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cleavage of an N-acetyl or N-formyl amino acid from the N-terminus of a polypeptide
substrate binding and catalytic mechanisms, overview. Three main pathways are observed most frequently, namely P1, P2A, and P3, evaluation by comparing the average force profiles and potential of mean force calculations revealing that P3 is the unbinding pathway. P1 is located in a tunnel in the beta-propeller domain and contained the D158, R160, S157, S201, A200, S199, W250, D69, Q28, and R287 residues. P2A is located between blades 1 and 2 (G86, E88, K85, H90, D82, and N65), whereas P2D penetrates through blades 1 and 2 formed by loop A, which is close to P2A (S481, F485, D482, L115, I114, R113, H90, E88, R526, and S525). P3 is located between the beta-propeller domain and alpha/beta hydrolase containing the residues M561, A564, L568, F381, T380, I20, A21, F41, K24, G40, G44, and V46
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2-aminobenzoyl-Ala-Leu-Phe-Gln-Gly-Pro-Phe(NO2)-Ala + H2O
2-aminobenzoyl-Ala-Leu-Phe + Gln-Gly-Pro-Phe(NO2)-Ala
endopeptidase activity
-
-
?
4-nitrophenyl caprylate + H2O
4-nitrophenol + caprylate
-
-
-
?
Ac-Ala-Ala + H2O
Ac-Ala + Ala
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-
-
?
Ac-Ala-Ala-Ala + H2O
Ac-Ala + Ala-Ala
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-
-
?
Ac-Ala-Ala-Ala-Ala + H2O
Ac-Ala + Ala-Ala-Ala
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-
-
?
Ac-Leu-4-nitroanilide + H2O
Ac-Leu + 4-nitroaniline
-
-
-
?
acetyl-Phe-2-naphthylamide + H2O
acetyl-Phe + 2-naphthylamine
-
-
-
?
N-acetyl-L-Leu-4-nitroanilide + H2O
N-acetyl-L-Leu + 4-nitroaniline
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-
-
?
N-acetyl-Leu-4-nitroanilide + H2O
N-acetyl-L-Leu + 4-nitroaniline
switch of substrate specificity of hyperthermophilic promiscuous acylaminoacyl peptidase by combination of protein and solvent engineering into a specific carboxylesterase
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?
N-acetyl-Leu-p-nitroanilide + H2O
N-acetyl-Leu + p-nitroaniline
esterase activity of wild-type enzyme with p-nitrophenyl caprylate as substrate is 7times higher than peptidase activity with N-acetyl-Leu-p-nitroanilide as substrate, 150fold higher for mutant enzyme R526V, peptidase activity for mutant R526E is abolished
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?
N-acetyl-Phe-2-naphthylamide + H2O
N-acetyl-Phe + 2-naphthylamine
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-
-
?
p-nitrophenyl caprylate + H2O
nitrophenol + caprylate
esterase activity of wild-type enzyme with p-nitrophenyl caprylate as substrate is 7times higher than peptidase activity with N-acetyl-Leu-p-nitroanilide as substrate, 150fold higher for mutant enzyme R526V, peptidase activity for mutant R526E is abolished
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-
?
additional information
?
-
additional information
?
-
hundreds nanosecond all-atom atomistic molecular dynamics simulations of a representative member of the acylaminoacyl peptidase subfamily (Aeropyrum pernix K1) allow to identify the presence of a tunnel which from the surrounding of the N-terminal alpha1-helix bring to the catalytic site and it is regulated by conformational changes of the N-terminal alpha-helix itself and its surroundings in the native conformational ensemble
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?
additional information
?
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acylaminoacyl peptidase (AAP) is an oligopeptidase that only cleaves short peptides or protein segments
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?
additional information
?
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acylaminoacyl peptidase (AAP) is an oligopeptidase that only cleaves short peptides or protein segments
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?
additional information
?
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enzyme APH catalyzes the N-terminal hydrolysis of Nalpha-acylpeptides to release Nalpha-acylated amino acids
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?
additional information
?
