Structural Analysis of the QB Pocket of the D 1 Subunit of Photosystem II in Synechocystis PCC 6714 and 6803

1993 ◽  
Vol 48 (3-4) ◽  
pp. 199-204 ◽  
Author(s):  
Chantal Astier ◽  
Irene Perewoska ◽  
Martine Picaud ◽  
Diana Kirilovsky ◽  
Keyword(s):  
Amino Acid ◽  
Photosystem Ii ◽  
Binding Site ◽  
Herbicide Resistance ◽  
Point Mutations ◽  
Amino Acid Substitutions ◽  
Amino Acid Residues ◽  
Oscillatory Pattern ◽  
Mutant Phenotypes ◽  
Synechocystis Pcc 6714

Abstract Various herbicides inhibit photosynthesis by displacing the second electron acceptor QB from its binding site at the D 1 protein. Different amino acid substitutions within this binding site have been found to reduce herbicide affinities, thereby conferring herbicide resistance. In Synechocystis PCC 6714 we have selected 7 single mutants and 6 double mutants resistant to various herbicides due to amino acid substitutions at different positions in the QB pocket. Characterization of these mutants consists in molecular determination of the mutations in the psbAl genes and in transformation of Synechocystis PCC 6803 by the cloned mutated genes to analyze the role of the mutations in the mutant phenotypes. Comparison with equivalent Chlamydomonas mutants is presented. These studies allow us to specify the interactions of several amino acid residues with herbicides and QB and with each other. Furthermore some Synechocystis mutants present additional characteristics such as an increased sensitivity to photoinhibition, or resistance to formate or modification of the oscillatory pattern of oxygen evolution. Among the 6 point-mutations giving herbicide resistance, only those located at the limit of the loop and the parallel helix produced additional effects on photosystem II function.

scholarly journals The Application of a Homologous Recombination Assay Revealed Amino Acid Residues in an LTR-Retrotransposon That Were Critical for Integration

1998 ◽  
Vol 72 (2) ◽  
pp. 1324-1333 ◽  
Author(s):  
Angela Atwood ◽  
Jeannie Choi ◽  
Henry L. Levin
Keyword(s):  
Amino Acid ◽  
Point Mutations ◽  
Rnase H ◽  
Host Cells ◽  
Amino Acid Substitutions ◽  
Integration Step ◽  
Ltr Retrotransposon ◽  
Amino Acid Residues ◽  
Catalytic Core ◽  
Identify Amino Acid

ABSTRACT Retroviruses and their relatives, the LTR-retrotransposons, possess an integrase protein (IN) that is required for the insertion of reverse transcripts into the genome of host cells. Schizosaccharomyces pombe is the host of Tf1, an LTR-retrotransposon with integration activity that can be studied by using techniques of yeast genetics. In this study, we sought to identify amino acid substitutions in Tf1 that specifically affected the integration step of transposition. In addition to seeking amino acid substitutions in IN, we also explored the possibility that other Tf1 proteins contributed to integration. By comparing the results of genetic assays that monitored both transposition and reverse transcription, we were able to seek point mutations throughout Tf1 that blocked transposition but not the synthesis of reverse transcripts. These mutant versions of Tf1 were candidates of elements that possessed defects in the integration step of transposition. Five mutations in Tf1 that resulted in low levels of integration were found to be located in the IN protein: two substitutions in the N-terminal Zn domain, two in the catalytic core, and one in the C-terminal domain. These results suggested that each of the three IN domains was required for Tf1 transposition. The potential role of these five amino acid residues in the function of IN is discussed. Two of the mutations that reduced integration mapped to the RNase H (RH) domain of Tf1 reverse transcriptase. The Tf1 elements with the RH mutations produced high levels of reverse transcripts, as determined by recombination and DNA blot analysis. These results indicated that the RH of Tf1 possesses a function critical for transposition that is independent of the accumulation of reverse transcripts.

