-
1
-
-
0032692877
-
Occurrence of free D-amino acids and aspartate racemases in hyperthermophilic archaea
-
Matsumoto M, Homma H, Long Z, Imai K, Iida T, Maruyama T, Aikawa Y, Endo I, Yohda M. Occurrence of free D-amino acids and aspartate racemases in hyperthermophilic archaea. J Bacteriol 1999;181:6560-6563.
-
(1999)
J Bacteriol
, vol.181
, pp. 6560-6563
-
-
Matsumoto, M.1
Homma, H.2
Long, Z.3
Imai, K.4
Iida, T.5
Maruyama, T.6
Aikawa, Y.7
Endo, I.8
Yohda, M.9
-
2
-
-
0031827219
-
Occurrence of free D-aspartate and aspartate racemase in the blood shell Scapharca broughtonii
-
Watanabe T, Shibata K, Kera Y, Yamada R. Occurrence of free D-aspartate and aspartate racemase in the blood shell Scapharca broughtonii. Amino Acids 1998;14:353-360.
-
(1998)
Amino Acids
, vol.14
, pp. 353-360
-
-
Watanabe, T.1
Shibata, K.2
Kera, Y.3
Yamada, R.4
-
3
-
-
0027484142
-
Presence of the N-methyl-D-aspartate-associated glycine receptor agonist, D-serine, in human temporal cortex: Comparison of normal, Parkinson, and Alzheimer tissues
-
Chouinard ML, Gaitan D, Wood PL. Presence of the N-methyl-D-aspartate- associated glycine receptor agonist, D-serine, in human temporal cortex: comparison of normal, Parkinson, and Alzheimer tissues. J Neurochem 1993;61:1561-1564.
-
(1993)
J Neurochem
, vol.61
, pp. 1561-1564
-
-
Chouinard, M.L.1
Gaitan, D.2
Wood, P.L.3
-
4
-
-
0037636496
-
D-serine and serine racemase are present in the vertebrate retina and contribute to the physiological activation of NMDA receptors
-
Stevens ER, Esguerra M, Kim PM, Newman EA, Snyder SH, Zahs KR, Miller RF. D-serine and serine racemase are present in the vertebrate retina and contribute to the physiological activation of NMDA receptors. Proc Natl Acad Sci U S A 2003;100:6789-6794.
-
(2003)
Proc Natl Acad Sci U S A
, vol.100
, pp. 6789-6794
-
-
Stevens, E.R.1
Esguerra, M.2
Kim, P.M.3
Newman, E.A.4
Snyder, S.H.5
Zahs, K.R.6
Miller, R.F.7
-
5
-
-
0037306393
-
Purification and characterization of aspartate racemase from the bivalve mollusk Scapharca broughtonii
-
Shibata K, Watanabe T, Yoshikawa H, Abe K, Takahashi S, Kera Y, Yamada RH. Purification and characterization of aspartate racemase from the bivalve mollusk Scapharca broughtonii. Comp Biochem Physiol B Biochem Mol Biol 2003;134:307-314.
-
(2003)
Comp Biochem Physiol B Biochem Mol Biol
, vol.134
, pp. 307-314
-
-
Shibata, K.1
Watanabe, T.2
Yoshikawa, H.3
Abe, K.4
Takahashi, S.5
Kera, Y.6
Yamada, R.H.7
-
6
-
-
0000950510
-
Mandelate racemase and class-related enzymes
-
Gerlt JA, Kenyon GL, Kozarich JW, Neidhart DJ, Petsko GA, Powers VM. Mandelate racemase and class-related enzymes. Current Opin Struct Biol 1992;2:736-742.
-
(1992)
Current Opin Struct Biol
, vol.2
, pp. 736-742
-
-
Gerlt, J.A.1
Kenyon, G.L.2
Kozarich, J.W.3
Neidhart, D.J.4
Petsko, G.A.5
Powers, V.M.6
-
7
-
-
84961472980
-
Pyridoxal enzymes acting on D-amino acids
-
Soda K, Esaki N. Pyridoxal enzymes acting on D-amino acids. Pure Appl Chem 1994;66:709-714.