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the acylpeptide hydrolase and esterase activity of wild-type and the mutants is tested with acetyl-amino acid-4-nitroanilides (Ac-Ala2, Ac-Ala3, Ac-Ala4) as the APH substrate and 4-nitrophenyl fatty acid esters (pNPC2, pNPC3, pNPC4, pNPC8, pNPC12, pNPC16) as esterase substrate. Substrate specificity of wild-type and mutant enzymes, overview
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?
additional information
?
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the enzyme is also active with fatty acid esters, e.g. with 4-nitrophenyl caprylate. Substrate binding mechanism analysis, and random acceleration and steered molecular dynamics simulations of ligands unbinding pathways from APH. Three main pathways are observed most frequently, namely P1, P2A, and P3, evaluation by comparing the average force profiles and potential of mean force calculations revealing that P3 is the unbinding pathway. Overview
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?
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0.00129 - 0.0071
2-aminobenzoyl-Ala-Leu-Phe-Gln-Gly-Pro-Phe(NO2)-Ala
0.0082 - 0.1
acetyl-Phe-2-naphthylamide
0.4 - 10.5
N-acetyl-Leu-p-nitroanilide
0.00566
N-acetyl-Phe-2-naphthylamide
pH 7.0, 70°C, wild-type enzyme
35.7 - 114.6
p-nitrophenyl caprylate
additional information
additional information
thermodynamics
-
0.00129
2-aminobenzoyl-Ala-Leu-Phe-Gln-Gly-Pro-Phe(NO2)-Ala
pH 7.0, 70°C, wild-type enzyme
0.00281
2-aminobenzoyl-Ala-Leu-Phe-Gln-Gly-Pro-Phe(NO2)-Ala
pH 7.0, 70°C, mutant enzyme D524N
0.0071
2-aminobenzoyl-Ala-Leu-Phe-Gln-Gly-Pro-Phe(NO2)-Ala
pH 7.0, 70°C, mutant enzyme D524A
0.0082
acetyl-Phe-2-naphthylamide
wild-type
0.1
acetyl-Phe-2-naphthylamide
mutant H367A
0.4
N-acetyl-Leu-p-nitroanilide
80°C, wild-type enzyme
1.3
N-acetyl-Leu-p-nitroanilide
80°C, mutant enzyme R526L
1.7
N-acetyl-Leu-p-nitroanilide
80°C, mutant enzyme R526V
2.1
N-acetyl-Leu-p-nitroanilide
80°C, mutant enzyme R526I
4.3
N-acetyl-Leu-p-nitroanilide
80°C, mutant enzyme R526A
5.8
N-acetyl-Leu-p-nitroanilide
80°C, mutant enzyme R526E
10.5
N-acetyl-Leu-p-nitroanilide
80°C, mutant enzyme R526K
35.7
p-nitrophenyl caprylate
80°C, mutant enzyme R526V
38.2
p-nitrophenyl caprylate
80°C, mutant enzyme R526K
38.2
p-nitrophenyl caprylate
80°C, mutant enzyme R526L
40.1
p-nitrophenyl caprylate
80°C, mutant enzyme R526I
41.6
p-nitrophenyl caprylate
80°C, mutant enzyme R526A
43.3
p-nitrophenyl caprylate
80°C, wild-type enzyme
114.6
p-nitrophenyl caprylate
80°C, mutant enzyme R526E
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0.000917 - 8.2
2-aminobenzoyl-Ala-Leu-Phe-Gln-Gly-Pro-Phe(NO2)-Ala
0.5 - 26.9
N-acetyl-Leu-p-nitroanilide
4.28
N-acetyl-Phe-2-naphthylamide
pH 7.0, 70°C, wild-type enzyme
6.6 - 30.9
p-nitrophenyl caprylate
0.000917
2-aminobenzoyl-Ala-Leu-Phe-Gln-Gly-Pro-Phe(NO2)-Ala
pH 7.0, 70°C, mutant enzyme D524A
0.00525
2-aminobenzoyl-Ala-Leu-Phe-Gln-Gly-Pro-Phe(NO2)-Ala
pH 7.0, 70°C, mutant enzyme D524N
8.2
2-aminobenzoyl-Ala-Leu-Phe-Gln-Gly-Pro-Phe(NO2)-Ala
pH 7.0, 70°C, wild-type enzyme
0.5
N-acetyl-Leu-p-nitroanilide
80°C, mutant enzyme R526E
9.2
N-acetyl-Leu-p-nitroanilide
80°C, mutant enzyme R526I
9.3
N-acetyl-Leu-p-nitroanilide
80°C, wild-type enzyme
9.6
N-acetyl-Leu-p-nitroanilide
80°C, mutant enzyme R526L
9.7
N-acetyl-Leu-p-nitroanilide
80°C, mutant enzyme R526V
12.6
N-acetyl-Leu-p-nitroanilide
