scholarly journals A Crystal Structure of the Dengue Virus Non-structural Protein 5 (NS5) Polymerase Delineates Interdomain Amino Acid Residues That Enhance Its Thermostability andde NovoInitiation Activities

2013 ◽  
Vol 288 (43) ◽  
pp. 31105-31114 ◽  
Author(s):  
Siew Pheng Lim ◽  
Jolene Hong Kiew Koh ◽  
Cheah Chen Seh ◽  
Chong Wai Liew ◽  
Andrew D. Davidson ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Amino Acid ◽  
Dengue Virus ◽  
Amino Acid Residues ◽  
Structural Protein

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 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 Structure of human nucleosome containing the testis-specific histone variant TSH2B

2014 ◽  
Vol 70 (4) ◽  
pp. 444-449 ◽  
Author(s):  
Takashi Urahama ◽  
Naoki Horikoshi ◽  
Akihisa Osakabe ◽  
Hiroaki Tachiwana ◽  
Hitoshi Kurumizaka
Keyword(s):  
Crystal Structure ◽  
Amino Acid ◽  
Structural Changes ◽  
Structural Difference ◽  
Histone Variants ◽  
The Other ◽  
Human Testis ◽  
Amino Acid Residues ◽  
Histone H2b ◽  
Specific Amino Acid

The human histone H2B variant TSH2B is highly expressed in testis and may function in the chromatin transition during spermatogenesis. In the present study, the crystal structure of the human testis-specific nucleosome containing TSH2B was determined at 2.8 Å resolution. A local structural difference between TSH2B and canonical H2B in nucleosomes was detected around the TSH2B-specific amino-acid residue Ser85. The TSH2B Ser85 residue does not interact with H4 in the nucleosome, but in the canonical nucleosome the H2B Asn84 residue (corresponding to the TSH2B Ser85 residue) forms water-mediated hydrogen bonds with the H4 Arg78 residue. In contrast, the other TSH2B-specific amino-acid residues did not induce any significant local structural changes in the TSH2B nucleosome. These findings may provide important information for understanding how testis-specific histone variants form nucleosomes during spermatogenesis.

scholarly journals Identification of amino acid residues important for anti-IFN activity of porcine reproductive and respiratory syndrome virus non-structural protein 1

Virology ◽  
2012 ◽  
Vol 433 (2) ◽  
pp. 431-439 ◽  
Author(s):  
Lalit K. Beura ◽  
Sakthivel Subramaniam ◽  
Hiep L.X. Vu ◽  
Byungjoon Kwon ◽  
Asit K. Pattnaik ◽  
...  
Keyword(s):  
Amino Acid ◽  
Respiratory Syndrome Virus ◽  
Amino Acid Residues ◽  
Structural Protein

scholarly journals Molecular Dynamics Simulations of a Cytochrome P450 from Tepidiphilus thermophilus (P450-TT) Reveal How Its Substrate-Binding Channel Opens

Molecules ◽  
2021 ◽  
Vol 26 (12) ◽  
pp. 3614
Author(s):  
Abayomi S. Faponle ◽  
Anupom Roy ◽  
Ayodeji A. Adelegan ◽  
James W. Gauld
Keyword(s):  
Crystal Structure ◽  
Molecular Dynamics ◽  
Cytochrome P450 ◽  
Amino Acid ◽  
Molecular Dynamics Simulations ◽  
Organic Molecules ◽  
Side Chain ◽  
Relative Solvent Accessibility ◽  
Amino Acid Residues ◽  
Dynamics Simulations

Cytochrome P450s (P450) are important enzymes in biology with useful biochemical reactions in, for instance, drug and xenobiotics metabolisms, biotechnology, and health. Recently, the crystal structure of a new member of the CYP116B family has been resolved. This enzyme is a cytochrome P450 (CYP116B46) from Tepidiphilus thermophilus (P450-TT) and has potential for the oxy-functionalization of organic molecules such as fatty acids, terpenes, steroids, and statins. However, it was thought that the opening to its hitherto identified substrate channel was too small to allow organic molecules to enter. To investigate this, we performed molecular dynamics simulations on the enzyme. The results suggest that the crystal structure is not relaxed, possibly due to crystal packing effects, and that its tunnel structure is constrained. In addition, the simulations revealed two key amino acid residues at the mouth of the channel; a glutamyl and an arginyl. The glutamyl’s side chain tightens and relaxes the opening to the channel in conjunction with the arginyl’s, though the latter’s side chain is less dramatically changed after the initial relaxation of its conformations. Additionally, it was observed that the effect of increased temperature did not considerably affect the dynamics of the enzyme fold, including the relative solvent accessibility of the amino acid residues that make up the substrate channel wall even as compared to the changes that occurred at room temperature. Interestingly, the substrate channel became distinguishable as a prominent tunnel that is likely to accommodate small- to medium-sized organic molecules for bioconversions. That is, P450-TT has the ability to pass appropriate organic substrates to its active site through its elaborate substrate channel, and notably, is able to control or gate any molecules at the opening to this channel.