Schistosomal Sulfotransferase Interaction with Oxamniquine Involves Hybrid Mechanism of Induced-fit and Conformational Selection

2020 ◽  
Vol 16 (4) ◽  
pp. 451-459 ◽  
Author(s):  
Fortunatus C. Ezebuo ◽  
Ikemefuna C. Uzochukwu
Keyword(s):  
Molecular Dynamics ◽  
Amino Acid ◽  
Binding Energy ◽  
Binding Site ◽  
Conformational Dynamics ◽  
Side Chain ◽  
Amino Acid Residues ◽  
Conformational Selection ◽  
Hybrid Mechanism ◽  
Dynamics Simulations

Background: Sulfotransferase family comprises key enzymes involved in drug metabolism. Oxamniquine is a pro-drug converted into its active form by schistosomal sulfotransferase. The conformational dynamics of side-chain amino acid residues at the binding site of schistosomal sulfotransferase towards activation of oxamniquine has not received attention. Objective: The study investigated the conformational dynamics of binding site residues in free and oxamniquine bound schistosomal sulfotransferase systems and their contribution to the mechanism of oxamniquine activation by schistosomal sulfotransferase using molecular dynamics simulations and binding energy calculations. Methods: Schistosomal sulfotransferase was obtained from Protein Data Bank and both the free and oxamniquine bound forms were subjected to molecular dynamics simulations using GROMACS-4.5.5 after modeling it’s missing amino acid residues with SWISS-MODEL. Amino acid residues at its binding site for oxamniquine was determined and used for Principal Component Analysis and calculations of side-chain dihedrals. In addition, binding energy of the oxamniquine bound system was calculated using g_MMPBSA. Results: The results showed that binding site amino acid residues in free and oxamniquine bound sulfotransferase sampled different conformational space involving several rotameric states. Importantly, Phe45, Ile145 and Leu241 generated newly induced conformations, whereas Phe41 exhibited shift in equilibrium of its conformational distribution. In addition, the result showed binding energy of -130.091 ± 8.800 KJ/mol and Phe45 contributed -9.8576 KJ/mol. Conclusion: The results showed that schistosomal sulfotransferase binds oxamniquine by relying on hybrid mechanism of induced fit and conformational selection models. The findings offer new insight into sulfotransferase engineering and design of new drugs that target sulfotransferase.

scholarly journals Mitigating the Adverse Effects of Polychlorinated Biphenyl Derivatives on Estrogenic Activity via Molecular Modification Techniques

2021 ◽  
Vol 18 (9) ◽  
pp. 4999
Author(s):  
Wei He ◽  
Wenhui Zhang ◽  
Zhenhua Chu ◽  
Yu Li
Keyword(s):  
Amino Acid ◽  
Binding Site ◽  
Hydrophobic Interaction ◽  
Oestrogen Receptor ◽  
Polychlorinated Biphenyl ◽  
Hydrophobic Interactions ◽  
Estrogenic Activity ◽  
Average Distance ◽  
Amino Acid Residues ◽  
Hydrophobic Amino Acid

The aim of this paper is to explore the mechanism of the change in oestrogenic activity of PCBs molecules before and after modification by designing new PCBs derivatives in combination with molecular docking techniques through the constructed model of oestrogenic activity of PCBs molecules. We found that the weakened hydrophobic interaction between the hydrophobic amino acid residues and hydrophobic substituents at the binding site of PCB derivatives and human oestrogen receptor alpha (hERα) was the main reason for the weakened binding force and reduced anti-oestrogenic activity. It was consistent with the information that the hydrophobic field displayed by the 3D contour maps in the constructed oestrogen activity CoMSIA model was one of the main influencing force fields. The hydrophobic interaction between PCB derivatives and oestrogen-active receptors was negatively correlated with the average distance between hydrophobic substituents and hydrophobic amino acid residues at the hERα-binding site, and positively correlated with the number of hydrophobic amino acid residues. In other words, the smaller the average distance between the hydrophobic amino acid residues at the binding sites between the two and the more the number of them, and the stronger the oestrogen activity expression degree of PCBS derivative molecules. Therefore, hydrophobic interactions between PCB derivatives and the oestrogen receptor can be reduced by altering the microenvironmental conditions in humans. This reduces the ability of PCB derivatives to bind to the oestrogen receptor and can effectively modulate the risk of residual PCB derivatives to produce oestrogenic activity in humans.