80°C, mutant enzyme R526A
26.9
N-acetyl-Leu-p-nitroanilide
80°C, mutant enzyme R526K
6.6
p-nitrophenyl caprylate
80°C, wild-type enzyme
8.1
p-nitrophenyl caprylate
80°C, mutant enzyme R526E
9.4
p-nitrophenyl caprylate
80°C, mutant enzyme R526K
9.6
p-nitrophenyl caprylate
80°C, mutant enzyme R526A
20.8
p-nitrophenyl caprylate
80°C, mutant enzyme R526I
28.5
p-nitrophenyl caprylate
80°C, mutant enzyme R526L
30.9
p-nitrophenyl caprylate
80°C, mutant enzyme R526V
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physiological function
acylpeptide hydrolases (APHs) catalyze the removal of N-acylated amino acids from blocked peptides
evolution
acylaminoacyl peptidase is a member of the prolyl oligopeptidase protein family
evolution
enzyme AAP belongs to alpha/beta-hydrolase enzyme superfamily
evolution
the enzyme belongs to a class of serine-type protease belonging to the prolyl oligopeptidase (POP) family. The members of the POP family are involved in numerous metabolic processes
evolution
the enzyme belongs to the prolyl oligopeptidase family of serine proteases
additional information
enzyme structure modeling and comparison with the enzyme structure from Sulfurisphaera tokodaii, overview. Both enzymes share a high structural homology
additional information
exploration of the chlorpyrifos escape pathway from acylpeptide hydrolases using steered molecular dynamics simulations, overview
additional information
molecular docking and molecular dynamics simulations using the structure with PDB ID 1VE7, substrate binding structures, overview
additional information
substrate binding structures of wild-type and mutant enzymes, docking study and molecular dynamics simulations, overview. Molecular mechanics/Poisson-Boltzmann surface area (MM/PBSA) calculations
additional information
the closed form of the enzyme is catalytically active, while opening deactivates the catalytic triad. Molecular-dynamics simulations are used to investigate the structure of the complexes formed with longer peptide substrates showing that their binding within the large crevice of the closed form of ApAAP leaves the enzyme structure unperturbed. Their accessing the binding site seems more probable when assisted by opening of the enzyme. Thus, the open form of ApAAP corresponds to a scavenger of possible substrates, the actual cleavage of which only takes place if the enzyme is able to re-close. Structure analysis, detailed overview
additional information
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the closed form of the enzyme is catalytically active, while opening deactivates the catalytic triad. Molecular-dynamics simulations are used to investigate the structure of the complexes formed with longer peptide substrates showing that their binding within the large crevice of the closed form of ApAAP leaves the enzyme structure unperturbed. Their accessing the binding site seems more probable when assisted by opening of the enzyme. Thus, the open form of ApAAP corresponds to a scavenger of possible substrates, the actual cleavage of which only takes place if the enzyme is able to re-close. Structure analysis, detailed overview
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crystals grown at 17.8°C using ammonium phosphate as a precipitant. Crystals belong to space group P1 with unit-cell parameters a = 107.5, b = 109.9, alpha = 108.1°, beta = 109.8° and gamma = 91.9°
