scholarly journals Decoding Essential Amino Acid Residues in the Substrate Groove of a Non-Specific Nuclease from Pseudomonas syringae

Catalysts ◽  
2019 ◽  
Vol 9 (11) ◽  
pp. 941 ◽  
Author(s):  
Lynn Sophie Schwardmann ◽  
Sarah Schmitz ◽  
Volker Nölle ◽  
Skander Elleuche
Keyword(s):  
Amino Acid ◽  
Pseudomonas Syringae ◽  
Metal Ion ◽  
Homology Model ◽  
Downstream Processing ◽  
Outer Ring ◽  
Amino Acid Residues ◽  
Independent Manner ◽  
Identify Amino Acid ◽  
Close Proximity

Non-specific nucleases (NSN) are of interest for biotechnological applications, including industrial downstream processing of crude protein extracts or cell-sorting approaches in microfabricated channels. Bacterial nucleases belonging to the superfamily of phospholipase D (PLD) are featured for their ability to catalyze the hydrolysis of nucleic acids in a metal-ion-independent manner. In order to gain a deeper insight into the composition of the substrate groove of a NSN from Pseudomonas syringae, semi-rational mutagenesis based on a structure homology model was applied to identify amino acid residues on the protein’s surface adjacent to the catalytic region. A collection of 12 mutant enzymes each with a substitution to a positively charged amino acid (arginine or lysine) was produced in recombinant form and biochemically characterized. Mutations in close proximity to the catalytic region (inner ring) either dramatically impaired or completely abolished the enzymatic performance, while amino acid residues located at the border of the substrate groove (outer ring) only had limited or no effects. A K119R substitution mutant displayed a relative turnover rate of 112% compared to the original nuclease. In conclusion, the well-defined outer ring of the substrate groove is a potential target for modulation of the enzymatic performance of NSNs belonging to the PLD superfamily.

scholarly journals The Differential Binding Affinities of the Luteinizing Hormone (LH)/Choriogonadotropin Receptor for LH and Choriogonadotropin Are Dictated by Different Extracellular Domain Residues

2005 ◽  
Vol 19 (5) ◽  
pp. 1263-1276 ◽  
Author(s):  
Colette Galet ◽  
Mario Ascoli
Keyword(s):  
Amino Acid ◽  
Ligand Binding ◽  
Binding Affinity ◽  
Extracellular Domain ◽  
Binding Affinities ◽  
Amino Acid Residues ◽  
Identify Amino Acid ◽  
Β Sheets ◽  
Leucine Rich Repeats ◽  
High Degree

Abstract The high degree of amino acid sequence homology and the divergent ligand binding affinities of the rat (r) and human (h) LH receptors (LHRs) allowed us to identify amino acid residues of their extracellular domain that are responsible for the different binding affinities of bovine (b) and hLH, and human choriogonadotropin (hCG) to the hLHR and rLHR. Because of the proposed importance of the β-sheets of the leucine-rich repeats (LRRs) of the extracellular domain of the LHR on hormone binding, we examined 10 divergent residues present in these regions by analyzing two complementary sets of mutants in which hLHR residues were substituted with the corresponding rLHR residues and vice versa. These experiments resulted in the identification of a single residue (a Ile or Ser in the C-terminal end of LRR2 of the hLHR or rLHR, respectively) that is important for hLH binding affinity. Surprisingly, however, this residue does not affect hCG or for bLH binding affinity. In fact, the results obtained with bLH and hCG show that several of the divergent residues in the β-sheets of LRR1–9 affect bLH binding affinity, but none of them affect hCG binding affinity. Importantly, our results also emphasize the involvement of residues outside of the β-sheets of the LRRs of the LHR in ligand binding affinity. This finding has to be considered in future models of the interaction of LH/CG with the LHR.