scholarly journals Mechanism of Metronidazole Resistance inHelicobacter pylori: Comparison of the rdxA Gene Sequences in 30 Strains

2000 ◽  
Vol 44 (8) ◽  
pp. 2207-2210 ◽  
Author(s):  
Nadia Maggi Solcà ◽  
Marco Valerio Bernasconi ◽  
Jean-Claude Piffaretti
Keyword(s):  
Phylogenetic Analysis ◽  
Helicobacter Pylori ◽  
Amino Acid ◽  
Resistant Strain ◽  
Point Mutations ◽  
Housekeeping Genes ◽  
Amino Acid Substitutions ◽  
Metronidazole Resistance ◽  
Nucleotide Mutation ◽  
Nucleotide Insertion

ABSTRACT The rdxA gene of 30 independently isolatedHelicobacter pylori strains was sequenced. A comparison of the rdxA sequences revealed a higher percentage of amino acid substitutions in the corresponding protein than in other housekeeping genes. Out of 122 point mutations, 41 were missense and 4 were nonsense. A resistant strain with a nucleotide insertion in therdxA sequence was also found. With the exception of the point mutations and the insertion generating a stop signal, no particular nucleotide mutation or amino acid substitution could be associated to metronidazole resistance. Moreover, phylogenetic analysis of the 30 nucleotide sequences did not demonstrate specific clusters associated with the resistance phenotype.

scholarly journals Identification of separate domains in the adenovirus E1A gene for immortalization activity and the activation of virus early genes.

1986 ◽  
Vol 6 (10) ◽  
pp. 3470-3480 ◽  
Author(s):  
E Moran ◽  
B Zerler ◽  
T M Harrison ◽  
M B Mathews
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Point Mutations ◽  
Apparent Molecular Weight ◽  
Amino Acid Position ◽  
Cysteine Residue ◽  
Transformation Function ◽  
Single Amino Acid ◽  
Amino Acid Substitutions ◽  
E1a Gene

The transformation and early adenovirus gene transactivation functions of the E1A region were analyzed with deletion and point mutations. Deletion of amino acids from position 86 through 120 had little effect on the lytic or transforming functions of the E1A products, while deletion of amino acids from position 121 through 150 significantly impaired both functions. The sensitivity of the transformation function to alterations in the region from amino acid position 121 to 150 was further indicated by the impairment of transforming activity resulting from single amino acid substitutions at positions 124 and 135. Interestingly, conversion of a cysteine residue at position 124 to glycine severely impaired the transformation function without affecting the early adenovirus gene activating functions. Single amino acid substitutions in a different region of the E1A gene had the converse effect. All the mutants produced polypeptides of sufficient stability to be detected by Western immunoblot analysis. The single amino acid substitutions at positions 124 and 135, although impairing the transformation functions, did not detectably alter the formation of the higher-apparent-molecular-weight forms of the E1A products.

scholarly journals Amino acid substitutions in human growth hormone affect coiled-coil content and receptor binding

2021 ◽  
Author(s):  
Andrei Rajkovic ◽  
Sandesh Kanchugal ◽  
Eldar Abdurakhmanov ◽  
Rebecca Howard ◽  
Astrid Gräslund ◽  
...  
Keyword(s):  
Growth Hormone ◽  
Amino Acid ◽  
Binding Site ◽  
Human Growth Hormone ◽  
Receptor Binding ◽  
Coiled Coil ◽  
Human Growth ◽  
Zinc Binding ◽  
Amino Acid Substitutions ◽  
Great Relevance