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crystals of the H367A mutant grown at 20°C in hanging drops, to 2.2 A resolution. Belongs to space group P212121
hanging drop method, crystal structure determination of the native and two mutant structures (D524N and D524A)
hanging-drop vapor-diffusion method. The best crystals were obtained from reservoir of 6% PEG4000, 50 mM/l NaAc (pH 4.6), 15 mM/l DTT, 0.2 mM/l EDTA
purified enzyme in complex with chloromethyl ketone inhibitor, hanging drop vapour diffusion method, for the complex crystal form: mixing of 0.003 ml of protein solution containing 0.221 mM ApAAP protein, and 0.56 mM inhibitor CMK in 20 mM Tris pH 7.5 buffer, with 0.003 ml of reservoir solution containing 78 mM sodium acetate, pH 4.5, 2.4% w/v PEG 4000, 6.7 mM dithiothreitol, and 0.44 mM EDTA, for apoenzyme crystal form: mixing of 0.003 ml of protein solution containing 0.158 mM ApAAP protein in 20 mM Tris pH 7.5 buffer, with 0.003 ml of reservoir solution containing 78 mM sodium acetate, pH 5.0, 2.2% w/v PEG 4000, 5.2 mM dithiothreitol, and 0.34 mM EDTA, 20°C, X-ray diffraction structure determination and analysis at 1.90A and 2.55A resolution, modeling
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D524A
the mutation affects the closed, active form of the enzyme, disrupting its catalytic triad. The wild-type enzyme exhibits a bell-shaped pH-rate profile (optimum at pH 7.5), whereas the rate constants for the D524A and D524N variants increase to about pH 9. The kcat/Km values is much lower compared with those of the wild-type enzyme
D524N
the mutation affects the closed, active form of the enzyme, disrupting its catalytic triad. The wild-type enzyme exhibits a bell-shaped pH-rate profile (optimum at pH 7.5), whereas the rate constants for the D524A and D524N variants increase to about pH 9. The kcat/Km values is much lower compared with those of the wild-type enzyme
F488G/R526V/T560W
1.55fold increase in activity with 4-nitrophenyl laurate compared to activity of mutant R526V/T560W
H367A
displays significantly reduced catalytic activity. Unlike the reaction of the wild-type, the reaction of the mutant displays completely linear temperature dependence. Its reaction is associated with unfavourable entropy of activation
R526 I
the ratio of kcat/Km for p-nitrophenyl caprylate to kcat/KM for N-acetyl-Leu-p-nitroanilide is 17.3fold higher than the wild-type ratio
R526A
the ratio of kcat/Km for p-nitrophenyl caprylate to kcat/KM for N-acetyl-Leu-p-nitroanilide is 11.7fold higher than the wild-type ratio
R526E
the ratio of kcat/Km for p-nitrophenyl caprylate to kcat/KM for N-acetyl-Leu-p-nitroanilide is 115.5fold higher than the wild-type ratio
R526K
the ratio of kcat/Km for p-nitrophenyl caprylate to kcat/KM for N-acetyl-Leu-p-nitroanilide is 13.9fold higher than the wild-type ratio
R526L
the ratio of kcat/Km for p-nitrophenyl caprylate to kcat/KM for N-acetyl-Leu-p-nitroanilide is 14.8fold higher than the wild-type ratio
R526V/T560W
1.5fold increase in activity with 4-nitrophenyl dodecanoate compared to activity of mutant R526V
W474V/F488G/R526V/T560W
the mutant enzyme has 7fold higher catalytic efficiency (kcat/Km) for 4-nitrophenyl dodecanoate than the mutant enzyme R526V
W474V/R526V/T560W
3.11fold increase in activity with 4-nitrophenyl laurate compared to activity of mutant R526V/T560W
R526V