scholarly journals Identification of Major Histocompatibility Complex Restriction and Anchor Residues of Foot-and-Mouth Disease Virus-Derived Bovine T-Cell Epitopes

2009 ◽  
Vol 83 (9) ◽  
pp. 4039-4050 ◽  
Author(s):  
Wilhelm Gerner ◽  
Sabine E. Hammer ◽  
Karl-Heinz Wiesmüller ◽  
Armin Saalmüller
Keyword(s):  
Major Histocompatibility Complex ◽  
Amino Acid ◽  
Mhc Class Ii ◽  
Foot And Mouth Disease ◽  
Amino Acid Residues ◽  
T Cell Epitopes ◽  
Structural Protein ◽  
Histocompatibility Complex ◽  
Mouth Disease Virus ◽  
Proliferation Assays

ABSTRACT Despite intensive research on the identification of T-cell epitopes in cattle after foot-and-mouth disease virus (FMDV) infection during the last 20 years, knowledge of major histocompatibility complex (MHC) restriction and anchor residues of such epitopes is still sparse. Therefore, as a first step, we tested lymphocytes from two experimentally FMDV serotype A24-vaccinated and -challenged cattle for recognition of FMDV-derived pentadecapeptides in proliferation assays. Two epitopes were identified: amino acid residues 66 to 80 within the structural protein 1D and amino acid residues 22 to 36 within the structural protein 1A. The latter epitope was recognized by lymphocytes from both cattle. Peptide-specific proliferation was caused by a response of CD4+ T helper cells as identified by carboxyfluorescein diacetate succinimidyl ester proliferation assays. Having identified one epitope that was recognized by two cattle, we hypothesized that these animals should have common MHC class II alleles. Cloning and sequencing of DRB3, DQA, and DQB alleles revealed that both animals possessed DQA allele 22021 and DQB allele 1301 but had no common DRB3 allele. A parallel analysis of amino acid residues involved in MHC presentation by peptides with alanine substitutions showed that the amino acid residues in positions 5 and 9 within the pentadecapeptide representing the 1A epitope were important for MHC binding in both cattle. These data indicate that the epitope located on FMDV protein 1A can be presented by MHC class II DQ molecules encoded by DQA allele 22021 and DQB allele 1301 and present the first evidence of the binding motif of this particular DQ molecule.

scholarly journals Identification of Channel-lining Amino Acid Residues in the Hydrophobic Segment of Colicin Ia

2008 ◽  
Vol 132 (6) ◽  
pp. 693-707 ◽  
Author(s):  
Paul K. Kienker ◽  
Karen S. Jakes ◽  
Alan Finkelstein
Keyword(s):  
Crystal Structure ◽  
Amino Acid ◽  
Lipid Bilayer ◽  
Open Channel ◽  
Structural Model ◽  
Water Soluble ◽  
Amino Acid Residues ◽  
Lipid Bilayer Membranes ◽  
Planar Bilayers ◽  
Colicin Ia

Colicin Ia is a bactericidal protein of 626 amino acid residues that kills its target cell by forming a channel in the inner membrane; it can also form voltage-dependent channels in planar lipid bilayer membranes. The channel-forming activity resides in the carboxy-terminal domain of ∼177 residues. In the crystal structure of the water-soluble conformation, this domain consists of a bundle of 10 α-helices, with eight mostly amphipathic helices surrounding a hydrophobic helical hairpin (helices H8-H9). We wish to know how this structure changes to form a channel in a lipid bilayer. Although there is evidence that the open channel has four transmembrane segments (H8, H9, and parts of H1 and H6-H7), their arrangement relative to the pore is largely unknown. Given the lack of a detailed structural model, it is imperative to better characterize the channel-lining protein segments. Here, we focus on a segment of 44 residues (573–616), which in the crystal structure comprises the H8-H9 hairpin and flanking regions. We mutated each of these residues to a unique cysteine, added the mutant colicins to the cis side of planar bilayers to form channels, and determined whether sulfhydryl-specific methanethiosulfonate reagents could alter the conduction of ions through the open channel. We found a pattern of reactivity consistent with parts of H8 and H9 lining the channel as α-helices, albeit rather short ones for spanning a lipid bilayer (12 residues). The effects of the reactions on channel conductance and selectivity tend to be greater for residues near the amino terminus of H8 and the carboxy terminus of H9, with particularly large effects for G577C, T581C, and G609C, suggesting that these residues may occupy a relatively constricted region near the cis end of the channel.

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