-
(1994)
Pure Appl Chem
, vol.66
, pp. 709-714
-
-
Soda, K.1
Esaki, N.2
-
8
-
-
0000506164
-
Cloning and expression in Escherichia coli of the glutamate racemase gene from Pediococcus pentosaceus
-
Nakajima N, Tanizawa K, Tanaka H, Soda K. Cloning and expression in Escherichia coli of the glutamate racemase gene from Pediococcus pentosaceus. Agric Biol Chem 1986;50:2823-2830.
-
(1986)
Agric Biol Chem
, vol.50
, pp. 2823-2830
-
-
Nakajima, N.1
Tanizawa, K.2
Tanaka, H.3
Soda, K.4
-
9
-
-
0027299709
-
Mechanism of the reaction catalyzed by glutamate racemase
-
Gallo KA, Tanner ME, Knowles JR. Mechanism of the reaction catalyzed by glutamate racemase. Biochemistry 1993;32:3991-3997.
-
(1993)
Biochemistry
, vol.32
, pp. 3991-3997
-
-
Gallo, K.A.1
Tanner, M.E.2
Knowles, J.R.3
-
10
-
-
0027155359
-
Isotope effects and the identification of catalytic residues in the reaction catalyzed by glutamate racemase
-
Tanner ME, Gallo KA, Knowles JR. Isotope effects and the identification of catalytic residues in the reaction catalyzed by glutamate racemase. Biochemistry 1993;32:3998-4006.
-
(1993)
Biochemistry
, vol.32
, pp. 3998-4006
-
-
Tanner, M.E.1
Gallo, K.A.2
Knowles, J.R.3
-
11
-
-
0033528712
-
Chemical mechanism of Haemophilus influenzae diaminopimelate epimerase
-
Koo CW, Blanchard JS. Chemical mechanism of Haemophilus influenzae diaminopimelate epimerase. Biochemistry 1999;38:4416-4422.
-
(1999)
Biochemistry
, vol.38
, pp. 4416-4422
-
-
Koo, C.W.1
Blanchard, J.S.2
-
12
-
-
0023043214
-
Energetics of proline racemase: Transition-state fractionation factors for the two protons involved in the catalytic steps
-
Fisher LM, Belasco JG, Bruice TW, Albery WJ, Knowles JR. Energetics of proline racemase: transition-state fractionation factors for the two protons involved in the catalytic steps. Biochemistry 1986;25:2543-2551.
-
(1986)
Biochemistry
, vol.25
, pp. 2543-2551
-
-
Fisher, L.M.1
Belasco, J.G.2
Bruice, T.W.3
Albery, W.J.4
Knowles, J.R.5
-
13
-
-
0026655552
-
Properties of aspartate racemase, a pyridoxal 5′-phosphate- independent amino acid racemase
-
Yamauchi T, Choi SY, Okada H, Yohda M, Kumagai H, Esaki N, Soda K. Properties of aspartate racemase, a pyridoxal 5′-phosphate-independent amino acid racemase. J Biol Chem 1992;267:18361-18364.
-
(1992)
J Biol Chem
, vol.267
, pp. 18361-18364
-
-
Yamauchi, T.1
Choi, S.Y.2
Okada, H.3
Yohda, M.4
Kumagai, H.5
Esaki, N.6
Soda, K.7
-
14
-
-
0036301494
-
Crystal structure of aspartate racemase from Pyrococcus horikoshii OT3 and its implications for molecular mechanism of PLP-independent racemization
-
Liu L, Iwata K, Kita A, Kawarabayasi Y, Yohda M, Miki K. Crystal structure of aspartate racemase from Pyrococcus horikoshii OT3 and its implications for molecular mechanism of PLP-independent racemization. J Mol Biol 2002;319:479-489.