the ratio of kcat/Km for p-nitrophenyl caprylate to kcat/KM for N-acetyl-Leu-p-nitroanilide is 22.3fold higher than the wild-type ratio
R526V
mutant enzyme with high esterase activity, extreme thermal stability, and high tolerance to organic solvents
additional information
construction of chimeras of a carboxylesterase (EC 3.1.1.1) from Archaeoglobus fulgidus and an acylpeptide hydrolase (EC 3.4.19.1) from Aeropyrum pernix K1. Their activities to hydrolyze 4-nitrophenyl esters (pNP) with different acyl chain lengths is explored. The chimeras inherit the thermophilic property of both parents. The substrate-binding domain is the dominant factor on enzyme substrate specificity, and the optimization of the newly formed domain interface is an important guarantee for successful domain swapping of proteins with low-sequence homology
additional information
the esterase activity of the mutant R526V (this mutation transforms a promiscuous acylaminoacyl peptidase into a specific carboxylesterase) towards substrates with long acyl chains is enhanced by protein engineering and solvent optimization. The substrate preference of the enzyme can be further changed from 4-nitrophenyl octanoate to 4-nitrophenyl dodecanoate by protein and solvent engineering
additional information
construction of mutant APE-DELTAEG by deletion of two residues E316 and G317, and of mutant APE-2G by inserted two Gly residues between residues L315 and E316 deleted residues F395 and V396. The catalytic activity of the APE-DELTAEG mutant toward 4-nitrophenyl butyrate (pNPC4) is 2.8fold more active compared to wild-type, whose preferred substrate is 4-nitrophenyl caprylate (pNPC8)
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Wang, G.; Gao, R.; Ding, Y.; Yang, H.; Cao, S.; Feng, Y.; Rao, Z.
Crystallization and preliminary crystallographic analysis of acylamino-acid releasing enzyme from the hyperthermophilic archaeon Aeropyrum pernix
Acta Crystallogr. Sect. D
58
1054-1055
2002
Aeropyrum pernix
brenda
Wang, Q.; Yang, G.; Liu, Y.; Feng, Y.
Discrimination of esterase and peptidase activities of acylaminoacyl peptidase from hyperthermophilic Aeropyrum pernix K1 by a single mutation
J. Biol. Chem.
281
18618-18625
2006
Aeropyrum pernix (Q9YBQ2)
brenda
Bartlam, M.; Wang, G.; Yang, H.; Gao, R.; Zhao, X.; Xie, G.; Cao, S.; Feng, Y.; Rao, Z.
Crystal structure of an acylpeptide hydrolase/esterase from Aeropyrum pernix K1
Structure
12
1481-1488
2004
Aeropyrum pernix (Q9YBQ2)
brenda
Kiss, A.L.; Pallo, A.; Naray-Szabo, G.; Harmat, V.; Polgar, L.
Structural and kinetic contributions of the oxyanion binding site to the catalytic activity of acylaminoacyl peptidase
J. Struct. Biol.
162
312-323
2008
Aeropyrum pernix (Q9YBQ2), Aeropyrum pernix, Aeropyrum pernix K1 (Q9YBQ2)
brenda
Zhou, X.; Wang, H.; Zhang, Y.; Gao, L.; Feng, Y.
Alteration of substrate specificities of thermophilic alpha/beta hydrolases through domain swapping and domain interface optimization
Acta Biochim. Biophys. Sin.
44
965-973
2012
Aeropyrum pernix (Q9YBQ2)
brenda
Harmat, V.; Domokos, K.; Menyhard, D.K.; Pallo, A.; Szeltner, Z.; Szamosi, I.; Beke-Somfai, T.; Naray-Szabo, G., Polgar, L.
Structure and catalysis of acylaminoacyl peptidase: closed and open subunits of a dimer oligopeptidase
J. Biol. Chem.
286
1987-1998
2011
Aeropyrum pernix (Q9YBQ2), Aeropyrum pernix, Aeropyrum pernix DSM 11879 (Q9YBQ2)
brenda
Papaleo, E.; Renzetti, G.
