Reshaping an Enzyme Binding Pocket for Enhanced and Inverted Stereoselectivity: Use of Smallest Amino Acid Alphabets in Directed Evolution

2015 ◽  
Vol 54 (42) ◽  
pp. 12410-12415 ◽  
Author(s):  
Zhoutong Sun ◽  
Richard Lonsdale ◽  
Xu-Dong Kong ◽  
Jian-He Xu ◽  
Jiahai Zhou ◽  
...  
Keyword(s):  
Amino Acid ◽  
Directed Evolution ◽  
Binding Pocket ◽  
Enzyme Binding

Reshaping an Enzyme Binding Pocket for Enhanced and Inverted Stereoselectivity: Use of Smallest Amino Acid Alphabets in Directed Evolution

2015 ◽  
Vol 127 (42) ◽  
pp. 12587-12592 ◽  
Author(s):  
Zhoutong Sun ◽  
Richard Lonsdale ◽  
Xu-Dong Kong ◽  
Jian-He Xu ◽  
Jiahai Zhou ◽  
...  
Keyword(s):  
Amino Acid ◽  
Directed Evolution ◽  
Binding Pocket ◽  
Enzyme Binding

scholarly journals Genetic risk factors for sclerotic graft-versus-host disease

Blood ◽  
2016 ◽  
Vol 128 (11) ◽  
pp. 1516-1524 ◽  
Author(s):  
Yoshihiro Inamoto ◽  
Paul J. Martin ◽  
Mary E. D. Flowers ◽  
Stephanie J. Lee ◽  
Paul A. Carpenter ◽  
...  
Keyword(s):  
Risk Factors ◽  
Amino Acid ◽  
Graft Versus Host Disease ◽  
Genetic Risk ◽  
Peptide Binding ◽  
Binding Pocket ◽  
Genetic Risk Factors ◽  
Amino Acid Substitutions ◽  
Graft Versus Host ◽  
Key Points

Key Points SNPs in BANK1, CD247, and HLA-DPA1 were associated with risk of sclerotic GVHD. HLA-DPA1∼B1 haplotypes and amino acid substitutions in the HLA-DP P1 peptide-binding pocket were associated with risk of sclerotic GVHD.

Structural and functional consequences of single amino acid substitutions in the pyrimidine base binding pocket of Escherichia coli CMP kinase

FEBS Journal ◽  
2007 ◽  
Vol 274 (13) ◽  
pp. 3363-3373 ◽  
Author(s):  
Augustin Ofiteru ◽  
Nadia Bucurenci ◽  
Emil Alexov ◽  
Thomas Bertrand ◽  
Pierre Briozzo ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Amino Acid ◽  
Binding Pocket ◽  
Single Amino Acid ◽  
Amino Acid Substitutions ◽  
Pyrimidine Base ◽  
Functional Consequences

scholarly journals Structural basis for amino acid exchange by a human heteromeric amino acid transporter

2020 ◽  
Vol 117 (35) ◽  
pp. 21281-21287 ◽  
Author(s):  
Di Wu ◽  
Tamara N. Grund ◽  
Sonja Welsch ◽  
Deryck J. Mills ◽  
Max Michel ◽  
...  
Keyword(s):  
Amino Acid ◽  
Heavy Chain ◽  
Light Chain ◽  
Basic Amino Acid ◽  
Binding Pocket ◽  
Structural Basis ◽  
Amino Acid Transporters ◽  
Wide Range ◽  
Functional Complex ◽  
Protein Components

Heteromeric amino acid transporters (HATs) comprise a group of membrane proteins that belong to the solute carrier (SLC) superfamily. They are formed by two different protein components: a light chain subunit from an SLC7 family member and a heavy chain subunit from the SLC3 family. The light chain constitutes the transport subunit whereas the heavy chain mediates trafficking to the plasma membrane and maturation of the functional complex. Mutation, malfunction, and dysregulation of HATs are associated with a wide range of pathologies or represent the direct cause of inherited and acquired disorders. Here we report the cryogenic electron microscopy structure of the neutral and basic amino acid transport complex (b[0,+]AT1-rBAT) which reveals a heterotetrameric protein assembly composed of two heavy and light chain subunits, respectively. The previously uncharacterized interaction between two HAT units is mediated via dimerization of the heavy chain subunits and does not include participation of the light chain subunits. The b(0,+)AT1 transporter adopts a LeuT fold and is captured in an inward-facing conformation. We identify an amino-acid–binding pocket that is formed by transmembrane helices 1, 6, and 10 and conserved among SLC7 transporters.