The interaction between human Growth Hormone (hGH) and hGH Receptor (hGHR) has great relevance to human diseases such as acromegaly and cancer. HGH has been extensively engineered by other workers to improve binding and other properties. We used a computational screen to select substitutions at single hGH positions within the hGHR-binding site. We find that, while many successfully slow down dissociation of the hGH-hGHR complex once bound, they also slow down the association of hGH to hGHR. We are particularly interested in E174 which belongs to the hGH zinc-binding triad, and which spans coiled-coil helices and obeys the coiled-coil heptad pattern. Surprisingly, substituting E174 with A leads to substantial increase in an experimental measure of coiled-coil content. E174A is known to increase affinity of hGH against hGHR; here we show that this is simply because the off-rate is slowed down more than the on-rate, in line with what has been found for other affinity-improving mutations. For E174Y (and mutations at other sites) the slowdown in on-rate was greater, leading to decreased affinity. The results point to a link between coiled-coiling, zinc binding, and hGHR-binding affinity in hGH, and also suggest rules for choosing affinity-increasing substitutions.

Identification of amino acid residues responsible for the α5  subunit binding selectivity of L-655,708, a benzodiazepine binding site ligand at the GABAA receptor

2001 ◽  
Vol 77 (2) ◽  
pp. 445-451 ◽  
Author(s):  
M. Anna Casula ◽  
Frances A. Bromidge ◽  
Gopalan V. Pillai ◽  
Peter B. Wingrove ◽  
Karine Martin ◽  
...  
Keyword(s):  
Amino Acid ◽  
Binding Site ◽  
Gabaa Receptor ◽  
Amino Acid Residues ◽  
Binding Selectivity ◽  
Benzodiazepine Binding

Protein truncation is required for the activation of the c-myb proto-oncogene

1991 ◽  
Vol 11 (8) ◽  
pp. 3987-3996
Author(s):  
F A Grässer ◽  
T Graf ◽  
J S Lipsick
Keyword(s):  
Amino Acid ◽  
Bone Marrow Cells ◽  
Protein Product ◽  
Full Length ◽  
Carboxyl Terminus ◽  
Amino Acid Substitutions ◽  
Amino Acid Residues ◽  
Avian Myeloblastosis Virus ◽  
Virally Encoded ◽  
Myb Proteins

The protein product of the v-myb oncogene of avian myeloblastosis virus, v-Myb, differs from its normal cellular counterpart, c-Myb, by (i) expression under the control of a strong viral long terminal repeat, (ii) truncation of both its amino and carboxyl termini, (iii) replacement of these termini by virally encoded residues, and (iv) substitution of 11 amino acid residues. We had previously shown that neither the virally encoded termini nor the amino acid substitutions are required for transformation by v-Myb. We have now constructed avian retroviruses that express full-length or singly truncated forms of c-Myb and have tested them for the transformation of chicken bone marrow cells. We conclude that truncation of either the amino or carboxyl terminus of c-Myb is sufficient for transformation. In contrast, the overexpression of full-length c-Myb does not result in transformation. We have also shown that the amino acid substitutions of v-Myb by themselves are not sufficient for the activation of c-Myb. Rather, the presence of either the normal amino or carboxyl terminus of c-Myb can suppress transformation when fused to v-Myb. Cells transformed by c-Myb proteins truncated at either their amino or carboxyl terminus appear to be granulated promyelocytes that express the Mim-1 protein. Cells transformed by a doubly truncated c-Myb protein are not granulated but do express the Mim-1 protein, in contrast to monoblasts transformed by v-Myb that neither contain granules nor express Mim-1. These results suggest that various alterations of c-Myb itself may determine the lineage of differentiating hematopoietic cells.

Sign in / Sign up

Export Citation Format

Share Document