Coupled motions during dynamics reveal a tunnel toward the active site regulated by the N-terminal alpha-helix in an acylaminoacyl peptidase
J. Mol. Graph. Model.
38
226-234
2012
Aeropyrum pernix (Q9YBQ2), Aeropyrum pernix DSM 11879 (Q9YBQ2)
brenda
Liu, C.; Yang, G.; Wu, L.; Tian, G.; Zhang, Z.; Feng, Y.
Switch of substrate specificity of hyperthermophilic acylaminoacyl peptidase by combination of protein and solvent engineering
Protein Cell
2
497-506
2011
Aeropyrum pernix (Q9YBQ2), Aeropyrum pernix DSM 11879 (Q9YBQ2)
brenda
Menyhard, D.K.; Orgovan, Z.; Szeltner, Z.; Szamosi, I.; Harmat, V.
Catalytically distinct states captured in a crystal lattice the substrate-bound and scavenger states of acylaminoacyl peptidase and their implications for functionality
Acta Crystallogr. Sect. D
71
461-472
2015
Aeropyrum pernix (Q9YBQ2), Aeropyrum pernix, Aeropyrum pernix ATCC 700893 (Q9YBQ2), Aeropyrum pernix DSM 11879 (Q9YBQ2), Aeropyrum pernix JCM 9820 (Q9YBQ2), Aeropyrum pernix NBRC 100138 (Q9YBQ2)
brenda
Liu, D.; Deng, L.; Wang, D.; Li, W.; Gao, R.
"Bridge regions" regulate catalysis and protein stability of acylpeptide hydrolase
Biochem. Eng. J.
145
42-52
2019
Aeropyrum pernix (Q9YBQ2), Aeropyrum pernix ATCC 700893 (Q9YBQ2), Aeropyrum pernix DSM 11879 (Q9YBQ2), Aeropyrum pernix JCM 9820 (Q9YBQ2), Aeropyrum pernix NBRC 100138 (Q9YBQ2), Sulfurisphaera tokodaii (Q973W9), Sulfurisphaera tokodaii 7 (Q973W9), Sulfurisphaera tokodaii DSM 16993 (Q973W9), Sulfurisphaera tokodaii JCM 10545 (Q973W9), Sulfurisphaera tokodaii NBRC 100140 (Q973W9)
-
brenda
Jin, H.; Zhou, Z.; Wang, D.; Guan, S.; Han, W.
Molecular dynamics simulations of acylpeptide hydrolase bound to chlorpyrifosmethyl oxon and dichlorvos
Int. J. Mol. Sci.
16
6217-6234
2015
Aeropyrum pernix (Q9YBQ2)
brenda
Wang, D.; Jin, H.; Wang, J.; Guan, S.; Zhang, Z.; Han, W.
Exploration of the chlorpyrifos escape pathway from acylpeptide hydrolases using steered molecular dynamics simulations
J. Biomol. Struct. Dyn.
34
749-761
2016
Aeropyrum pernix (Q9YBQ2)
brenda
Zhu, J.; Wang, Y.; Li, X.; Han, W.; Zhao, L.
Understanding the interactions of different substrates with wild-type and mutant acylaminoacyl peptidase using molecular dynamics simulations
J. Biomol. Struct. Dyn.
36
4285-4302
2018
Aeropyrum pernix (Q9YBQ2), Aeropyrum pernix ATCC 700893 (Q9YBQ2), Aeropyrum pernix DSM 11879 (Q9YBQ2), Aeropyrum pernix JCM 9820 (Q9YBQ2), Aeropyrum pernix NBRC 100138 (Q9YBQ2), Homo sapiens (P13798), Homo sapiens
brenda
Jin, H.; Zhu, J.; Dong, Y.; Han, W.
Exploring the different ligand escape pathways in acylaminoacyl peptidase by random acceleration and steered molecular dynamics simulations
RSC Adv.
6
10987-10996
2016
Aeropyrum pernix (Q9YBQ2)
-
brenda