scholarly journals Engineering Improves Enzymatic Synthesis of L-Tryptophan by Tryptophan Synthase from Escherichia coli

2020 ◽  
Vol 8 (4) ◽  
pp. 519
Author(s):  
Lisheng Xu ◽  
Fangkai Han ◽  
Zeng Dong ◽  
Zhaojun Wei
Keyword(s):  
Thermal Stability ◽  
Amino Acid ◽  
Directed Evolution ◽  
Amino Acid Residue ◽  
Rational Design ◽  
Molecular Engineering ◽  
Mutant Enzyme ◽  
Tryptophan Synthase ◽  
Mutant Library ◽  
Thermal Stability Of

To improve the thermostability of tryptophan synthase, the molecular modification of tryptophan synthase was carried out by rational molecular engineering. First, B-FITTER software was used to analyze the temperature factor (B-factor) of each amino acid residue in the crystal structure of tryptophan synthase. A key amino acid residue, G395, which adversely affected the thermal stability of the enzyme, was identified, and then, a mutant library was constructed by site-specific saturation mutation. A mutant (G395S) enzyme with significantly improved thermal stability was screened from the saturated mutant library. Error-prone PCR was used to conduct a directed evolution of the mutant enzyme (G395S). Compared with the parent, the mutant enzyme (G395S /A191T) had a Km of 0.21 mM and a catalytic efficiency kcat/Km of 5.38 mM−1∙s−1, which was 4.8 times higher than that of the wild-type strain. The conditions for L-tryptophan synthesis by the mutated enzyme were a L-serine concentration of 50 mmol/L, a reaction temperature of 40 °C, pH of 8, a reaction time of 12 h, and an L-tryptophan yield of 81%. The thermal stability of the enzyme can be improved by using an appropriate rational design strategy to modify the correct site. The catalytic activity of tryptophan synthase was increased by directed evolution.

scholarly journals Synthesis and Biochemical Evaluation of Lid-Open D-Amino Acid Oxidase Inhibitors

Molecules ◽  
2019 ◽  
Vol 24 (2) ◽  
pp. 290
Author(s):  
Bence Szilágyi ◽  
Csilla Hargitai ◽  
Ádám A. Kelemen ◽  
Anita Rácz ◽  
György G. Ferenczy ◽  
...  
Keyword(s):  
Amino Acid ◽  
Physicochemical Properties ◽  
Active Site ◽  
Binding Pocket ◽  
Acid Oxidase ◽  
Amino Acid Oxidase ◽  
New Class ◽  
Biochemical Evaluation ◽  
Low Sensitivity ◽  
Adme Profile

Most of the known inhibitors of D-amino acid oxidase (DAAO) are small polar molecules recognized by the active site of the enzyme. More recently a new class of DAAO inhibitors has been disclosed that interacts with loop 218−224 at the top of the binding pocket. These compounds have a significantly larger size and more beneficial physicochemical properties than most reported DAAO inhibitors, however, their structure-activity relationship is poorly explored. Here we report the synthesis and evaluation of this type of DAAO inhibitors that open the lid over the active site of DAAO. In order to collect relevant SAR data we varied two distinct parts of the inhibitors. A systematic variation of the pendant aromatic substituents according to the Topliss scheme resulted in DAAO inhibitors with low nanomolar activity. The activity showed low sensitivity to the substituents investigated. The variation of the linker connecting the pendant aromatic moiety and the acidic headgroup revealed that the interactions of the linker with the enzyme were crucial for achieving significant inhibitory activity. Structures and activities were analyzed based on available X-ray structures of the complexes. Our findings might support the design of drug-like DAAO inhibitors with advantageous physicochemical properties and ADME profile.