Amino Acid Residues His183 and Glu264 inBacillus subtilisFerrochelatase Direct and Facilitate the Insertion of Metal Ion into Protoporphyrin IX†,‡

Biochemistry ◽  
2007 ◽  
Vol 46 (1) ◽  
pp. 87-94 ◽  
Author(s):  
Mattias D. Hansson ◽  
Tobias Karlberg ◽  
Muhammad Arys Rahardja ◽  
Salam Al-Karadaghi ◽  
Mats Hansson
Keyword(s):  
Amino Acid ◽  
Metal Ion ◽  
Protoporphyrin Ix ◽  
Amino Acid Residues

scholarly journals Reconstruction of Mycobacterial Dehalogenase Rv2579 by Cumulative Mutagenesis of Haloalkane Dehalogenase LinB

2003 ◽  
Vol 69 (4) ◽  
pp. 2349-2355 ◽  
Author(s):  
Yuji Nagata ◽  
Zbyněk Prokop ◽  
Soňa Marvanová ◽  
Jana Sýkorová ◽  
Marta Monincová ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Mycobacterium Tuberculosis ◽  
Amino Acid ◽  
Active Site ◽  
Homology Model ◽  
Protein Family ◽  
Sphingomonas Paucimobilis ◽  
Amino Acid Residues ◽  
Haloalkane Dehalogenase

ABSTRACT The homology model of protein Rv2579 from Mycobacterium tuberculosis H37Rv was compared with the crystal structure of haloalkane dehalogenase LinB from Sphingomonas paucimobilis UT26, and this analysis revealed that 6 of 19 amino acid residues which form an active site and entrance tunnel are different in LinB and Rv2579. To characterize the effect of replacement of these six amino acid residues, mutations were introduced cumulatively into the six amino acid residues of LinB. The sixfold mutant, which was supposed to have the active site of Rv2579, exhibited haloalkane dehalogenase activity with the haloalkanes tested, confirming that Rv2579 is a member of the haloalkane dehalogenase protein family.

scholarly journals Construction of immunoglobulin-binding peptides based on analysis of the protein A of Staphylococcus aureus interaction with immunoglobulins Fc fragment

2019 ◽  
Vol 55 (4) ◽  
pp. 447-454
Author(s):  
A. V. Lapko ◽  
E. S. Pustyul’ga ◽  
V. P. Golubovich
Keyword(s):  
Staphylococcus Aureus ◽  
Molecular Docking ◽  
Amino Acid ◽  
Protein A ◽  
New Drugs ◽  
Amino Acid Residues ◽  
Fc Fragment ◽  
Peptide Analog ◽  
Identify Amino Acid ◽  
Starting Point

Over the past decades, molecular docking has become an increasingly popular tool for the development of new drugs. To search and design new compounds, a detailed study of the interaction of existing complexes of ligands with the target protein is necessary. According to the purpose to identify amino acid residues of the B domain of protein A of Staphylococcus aureus involved in interaction with immunoglobulins G, we studied the interaction mechanisms during the formation of a complex of protein A of the Staphylococcus aureus cell wall and immunoglobulins G by molecular docking. By the means of molecular docking we selected four amino acid residues of Phe132, Gln129, Tyr133 and Phe124, which we can use to construct a peptide analog of the active binding site of protein A with the Fc fragment of immunoglobulins G. The obtained results can serve as starting point for an effective strategy for finding new medicines, in particular, they can be used to further develop biospecific sorbent for the selective removal of immunoglobulins G from human blood.

In vitro and in silico study of 1,3-oxazol-4-yltriphenylphosphonium salts as potential inhibitors of Candida albicans transglycosylase

2021 ◽  
Vol 16 (1) ◽  
pp. 25-33
Author(s):  
Ivan Semenyuta ◽  
Maria Trush ◽  
Diana Hodyna ◽  
Maryna Kachaeva ◽  
Larysa Metelytsia ◽  
...  
Keyword(s):  
Candida Albicans ◽  
Amino Acid ◽  
Protein Complexes ◽  
Homology Model ◽  
Binding Energies ◽  
Amino Acid Residues ◽  
Plot Analysis ◽  
Potential Inhibitors ◽  
Dual Mechanism