-
(2002)
J Mol Biol
, vol.319
, pp. 479-489
-
-
Liu, L.1
Iwata, K.2
Kita, A.3
Kawarabayasi, Y.4
Yohda, M.5
Miki, K.6
-
15
-
-
0037174167
-
Structural insight into gene duplication, gene fusion and domain swapping in the evolution of PLP-independent amino acid racemases
-
Liu L, Iwata K, Yohda M, Miki K. Structural insight into gene duplication, gene fusion and domain swapping in the evolution of PLP-independent amino acid racemases. FEBS Lett 2002;528:114-118.
-
(2002)
FEBS Lett
, vol.528
, pp. 114-118
-
-
Liu, L.1
Iwata, K.2
Yohda, M.3
Miki, K.4
-
16
-
-
0034640453
-
Hydrogen bonds and proton transfer in general-catalytic transition-state stabilization in enzyme catalysis
-
Schowen KB, Limbach HH, Denisov GS, Schowen RL. Hydrogen bonds and proton transfer in general-catalytic transition-state stabilization in enzyme catalysis. Biochim Biophys Acta 2000;1458:43-62.
-
(2000)
Biochim Biophys Acta
, vol.1458
, pp. 43-62
-
-
Schowen, K.B.1
Limbach, H.H.2
Denisov, G.S.3
Schowen, R.L.4
-
18
-
-
0032915050
-
Structure and mechanism of glutamate racemase from Aquifex pyrophilus
-
Hwang KY, Cho CS, Kim SS, Sung HC, Yu YG, Cho Y. Structure and mechanism of glutamate racemase from Aquifex pyrophilus. Nat Struct Biol 1999;6:422-426.
-
(1999)
Nat Struct Biol
, vol.6
, pp. 422-426
-
-
Hwang, K.Y.1
Cho, C.S.2
Kim, S.S.3
Sung, H.C.4
Yu, Y.G.5
Cho, Y.6
-
19
-
-
0036688941
-
L-aspartate oxidase is present in the anaerobic hyperthermophilic archaeon Pyrococcus horikoshii OT-3: Characteristics and role in the de novo biosynthesis of nicotinamide adenine dinucleotide proposed by genome sequencing
-
Sakuraba H, Satomura T, Kawakami R, Yamamoto S, Kawarabayasi Y, Kikuchi H, Ohshima T. L-aspartate oxidase is present in the anaerobic hyperthermophilic archaeon Pyrococcus horikoshii OT-3: characteristics and role in the de novo biosynthesis of nicotinamide adenine dinucleotide proposed by genome sequencing. Extremophiles 2002;6:275-281.
-
(2002)
Extremophiles
, vol.6
, pp. 275-281
-
-
Sakuraba, H.1
Satomura, T.2
Kawakami, R.3
Yamamoto, S.4
Kawarabayasi, Y.5
Kikuchi, H.6
Ohshima, T.7
-
20
-
-
0034754658
-
Crystallization and preliminary X-ray analysis of aspartate racemase from Pyrococcus horikoshii OT3
-
Liu L, Iwata K, Kawarabayasi Y, Kikuchi H, Kita A, Yohda M, Miki K. Crystallization and preliminary X-ray analysis of aspartate racemase from Pyrococcus horikoshii OT3. Acta Crystallogr D Biol Crystallogr 2001;57:1674-1676.
-
(2001)
Acta Crystallogr D Biol Crystallogr
, vol.57
, pp. 1674-1676
-
-
Liu, L.1
Iwata, K.2
Kawarabayasi, Y.3
Kikuchi, H.4
Kita, A.5
Yohda, M.6
Miki, K.7
-
21
-
-
0034808464
-
Occurrence of D-amino acids and a pyridoxal 5′-phosphate-dependent aspartate racemase in the acidothermophilic archaeon, Thermoplasma acidophilum
-
Long Z, Lee JA, Okamoto T, Sekine M, Nimura N, Imai K, Yohda M, Maruyama T, Sumi M, Kamo N, Yamagishi A, Oshima T, Homma H. Occurrence of D-amino acids and a pyridoxal 5′-phosphate-dependent aspartate racemase in the acidothermophilic archaeon, Thermoplasma acidophilum. Biochem Biophys Res Commun 2001;281:317-321.