Tetranectin-Binding Site on Plasminogen Kringle 4 Involves the Lysine-Binding Pocket and at Least One Additional Amino Acid Residue†

Biochemistry ◽  
2000 ◽  
Vol 39 (25) ◽  
pp. 7414-7419 ◽  
Author(s):  
Jonas H. Graversen ◽  
Bent W. Sigurskjold ◽  
Hans C. Thøgersen ◽  
Michael Etzerodt
Keyword(s):  
Amino Acid ◽  
Binding Site ◽  
Amino Acid Residue ◽  
Binding Pocket ◽  
Additional Amino Acid

scholarly journals Structure–function studies of human deoxyhypusine synthase: identification of amino acid residues critical for the binding of spermidine and NAD

2001 ◽  
Vol 355 (3) ◽  
pp. 841-849 ◽  
Author(s):  
Chang Hoon LEE ◽  
Patrick Y. UM ◽  
Myung Hee PARK
Keyword(s):  
Crystal Structure ◽  
Enzyme Activity ◽  
Amino Acid ◽  
Binding Sites ◽  
Binding Pocket ◽  
Complete Loss ◽  
Amino Acid Residues ◽  
Deoxyhypusine Synthase ◽  
Positive Identification ◽  
Insight Into

Deoxyhypusine synthase catalyses the first step in the biosynthesis of hypusine [Nε-(4-amino-2-hydroxybutyl)lysine]. The crystal structure of human deoxyhypusine synthase in complex with NAD revealed four NAD-binding sites per enzyme tetramer, and led to a prediction of the spermidine-binding pocket. We have replaced each of the seven amino acid residues at the predicted spermidine-binding site, and eleven residues that contact NAD, on an individual basis with alanine. Of the amino acid residues at the spermidine site, substitution of Asp-243, Trp-327, His-288, Asp-316 or Glu-323 with alanine caused an almost complete loss of spermidine binding and enzyme activity; only the mutation Tyr-305 → Ala showed partial binding and activity. His-288 → Ala was also deficient in terms of binding NAD. NAD binding was significantly reduced in all of the NAD-site mutant enzymes, except for Glu-137 → Ala, which showed a normal binding of NAD, but was totally lacking in spermidine binding. Of the NAD-site mutant enzymes, Asp-342 → Ala, Asp-313 → Ala and Asp-238 → Ala displayed the lowest binding of NAD. These enzymes and His-288Ala also showed a reduced binding of spermidine, presumably because spermidine binding is dependent on NAD. These findings permit the positive identification of amino acid residues critical for binding of spermidine and NAD, and provide a new insight into the complex molecular interactions involved in the deoxyhypusine synthase reaction.

scholarly journals Cd-Specific Mutants of Mercury-Sensing Regulatory Protein MerR, Generated by Directed Evolution

2011 ◽  
Vol 77 (17) ◽  
pp. 6215-6224 ◽  
Author(s):  
Kaisa M. Hakkila ◽  
Pia A. Nikander ◽  
Sini M. Junttila ◽  
Urpo J. Lamminmäki ◽  
Marko P. Virta
Keyword(s):  
Amino Acid ◽  
Directed Evolution ◽  
Metal Binding ◽  
Fluorescent Protein ◽  
Regulatory Protein ◽  
Screening Strategy ◽  
Mercury Resistance ◽  
Content Type ◽  
Green Fluorescent ◽  
Mercury Sensing

ABSTRACTThe mercury-sensing regulatory protein, MerR (Tn21), which regulates mercury resistance operons in Gram-negative bacteria, was subjected to directed evolution in an effort to generate a MerR mutant that responds to Cd but not Hg. Oligonucleotide-directed mutagenesis was used to introduce random mutations into the key metal-binding regions of MerR. The effects of these mutations were assessed using a vector in which MerR controlled the expression of green fluorescent protein (GFP) and luciferase via themeroperator/promoter. AnEscherichia colicell library was screened by fluorescence-activated cell sorting, using a fluorescence-based dual screening strategy that selected for MerR mutants that showed GFP repression when cells were induced with Hg but GFP activation in the presence of Cd. Two Cd-responsive MerR mutants with decreased responses toward Hg were identified through the first mutagenesis/selection round. These mutants were used for a second mutagenesis/selection round, which yielded eight Cd-specific mutants that had no significant response to Hg, Zn, or the other tested metal(loid)s. Seven of the eight Cd-specific MerR mutants showed repressor activities equal to that of wild-type (wt) MerR. These Cd-specific mutants harbored multiple mutations (12 to 22) in MerR, indicating that the alteration of metal specificity with maintenance of repressor function was due to the combined effect of many mutations rather than just a few amino acid changes. The amino acid changes were studied by alignment against the sequences of MerR and other metal-responsive MerR family proteins. The analysis indicated that the generated Cd-specific MerR mutants appear to be unique among the MerR family members characterized to date.

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