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Shapovalov YA, Gladyshev PP, Tuleukhanov ST, Shvetsova EV, Abdrasulova ZT. Radicals in Cellular Structures. Biophysics (Nagoya-shi) 2020. [DOI: 10.1134/s000635092004020x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Chou PY, Fasman GD. Prediction of the secondary structure of proteins from their amino acid sequence. ADVANCES IN ENZYMOLOGY AND RELATED AREAS OF MOLECULAR BIOLOGY 2006; 47:45-148. [PMID: 364941 DOI: 10.1002/9780470122921.ch2] [Citation(s) in RCA: 878] [Impact Index Per Article: 48.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Affiliation(s)
- A V Efimov
- Institute of Protein Research, Russian Academy of Sciences, Moscow Region
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Abstract
A survey of 40 multisubunit proteins and 2 protein-protein complexes was performed to assay quantitatively the distribution of hydropathy among the exterior surface, interior, contact surface, and noncontact exterior surface of the isolated subunits. We suggest a useful way to present this distribution by using a "hydropathy level diagram." Additionally, we have devised a function called "hydropathy complementarity" to quantitate the degree to which interacting surfaces have matching hydropathy distributions. Our survey revealed the following patterns: (1) The difference in hydropathy between the interior and exterior of subunits is a fairly invariant quantity. (2) On average, the hydropathy of the contact surface is higher than that of the exterior surface, but is not greater than that of the protein as a whole. There was variation, however, among the proteins. In some instances, the contact surface was more hydrophilic than the noncontact exterior, and in a few cases the contact surface was as hydrophobic as the protein interior. (3) The average interface manifests significant hydropathy complementarity, signifying that proteins interact by placing hydrophobic centers of one surface against hydrophobic centers of the other surface, and by similarly matching hydrophilic centers. As a measure of recognition and specificity, hydropathy complementarity could be a useful tool for predicting correct docking of interacting proteins. We suggest that high hydropathy complementarity is associated with static inflexible interactions. (4) We have found that some subunits that bind predominantly through hydrophilic forces, such as hydrogen bonds, ionic pairs, and water and metal bridges, are involved in dynamic quaternary organization and allostery.
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Affiliation(s)
- A P Korn
- Wistar Institute, Philadelphia, Pennsylvania 19104
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Tohá JC, Soto MA, Chinga H. Pattern recognition of the secondary structure of proteins (alpha-helix and beta-structure). J Theor Biol 1990; 146:145-56. [PMID: 2259198 DOI: 10.1016/s0022-5193(05)80132-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
In this paper, an algorithm for the pattern recognition of secondary structure of proteins is proposed. The procedure simultaneously evaluates the contribution of all the residues of a given peptide to its conformation. By means of the algorithm it is possible to select from a universe of well known proteins the most representative alpha-helix and beta-structure peptides, and to use these peptides, as screening matrices to define the unknown structure of any peptide.
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Affiliation(s)
- J C Tohá
- Departamento de Física, Facultad de Ciencias Físicas y Matemáticas, Universidad de Chile, Santiago
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A statistical method for predicting alpha-helical and beta-sheet regions in proteins from their amino acidic sequences. ACTA ACUST UNITED AC 1984. [DOI: 10.1007/bf02457469] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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8
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Efimov AV. A novel super-secondary structure of proteins and the relation between the structure and the amino acid sequence. FEBS Lett 1984; 166:33-8. [PMID: 6692923 DOI: 10.1016/0014-5793(84)80039-3] [Citation(s) in RCA: 62] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
A novel protein super-secondary structure which is referred to as an alpha alpha-corner is considered. The alpha alpha-corner is formed by two consecutive alpha-helices packed approximately crosswise and connected by two or more peptide units. It is shown that the amino acid sequences coding for the alpha alpha-corners have a strictly definite order of hydrophobic, hydrophilic and glycine residues. A hypothesis is suggested that the alpha alpha-corner can be an embryo of protein folding.
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Borisov VV, Borisova SN, Sosfenov NI, Vainshtein BK. Electron density map of chicken heart cytosol aspartate transaminase at 3.5 A resolution. Nature 1980; 284:189-90. [PMID: 7360247 DOI: 10.1038/284189a0] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Aspartate transaminase (EC 2.6.1.1., Asp-transaminase) has been studied extensively, and much is now known about its physico-chemical, catalytic and other properties. X-ray studies that can provide a structural foundation for the events that occur during the transamination reaction are under way on three species of Asp-transaminase: the cytosolic enzyme from pig and chicken hearts, and the mitochondrial chicken heart enzyme. We describe here the interpretation of an electron density map of Asp-transaminase from chicken heart cytosol at 3.5 A.