The previously established in vitro high antimicrobial potential of triphenylphosphonium salts (TPPs) against bacterial (Staphylococcus aureus ATCC 25923 and multi-drug resistant (MDR)) and fungal (Candida albicans ATCC 10231 and MDR) strains made it possible to propose a molecular mechanism of action of these compounds associated with transglycosylase (TG) activity. The hypothesis was based on the well-known literature data on TPPs as inhibitors of S. aureus TG. The created homology model of TG C. albicans is optimal in terms of such quality indicators as GMQE (0.61), ERRAT (overall quality factor 95.904) and Ramachandran plot analysis (90% amino acid residues in the favored regions). Molecular docking of the most active ligands 1a-d, 3c into the active center of the created homology C. albicans TG model demonstrated the formation of stable ligand-protein complexes with binding energies in the range from -8.9 to -9.7 kcal/mol due to the various types of interactions. An important role in complex formation belongs to amino acid residues TYR307, TYR107, GLU275, ALA108 and PRO136. The presented qualitative homologous model of C. albicans TG can be used to search and create new agents with a dual mechanism of antimicrobial action. 1,3-oxazol-4-yltriphenylphosphonium salts 1a-d, 3c perform the perspective objects for further study as antimicrobials against infectious MDR pathogens.

Acid-base and metal ion complex formation properties of polymers containing amino acid residues

1986 ◽  
Vol 19 (1) ◽  
pp. 37-42 ◽  
Author(s):  
Rolando Barbucci ◽  
Mario Casolaro ◽  
Mila Nocentini ◽  
Silvia Corezzi ◽  
Paolo Ferruti ◽  
...  
Keyword(s):  
Amino Acid ◽  
Complex Formation ◽  
Metal Ion ◽  
Amino Acid Residues ◽  
Acid Base ◽  
Polymers Containing Amino Acid ◽  
Metal Ion Complex

scholarly journals Binding of ATP to the CBS domains in the C-terminal region of CLC-1

2011 ◽  
Vol 137 (4) ◽  
pp. 357-368 ◽  
Author(s):  
Pang-Yen Tseng ◽  
Wei-Ping Yu ◽  
Hao-Yang Liu ◽  
Xiao-Dong Zhang ◽  
Xiaoqin Zou ◽  
...  
Keyword(s):  
Amino Acid ◽  
Aromatic Amino Acids ◽  
Homology Model ◽  
Atp Binding ◽  
Amino Acid Residues ◽  
Atp Binding Site ◽  
Cbs Domain ◽  
C Terminus ◽  
Atp Inhibition ◽  
Cbs Domains

The common gating of CLC-1 has been shown to be inhibited by intracellular adenosine triphosphate (ATP) in acidic pH conditions. Such modulation is thought to be mediated by direct binding of ATP to the cystathionine β-synthase (CBS) domains at the C-terminal cytoplasmic region of CLC-1. Guided by the crystal structure of the C-terminal domain of CLC-5, we constructed a homology model of CLC-1’s C terminus and mutated critical amino acid residues lining the potential ATP-binding site. The CLC-1 mutations V634A and E865A completely abolished the ATP inhibition of CLC-1, consistent with the loss of ATP binding seen with the corresponding mutations in CLC-5. Mutating two other residues, V613 and V860, also disrupted the ATP modulation of CLC-1. However, placing aromatic amino acids at position 634 increases the apparent ATP affinity. Mutant cycle analyses showed that the modulation effects of ATP and cytidine triphosphate on wild-type CLC-1 and the V634F mutant were nonadditive, suggesting that the side chain of amino acid at position 634 interacts with the base moiety of the nucleotide. The mutation effects of V634F and V613A on the ATP modulation were also nonadditive, which is consistent with the assertion suggested from the homology model that these two residues may both interact with the bound nucleotide. These results provide evidence for a direct ATP binding for modulating the function of CLC-1 and suggest an overall conserved architecture of the ATP-binding sites in CLC-1 and CLC-5. This study also demonstrates that CLC-1 is a convenient experimental model for studying the interaction of nucleotides/nucleosides with the CBS domain.

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