Gene/Protein
Disease
Symptom
Drug
Enzyme
Compound
Pivot Concepts:
Gene/Protein
Disease
Symptom
Drug
Enzyme
Compound
Target Concepts:
Gene/Protein
Disease
Symptom
Drug
Enzyme
Compound
Query: EC:1.4.1.2 (
glutamate dehydrogenase
)
4,380
document(s) hit in 31,850,051 MEDLINE articles (0.00 seconds)
We developed a knowledge-based program to predict hydration structures around hydrophilic surfaces of proteins as probability density. In the program, we assume that the three-dimensional distribution of hydration water molecules on a hydrophilic surface is reconstructed by summing up the empirical hydration distribution function of each solvent-exposed polar atom composing the surface. The probability functions of polar atoms in the CO, NH(n) (n = 1,3), and OH groups were calculated from the 17 984 protein structures solved by X-ray crystallography better than resolutions of 2.2 A (Matsuoka, D.; Nakasako, M. J. Phys. Chem. B 2009, 113, 11274-11292). The program was first tested for human lysozyme. The predicted probability density enveloped more than 85% of crystal water sites found in the crystal structure refined at a resolution of 0.95 A, and the density peaks suggested as hydration sites were located within 1.5 A from more than 75% of the crystal water sites. The density reproduced the hydration structure in a solvent accessible narrow channel from the surface to the lysozyme interior. We also tested the feasibility of the program to predict the water clusters existing in the transmembrane channels of bacteriorhodopsin and
aquaporin
. In bacteriorhodopsin, the distributions were distinct between the ground state and the photoreaction intermediate indispensable for its function. The program reproduced the interfacial hydration in Per-Arnt-Sim-related protein-protein complex and the hydration of metastable conformations in domain motion of
glutamate dehydrogenase
. Taking the results for the various types of protein hydration, the present program may be a useful tool to characterize the surface properties of proteins and discuss the relevance of hydration structures to the biological functions of proteins. In addition, it will be used to predict hydration structures of proteins available at resolutions insufficient to identify water molecules.
...
PMID:Prediction of hydration structures around hydrophilic surfaces of proteins by using the empirical hydration distribution functions from a database analysis. 2020 97
In
Portunus trituberculatus
, a full-length cDNA of Rhesus-like glycoprotein (Rh protein), encoding the entire 478 amino acid protein, has been identified in gills, and plays an essential role in ammonia (NH
3
/NH
4
+
) excretion. Phylogenetic analysis of Rh-like proteins from crabs was clustered, showing high conservation of the ammonium transporter domain and transmembrane segments essential to the function of Rh protein. Rh protein of
P. trituberculatus
(
Pt
Rh) was detected in all tested tissues, and showed the highest expression in the gills. To further characterize the role of
Pt
Rh in ammonia metabolism and excretion, double-stranded RNA-mediated RNA interference of
Pt
Rh was employed. Knockdown of
Pt
Rh upregulated mRNA expression of ammonia excretion-related genes encoding
aquaporin
(AQP), K
+
channels and vesicle-associated membrane protein (VAMP), increased the activity of Na
+
/K
+
-ATPase (NKA) and V-type H
+
-ATPase (V-ATPase), and initially reduced then elevated the expression of the Na
+
/H
+
-exchanger (NHE). dsRNA-mediated reduction in
Pt
Rh significantly reduced ammonia excretion rate and increased ammonia and glutamine (Gln) levels in the hemolymph, together with an increase of
glutamate dehydrogenase
(
GDH
) and glutamine synthetase (GS) activity, indicating a central role for
Pt
Rh in ammonia excretion and detoxification mechanisms. Taken together, we conclude that Rh protein is a primary contributor to ammonia excretion of
P. trituberculatus
, which may be the basis of their ability to inhabit benthic water with high ammonia levels.
...
PMID:Identification of the role of Rh protein in ammonia excretion of the swimming crab
Portunus trituberculatus
. 3017 Oct 94
The eyestalks of crustaceans play an essential role in controlling a variety of physiological functions by converting light into hormonal signals. To obtain a more complete description of eyestalk biology in the commercially important Chinese mitten crab (Eriocheir sinensis), we conducted comparative transcriptome analysis of eyestalks during the day and at night using high-throughput sequencing on an Illumina HiSeq 4000 platform. We obtained 47,092 unigenes-including 4771 differentially expressed genes (DEGs)-from eyestalks during the day and at night. We found that 4269 DEGs were upregulated during the day and 502 DEGs were upregulated at night. We identified five DEGs that may contribute to molting, including molt-inhibiting hormone, cuticle, catalase,
aquaporin
, and ubiquitin-conjugating enzyme; hence, similar to other crustaceans, Eriocheir sinensis may molt at night. We further identified eight DEGs related to behavior regulation, including three
glutamate dehydrogenase
genes that were upregulated during the day. Thus, changes in the eyestalks may partially compensate for daily changes in illumination in the Chinese mitten crab's normal environment. Our present study is the first genome-wide transcriptome analysis of the eyestalks of Eriocheir sinensis during the day and at night. Our findings provide a valuable insight into the molecular basis of circadian cycle regulation in crustaceans.
...
PMID:Comparative transcriptome analysis provides insights into the molecular basis of circadian cycle regulation in Eriocheir sinensis. 3071 37