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Kolaskar AS, Prashanth D. Empirical torsional potential functions from protein structure data. Phi- and psi-potentials for non-glycyl amino acid residues. INTERNATIONAL JOURNAL OF PEPTIDE AND PROTEIN RESEARCH 1979; 14:88-98. [PMID: 489256 DOI: 10.1111/j.1399-3011.1979.tb01731.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The torsional potential functions Vt(phi) and Vt(psi) around single bonds N--C alpha and C alpha--C, which can be used in conformational studies of oligopeptides, polypeptides and proteins, have been derived, using crystal structure data of 22 globular proteins, fitting the observed distribution in the (phi, psi)-plane with the value of Vtot(phi, psi), using the Boltzmann distribution. The averaged torsional potential functions, obtained from various amino acid residues in L-configuration, are Vt(phi) = 1.0 cos (phi + 60 degrees); Vt(psi) = 0.5 cos (psi + 60 degrees) - 1.0 cos (2 psi + 30 degrees) - 0.5 cos (3 psi + 30 degrees). The dipeptide energy maps Vtot(phi, psi) obtained using these functions, instead of the normally accepted torsional functions, were found to explain various observations, such as the absence of the left-handed alpha helix and the C7 conformation, and the relatively high density of points near the line psi = 0 degrees. These functions derived from observational data on protein structures, will, it is hoped, explain various previously unexplained facts in polypeptide conformation.
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Bhat TN, Sasisekharan V, Vijayan M. An analysis of side-chain conformation in proteins. INTERNATIONAL JOURNAL OF PEPTIDE AND PROTEIN RESEARCH 1979; 13:170-84. [PMID: 429093 DOI: 10.1111/j.1399-3011.1979.tb01866.x] [Citation(s) in RCA: 136] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The crystal structures of a number of globular proteins are currently available. An analysis of the distribution of side-chains among different allowed conformations in these proteins has been carried out. The observed conformations of individual residues are discussed on the basis of well-known stereochemical criteria. The population distribution of side-chains in different allowed regions in conformational space can be explained largely on the basis of simple steric considerations. In addition to examining the conformational behaviour of individual residues, some population distributions of conformational angles of general interest involving groups of residues have also been analyzed.
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12
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Woody RW. Aromatic side-chain contributions to the far ultraviolet circular dichroism of peptides and proteins. Biopolymers 1978. [DOI: 10.1002/bip.1978.360170606] [Citation(s) in RCA: 206] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Phillips DC, Sternberg MJ, Thornton JM, Wilson IA. An analysis of the structure of triose phosphate isomerase and its comparison with lactate dehydrogenase. J Mol Biol 1978; 119:329-51. [PMID: 633372 DOI: 10.1016/0022-2836(78)90440-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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Manavalan P, Ponnuswamy PK. A study of the preferred environment of amino acid residues in globular proteins. Arch Biochem Biophys 1977; 184:476-87. [PMID: 596883 DOI: 10.1016/0003-9861(77)90457-x] [Citation(s) in RCA: 85] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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Biesecker G, Harris JI, Thierry JC, Walker JE, Wonacott AJ. Sequence and structure of D-glyceraldehyde 3-phosphate dehydrogenase from Bacillus stearothermophilus. Nature 1977; 266:328-33. [PMID: 193030 DOI: 10.1038/266328a0] [Citation(s) in RCA: 232] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The glyceraldehyde 3-phosphate dehydogenase holoenzyme of Bacillus stearothermophilus possesses precise 222 symmetry: in this respect it differs from the reported structure of the lobster muscle enzyme. Pairs of active sites are linked through a flexible polypeptide loop which probably mediates the structural changes giving rise to cooperative effects. Three additional salt bridges made by each subunit to others would make a major contribution to thermostability of the tetramer.