-
(2001)
Biochem Biophys Res Commun
, vol.281
, pp. 317-321
-
-
Long, Z.1
Lee, J.A.2
Okamoto, T.3
Sekine, M.4
Nimura, N.5
Imai, K.6
Yohda, M.7
Maruyama, T.8
Sumi, M.9
Kamo, N.10
Yamagishi, A.11
Oshima, T.12
Homma, H.13
-
22
-
-
0004268506
-
-
San Francisco: University of California
-
Case D, Pearlman D, Caldwell J, Cheatham III T, Ross W, Simmerling C, Darden T, Merz K, Stanton R, Cheng A, Vincent J, Crowley M, Ferguson D, Radmer R, Seibel G, Singh U, Weiner P, Kollman P. AMBER 6. San Francisco: University of California; 2000.
-
(2000)
AMBER 6
-
-
Case, D.1
Pearlman, D.2
Caldwell, J.3
Cheatham III, T.4
Ross, W.5
Simmerling, C.6
Darden, T.7
Merz, K.8
Stanton, R.9
Cheng, A.10
Vincent, J.11
Crowley, M.12
Ferguson, D.13
Radmer, R.14
Seibel, G.15
Singh, U.16
Weiner, P.17
Kollman, P.18
-
23
-
-
0029011701
-
A 2nd generation force-field for the simulation of proteins, nucleic acids, and organic molecules
-
Cornell WD, Cieplak P, Bayly CI, Gould IR, Merz KM, Ferguson DM, Spellmeyer DC, Fox T, Caldwell JW, Kollman PA. A 2nd generation force-field for the simulation of proteins, nucleic acids, and organic molecules. J Am Chem Soc 1995;117:5179-5197.
-
(1995)
J Am Chem Soc
, vol.117
, pp. 5179-5197
-
-
Cornell, W.D.1
Cieplak, P.2
Bayly, C.I.3
Gould, I.R.4
Merz, K.M.5
Ferguson, D.M.6
Spellmeyer, D.C.7
Fox, T.8
Caldwell, J.W.9
Kollman, P.A.10
-
24
-
-
0002098417
-
The development/application of a 'minimalist' organic/biochemical molecular mechanic force field using a combination of ab initio calculations and experimental data
-
A. W, P. W, W. vG, editors. New York: Elsevier
-
Kollman P, Dixon R, Cornell W, Fox T, Chipot C, Phorille A. The development/application of a 'minimalist' organic/biochemical molecular mechanic force field using a combination of ab initio calculations and experimental data. In: A. W, P. W, W. vG, editors. Computer simulation of biomolecular systems. New York: Elsevier; 1997. p 83-96.
-
(1997)
Computer Simulation of Biomolecular Systems
, pp. 83-96
-
-
Kollman, P.1
Dixon, R.2
Cornell, W.3
Fox, T.4
Chipot, C.5
Phorille, A.6
-
25
-
-
0004016501
-
Comparison of simple potential functions for simulating liquid water
-
Jorgensen W, Chandrasekhar J, Madura J, Klein M. Comparison of simple potential functions for simulating liquid water. J Chem Phys 1983;79:926-935.
-
(1983)
J Chem Phys
, vol.79
, pp. 926-935
-
-
Jorgensen, W.1
Chandrasekhar, J.2
Madura, J.3
Klein, M.4
-
26
-
-
22944463454
-
Two algorithms designed for realizing efficient combination of fast multipole method and dedicated hardware for molecular dynamics simulations
-
Amisaki T, Toyoda S, Miyagawa H, Kitamura K. Two algorithms designed for realizing efficient combination of fast multipole method and dedicated hardware for molecular dynamics simulations. J Comput Chem 2002;1:73-82.
