DHFR are distributed over the entire range of those for reported globular proteins (Gekko & Hasegawa, 1986). The correlation between p, and Go falls onto a positive linear relationship as found for other protein systems.…”

supporting

confidence: 51%

“…The compressibility measurements on DHFR and AspAT enzymes were performed without NADPH and with pyridoxal 5'-phosphate, at 15 and 25 "C, respectively. The apparatus and procedures used for compressibility measurements were same as our previous studies (Gekko & Noguchi, 1979;Gekko & Hasegawa, 1986, 1989Tamura et al, 1993;Tamura & Gekko, 1995). The sound velocity in protein solution, u, and the solution density, d, were measured by means of the "sing-around pulse method" at 5 MHz and with a precision density meter, DMA-02C (Anton Paar, Gratz), respectively.…”

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confidence: 99%

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

et al. 1996

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The adiabatic compressibility (βs) was determined, by means of the precise sound velocity and density measurements, for a series of single amino acid substituted mutant enzymes of Escherichia coli dihydrofolate reductase (DHFR) and aspartate aminotransferase (AspAT). Interestingly, the βs values of both DHFR and AspAT were influenced markedly by the mutations at glycine‐121 and valine‐39, respectively, in which the magnitude of the change was proportional to the enzyme activity. This result demonstrates that the local change of the primary structure plays an important role in atomic packing and protein dynamics, which leads to the modified stability and enzymatic function. This is the first report on the compressibility of mutant proteins.

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Section: K Gekko Et Alsupporting

confidence: 56%

supporting

confidence: 58%

supporting

confidence: 51%

mentioning

confidence: 99%

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

et al. 1996

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“…As predicted from the compressibility [19], Cyt c exhibits higher S 2 values, corresponding to more rigid structures than other proteins. In the reduced state, only eight amino acid residues showing S 2 ≤ 0.80 (Val3, Thr19, Val20, His26, Lys27, Gln42, Ile57, and Asn70) were observed, which are located in the loop regions.…”

Section: Backbone Dynamics Of Reduced and Oxidized Cyt Cmentioning

confidence: 57%

Redox-controlled backbone dynamics of human cytochrome c revealed by 15N NMR relaxation measurements

Sakamoto

Kamiya

Uchida

et al. 2010

Biochemical and Biophysical Research Communications

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Redox-controlled backbone dynamics in cytochrome c (Cyt c) were revealed by 2D 15 N NMR relaxation experiments. 15 N T 1 and T 2 values and 1 H-15 N NOEs of uniformly 15 N-labeled reduced and oxidized Cyt c were measured, and the generalized order parameters (S 2 ), the effective correlation time for internal motion (τ e ), the 15 N exchalnge broadening contributions (R ex ) for each residue, and the overal correlation time (τ m ) were estimated by model-free dynamics formalism. These dynamic parameters clearly showed that the backbone dynamics of Cyt c are highly restricted due to the covalently bound heme that functions as the stable hydrophobic core. Upon the oxidation of the heme iron in Cyt c, the average S 2 value was increased from 0.88±0.01 to 0.92±0.01, demonstrating that the mobility of the backbone is further restricted in the oxidized form. Such increases in the S 2 values were more prominent in the loop regions, including amino acid residues near the thioether bonds to the heme moiety and positively charged region around Lys87. Both of the regions are supposed to form the interaction site for cytochrome c oxidase (CcO) and the electron pathway from Cyt c to CcO. The redox-dependent mobility of the backbone in the interaction site for the electron transfer to CcO suggests an electron transfer mechanism regulated by the backbone dynamics in the Cyt c -CcO system.

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Mechanical property of a TIM-barrel protein

1997

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The mechanical response of a TIM-barrel protein to an applied pressure has been studied. We generated structures under an applied pressure by assuming the volume change to be a linear function of normal mode variables. By Delaunay tessellation, the space occupied by protein atoms is divided uniquely into tetrahedra, whose four vertices correspond to atomic positions. Based on the atoms that define them, the resulting Delaunay tetrahedra are classified as belonging to various secondary structures in the protein. The compressibility of various regions identified with respect to secondary structural elements in this protein is obtained from volume changes of respective regions in two structures with and without an applied pressure. We found that the beta barrel region located at the core of the protein is quite soft. The interior of the beta barrel, occupied by side chains of beta strands, is the softest. The helix, strand, and loop segments themselves are extremely rigid, while the regions existing between these secondary structural elements are soft. These results suggest that the regions between secondary structural elements play an important role in protein dynamics. Another aspect of tetrahedra, referred to as bond distance, is introduced to account for rigidities of the tetrahedra. Bond distance is a measure of separation of the atoms of a tetrahedron in terms of number of bonds along the polypeptide chain or side chains. Tetrahedra with longer bond distances are found to be softer on average. From this behavior, we derive a simple empirical equation, which well describes the compressibilities of various regions.

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Compressibility-structure relationship of globular proteins

Cited by 441 publications

References 58 publications

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

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

Redox-controlled backbone dynamics of human cytochrome c revealed by 15N NMR relaxation measurements

Mechanical property of a TIM-barrel protein

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