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Mattice WL, Carpenter DK. Effect of the fluctuations in electron density within a globular protein on the excess small-angle X-ray scattering. Biopolymers 1977. [DOI: 10.1002/bip.1977.360160107] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Sternberg MJ, Thornton JM. On the conformation of proteins: the handedness of the beta-strand-alpha-helix-beta-strand unit. J Mol Biol 1976; 105:367-82. [PMID: 972389 DOI: 10.1016/0022-2836(76)90099-1] [Citation(s) in RCA: 134] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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Taylor SS, Oxley SS. Homologies in the active site regions of lactate dehydrogenases. Arch Biochem Biophys 1976; 175:373-83. [PMID: 962329 DOI: 10.1016/0003-9861(76)90524-5] [Citation(s) in RCA: 33] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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22
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Abstract
A simple diagrammatic representation has been used to show the arrangement of alpha helices and beta sheets in 31 globular proteins, which are classified into four clearly separated classes. The observed arrangements are significantly non-random in that pieces of secondary structure adjacent in sequence along the polypeptide chain are also often in contact in three dimensions.
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White JL, Hackert ML, Buehner M, Adams MJ, Ford GC, Lentz PJ, Smiley IE, Steindel SJ, Rossmann MG. A comparison of the structures of apo dogfish M4 lactate dehydrogenase and its ternary complexes. J Mol Biol 1976; 102:759-79. [PMID: 940154 DOI: 10.1016/0022-2836(76)90290-4] [Citation(s) in RCA: 161] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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Greer J. Automated interpretation of electron density maps of proteins: derivation of atomic co-ordinates for the main chain. J Mol Biol 1976; 100:427-58. [PMID: 1255726 DOI: 10.1016/s0022-2836(76)80039-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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Chou PY, Adler AJ, Fasman GD. Conformational prediction and circular dichroism studies on the lac repressor. J Mol Biol 1975; 96:29-45. [PMID: 1099214 DOI: 10.1016/0022-2836(75)90180-1] [Citation(s) in RCA: 78] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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Chen SS, Engel PC. Modification of pig M4 lactate dehydrogenase by pyridoxal 5'-phosphate. Demonstration of an essential lysine residue. Biochem J 1975; 149:107-13. [PMID: 1238085 PMCID: PMC1165597 DOI: 10.1042/bj1490107] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
1. Pig M4 lactate dehydrogenase treated in the dark with pyridoxal 5'-phosphate at pH8.5 and 25 degrees C loses activity gradually. The maximum inactivation was 66%, and this did not increase with concentrations of pyridoxal 5'-phosphate above 1 mM. 2. Inactivation may be reversed by dialysis or made permanent by reducing the enzyme with NaBH4. 3. Spectral evidence indicates modification of lysine residues, and 6-N-pyridoxyl-lysine is present in the hydrolsate of inactivated, reduced enzyme. 4. A second cycle of treatment with pyridoxal 5'-phosphate and NaBH4 further decreases activity. After three cycles only 9% of the original activity remains. 5. Apparent Km values for lactate and NAD+ are unaltered in the partially inactivated enzyme. 6. These results suggest that the covalently modified enzyme is inactive; failure to achieve complete inactivation in a single treatment is due to the reversibility of Schiff-base formation and to the consequent presence of active non-covalently bonded enzyme-modifier complex in the equilibrium mixture. 7. Although several lysine residues per subunit are modified, only one appears to be essential for activity: pyruvate and NAD+ together (both 5mM) completely protect against inactivation, and there is a one-to-one relationship between enzyme protection and decreased lysine modification. 8. NAD+ or NADH alone gives only partial protection. Substrates give virtually none. 9. Pig H4 lactate dehydrogenase is also inactivated by pyridoxal 5'-phosphate. 10. The possible role of the essential lysine residue is discussed.
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Nagano K, Hasegawa K. Logical analysis of the mechanism of protein folding III. Prediction of the strong long-range interactions. J Mol Biol 1975; 94:257-81. [PMID: 1142442 DOI: 10.1016/0022-2836(75)90082-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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Ohlsson I, Nordström B, Brändén CI. Structural and functional similarities within the coenzyme binding domains of dehydrogenases. J Mol Biol 1974; 89:339-54. [PMID: 4374553 DOI: 10.1016/0022-2836(74)90523-3] [Citation(s) in RCA: 139] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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Lim VI. Algorithms for prediction of alpha-helical and beta-structural regions in globular proteins. J Mol Biol 1974; 88:873-94. [PMID: 4427384 DOI: 10.1016/0022-2836(74)90405-7] [Citation(s) in RCA: 395] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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Blake CC, Evans PR. Structure of horse muscle phosphoglycerate kinase. Some results on the chain conformation, substrate binding and evolution of the molecule from a 3 angstrom Fourier map. J Mol Biol 1974; 84:585-601. [PMID: 4841001 DOI: 10.1016/0022-2836(74)90118-1] [Citation(s) in RCA: 167] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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