-
(2002)
J Comput Chem
, vol.1
, pp. 73-82
-
-
Amisaki, T.1
Toyoda, S.2
Miyagawa, H.3
Kitamura, K.4
-
28
-
-
0029170114
-
Molecular-dynamics simulations on solvated biomolecular systems - The particle mesh Ewald method leads to stable trajectories of DNA, RNA, and proteins
-
Cheatham TE, Miller JL, Fox T, Darden TA, Kollman PA. Molecular-dynamics simulations on solvated biomolecular systems - the particle mesh Ewald method leads to stable trajectories of DNA, RNA, and proteins. J Am Chem Soc 1995;117:4193-4194.
-
(1995)
J Am Chem Soc
, vol.117
, pp. 4193-4194
-
-
Cheatham, T.E.1
Miller, J.L.2
Fox, T.3
Darden, T.A.4
Kollman, P.A.5
-
29
-
-
0029110156
-
Toward the aaccurate modeling of DNA - The importance of long-range electrostatics
-
York DM, Yang WT, Lee H, Darden T, Pedersen LG. Toward the aaccurate modeling of DNA - the importance of long-range electrostatics. J Am Chem Soc 1995;117:5001-5002.
-
(1995)
J Am Chem Soc
, vol.117
, pp. 5001-5002
-
-
York, D.M.1
Yang, W.T.2
Lee, H.3
Darden, T.4
Pedersen, L.G.5
-
30
-
-
33646940952
-
Numerical integration of the cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes
-
Ryckaert J, Ciccotti G, Berendsen H. Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. J Comput Phys 1977;23:327-341.
-
(1977)
J Comput Phys
, vol.23
, pp. 327-341
-
-
Ryckaert, J.1
Ciccotti, G.2
Berendsen, H.3
-
31
-
-
33750587438
-
Molecular dynamics with coupling to an external bath
-
Berendsen H, Postma J, van Grensteren W, DiNola A, Haak J. Molecular dynamics with coupling to an external bath. J Chem Phys 1984;81:3684-3690.
-
(1984)
J Chem Phys
, vol.81
, pp. 3684-3690
-
-
Berendsen, H.1
Postma, J.2
Van Grensteren, W.3
Dinola, A.4
Haak, J.5
-
32
-
-
0025064089
-
A theorem on amplitudes of thermal atomic fluctuations in large molecules assuming specific conformations calculated by normal mode analysis
-
Go N. A theorem on amplitudes of thermal atomic fluctuations in large molecules assuming specific conformations calculated by normal mode analysis. Biophys Chem 1990;35:105-112.
-
(1990)
Biophys Chem
, vol.35
, pp. 105-112
-
-
Go, N.1
-
33
-
-
0000998079
-
The effects of solvent on the conformation and the collective motions of protein: Normal mode analysis and molecular dynamics simulations of melittin in water and in vacuum
-
Kitao A, Hirata F, Go N. The effects of solvent on the conformation and the collective motions of protein: normal mode analysis and molecular dynamics simulations of melittin in water and in vacuum. Chem Phys 1991;158:447-472.
-
(1991)
Chem Phys
, vol.158
, pp. 447-472
-
-
Kitao, A.1
Hirata, F.2
Go, N.3
-
34
-
-
0000885331
-
Harmonic-analysis of large systems. 1. Methodology
-
Brooks BR, Janezic D, Karplus M. Harmonic-analysis of large systems. 1. Methodology. J Comput Chem 1995;16:1522-1542.
-
(1995)
J Comput Chem
, vol.16
, pp. 1522-1542
-
-
Brooks, B.R.1
Janezic, D.2
Karplus, M.3
-
35
-
-
3342957245
-
Multiple substrate binding states and chiral recognition in cofactor-independent glutamate racemase: A molecular dynamics study
-
Mobitz H, Bruice TC. Multiple substrate binding states and chiral recognition in cofactor-independent glutamate racemase: a molecular dynamics study. Biochemistry 2004;43:9685-9694.
-
(2004)
Biochemistry
, vol.43
, pp. 9685-9694
-
-
Mobitz, H.1
Bruice, T.C.2
|