Mutational Analysis of Conserved Hydrophobic Amino Acid Residues in the N-Terminal Region of DnaA Protein

We previously reported that a leucine-zipper-like structure (I26, L33 and L40) located in the N-terminal region of DnaA is essential for the duplex opening at oriC by DnaA. In this study, we focused on three other conserved hydrophobic amino acid residues, L3, L10 and L17, and examined the function of DnaA proteins mutated in these amino acid residues. DnaA427 (L17S) and DnaA413 (L3S, L10S and L17S) were inactive for oriC DNA replication both in vitro and in vivo. Although these mutant DnaA proteins maintained their binding activities for both ATP and oriC, they were unable to induce the opening of duplex DNA at oriC. Glutathione-S-transferase (GST)-fused wild-type DnaA interacted with wild-type DnaA but not with DnaA427 and DnaA413. Based on these results, we propose that conserved hydrophobic amino acid residues in the N-terminal region of DnaA are involved in DnaA oligomerization, in which DnaA—DnaA interaction is required.

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

International Journal of Environmental Research and Public Health ◽

10.3390/ijerph18094999 ◽

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.

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Identification and Mutational Analysis of Amino Acid Residues Involved in Dipyridamole Interactions with Human and Caenorhabditis elegans Equilibrative Nucleoside Transporters

Journal of Biological Chemistry ◽

10.1074/jbc.m410348200 ◽

2005 ◽

Vol 280 (12) ◽

pp. 11025-11034 ◽

Cited By ~ 25

Author(s):

Frank Visser ◽

Stephen A. Baldwin ◽

R. Elwyn Isaac ◽

James D. Young ◽

Carol E. Cass

Keyword(s):

Amino Acid ◽

Caenorhabditis Elegans ◽

Mutational Analysis ◽

Nucleoside Transporters ◽

Amino Acid Residues ◽

Equilibrative Nucleoside Transporters

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Peroxisome targeting signal of rat liver acyl-coenzyme A oxidase resides at the carboxy terminus

Molecular and Cellular Biology ◽

10.1128/mcb.9.1.83-91.1989 ◽

1989 ◽

Vol 9 (1) ◽

pp. 83-91

Author(s):

S Miyazawa ◽

T Osumi ◽

T Hashimoto ◽

K Ohno ◽

S Miura ◽

...

Keyword(s):

Amino Acid ◽

Rat Liver ◽

Coenzyme A ◽

Terminal Region ◽

Proteinase K ◽

Amino Acid Residues ◽

C Terminus ◽

Targeting Signal ◽

Acyl Coenzyme A

To identify the topogenic signal of peroxisomal acyl-coenzyme A oxidase (AOX) of rat liver, we carried out in vitro import experiments with mutant polypeptides of the enzyme. Full-length AOX and polypeptides that were truncated at the N-terminal region were efficiently imported into peroxisomes, as determined by resistance to externally added proteinase K. Polypeptides carrying internal deletions in the C-terminal region exhibited much lower import activities. Polypeptides that were truncated or mutated at the extreme C terminus were totally import negative. When the five amino acid residues at the extreme C terminus were attached to some of the import-negative polypeptides, the import activities were rescued. Moreover, the C-terminal 199 and 70 amino acid residues of AOX directed fusion proteins with two bacterial enzymes to peroxisomes. These results are interpreted to mean that the peroxisome targeting signal of AOX residues at the C terminus and the five or fewer residues at the extreme terminus have an obligatory function in targeting. The C-terminal internal region also has an important role for efficient import, possibly through a conformational effect.

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Stabilization of secondary structure elements by specific combinations of hydrophilic and hydrophobic amino acid residues is more important for proteins encoded by GC-poor genes

Biochimie ◽

10.1016/j.biochi.2012.08.008 ◽

2012 ◽

Vol 94 (12) ◽

pp. 2706-2715 ◽

Cited By ~ 12

Author(s):

Vladislav Victorovich Khrustalev ◽

Eugene Victorovich Barkovsky

Keyword(s):

Amino Acid ◽

Secondary Structure ◽

Amino Acid Residues ◽

Hydrophobic Amino Acid

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Modèle topologique de la structure d’un antiport vacuolaire de type NHX chez la vigne cultivée (Vitis vinifera)

Botany ◽

10.1139/b08-141 ◽

2009 ◽

Vol 87 (3) ◽

pp. 339-347 ◽

Cited By ~ 1

Author(s):

Mohsen Hanana ◽

Olivier Cagnac ◽

Ahmed Mliki ◽

Eduardo Blumwald

Keyword(s):

Amino Acid ◽

Vitis Vinifera ◽

Molecular Mass ◽

Electrostatic Interactions ◽

Functional Characterization ◽

Terminal Region ◽

Vitis Vinifera L ◽

Amino Acid Residues ◽

Transmembrane Segments ◽

Α Helix

After identifying and isolating a grapevine ( Vitis vinifera L.) NHX vacuolar antiporter and before initializing functional genomic studies, we juged necessary to acquire a minimum of knowledge about the VvNHX1 protein. Thus, we realized a bioinformatic analysis to determine its basic characteristics and to get structural informations that could guide us through the functional characterization. We have determined important physico-chemical parameters (molecular mass, isoelectric point, hydrophobic regions, etc.) and obtained interesting structural data (primary, secondary, and tertiary structures; conserved domains and interaction motives; etc.). The VvNHX1 gene, which encodes this 541 amino-acid protein with a predicted molecular mass of 60 kDa, is made of 14 exons and measures 6.5 kb. The amino-acidic composition of this protein is very important, in particular, for the establishment of the α-helix structure, which represents more than 50% of the protein, but also for charge distribution, which generates critical electrostatic interactions for the ionic flux. The secondary structure of VvNHX1 contains multiple transmembrane α-helix segments that are made of hydrophobic amino-acid residues, thus facilitating its insertion in the membrane. Globally, VvNHX1 has one hydrophobic N-terminal region, made of 10 transmembrane segments with 440 amino-acid residues, and one hydrophilic C-terminal region, made of 100 residues. The region located between the fourth and fifth transmembrane segments represents, with its structure mainly helicoidal and the presence of a favourable electrostatic environment, the pore where cation flux is performed across the membrane. VvNHX1 contains various interaction domains as well as several putative posttranslational modification sites, mainly at the C-terminus but also at the N-terminus, that play an important part in regulating protein activities, influence protein structural stability, or interact with other proteins or signalling molecules.

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