Gene Function Prediction/Annotator Group

Novel insights into the vancomycin-resistant Enterococcus faecalis (V583) alkylhydroperoxide reductase subunit F

Published date : 19 Sep 2017

The ability of the vancomycin-resistant Enterococcus faecalis (V583) to restore redox homeostasis via antioxidant defense mechanism is of importance, and knowledge into this defense is essential to understand its antibiotic-resistance and survival in hosts. The flavoprotein disulfide reductase AhpR, composed of the subunits AhpC and AhpF, represents one such vital part. Circular permutation was found to be a feature of the AhpF protein family. E.

type
Journal Paper
journal
Biochimica et Biophysica Acta (BBA), 2017 Sep 19, doi: 10.1016/j.bbagen.2017.09.011
Impact Factor
4.702

Prenylation of Viral Proteins by Enzymes of the Host: Virus-Driven Rationale for Therapy With Statins and FT/GGT1 Inhibitors

Published date : 08 Sep 2017

Intracellular bacteria were recently shown to employ eukaryotic prenylation system for modifying activity and ensuring proper intracellular localization of their own proteins. Following the same logic, the proteins of viruses may also serve as prenylation substrates.

type
Journal Paper
journal
BioEssays, 2017 Oct;39(10). doi: 10.1002/bies.201700014
Impact Factor
4.441

Charged residues next to transmembrane regions revisited: "Positive-inside rule" is complemented by the "negative inside depletion/outside enrichment rule"

Published date : 24 Jul 2017

BACKGROUND:
Transmembrane helices (TMHs) frequently occur amongst protein architectures as means for proteins to attach to or embed into biological membranes. Physical constraints such as the membrane's hydrophobicity and electrostatic potential apply uniform requirements to TMHs and their flanking regions; consequently, they are mirrored in their sequence patterns (in addition to TMHs being a span of generally hydrophobic residues) on top of variations enforced by the specific protein's biological functions.

RESULTS:

type
Journal Paper
journal
BMC Biology 2017 Jul 24;15(1):66. doi: 10.1186/s12915-017-0404-4
Impact Factor
6.779

Essential role of the flexible linker on the conformational equilibrium of bacterial peroxiredoxin reductase for effective regeneration of peroxiredoxin

Published date : 07 Mar 2017

Reactive oxygen species (ROS) can damage DNA, proteins, and lipids, so cells have antioxidant systems that regulate ROS. In many bacteria, a dedicated peroxiredoxin reductase, alkyl hydroperoxide reductase subunit F (AhpF), catalyzes the rapid reduction of the redox-active disulfide center of the antioxidant protein peroxiredoxin (AhpC) to detoxify ROS such as hydrogen peroxide, organic hydroperoxide, and peroxynitrite. AhpF is a flexible multi-domain protein that enables a series of electron transfers among the redox centers by accepting reducing equivalents from NADH.

type
Journal Paper
journal
The Journal of Biological Chemistry, 7 Mar 2017, doi : 10.1074/jbc.M117.775858
Impact Factor
4.258

Discovery of a novel splice variant of Fcar (CD89) unravels sequence segments necessary for efficient secretion: a story of bad signal peptides and good ones that nevertheless do not make it

Published date : 19 Jan 2017

The IgA receptor, Fcar (CD89) consists of five sequence segments: two segments (S1, S2) forming the potential signal peptide, two extracellular EC domains that include the IgA binding site, and the transmembrane and cytoplasmic tail (TM/C) region. Numerous Fcar splice variants have been reported with various combinations of the sequence segments mentioned above. Here, we report a novel splice variant termed variant APD isolated from a healthy volunteer that lacks only the IgA-binding EC1 domain.

type
Journal Paper
journal
Cell Cycle 2016, doi: 10.1080/15384101.2017.1281480
Impact Factor
3.952

Towards allosterically increased catalytic activity of insulin degrading enzyme (IDE) against amyloid peptides

Published date : 03 Dec 2016

Physiological role of insulin degrading enzyme (IDE) in the intracytosolic clearance of amyloid beta (Aβ) and other amyloid-like peptides supports a hypothesis that human IDE hyperactivation could be therapeutically beneficial in the treatment of the late onset Alzhimer’s disease (AD). The major challenge towards this goal is to increase specific catalytic activity of IDE against the Aβ-substrate.

type
Journal Paper
journal
Biochemistry 2016, doi: 10.1021/acs.biochem.6b00783
Impact Factor
2.87

xHMMER3x2: Utilizing HMMER3's speed and HMMER2's sensitivity and specificity in the glocal alignment mode for improved large-scale protein domain annotation

Published date : 29 Nov 2016

BACKGROUND:
While the local-mode HMMER3 is notable for its massive speed improvement, the slower glocal-mode HMMER2 is more exact for domain annotation by enforcing full domain-to-sequence alignments. Since a unit of domain necessarily implies a unit of function, local-mode HMMER3 alone remains insufficient for precise function annotation tasks. In addition, the incomparable E-values for the same domain model by different HMMER builds create difficulty when checking for domain annotation consistency on a large-scale basis.

RESULTS:

type
Journal Paper
journal
Biology Direct 2016, 11:63, DOI: 10.1186/s13062-016-0163-0
Impact Factor
3.016

Transition steps in peroxide reduction and a molecular switch for peroxide robustness of prokaryotic peroxiredoxins

Published date : 28 Nov 2016

In addition to their antioxidant function, the eukaryotic peroxiredoxins (Prxs) facilitate peroxide-mediated signaling by undergoing controlled inactivation by peroxide-driven over-oxidation. In general, the bacterial enzyme lacks this controlled inactivation mechanism, making it more resistant to high H2O2 concentrations. During peroxide reduction, the active site alternates between reduced, fully folded (FF), and oxidized, locally unfolded (LU) conformations.

type
Journal Paper
journal
Scientific Reports 6, 2016, doi: 10.1038/srep37610
Impact Factor
5.228

Protein function machinery: from basic structural units to modulation of activity

Published date : 16 Nov 2016

Contemporary protein structure is a result of the trade off between the laws of physics and the evolutionary selection. The polymer nature of proteins played a decisive role in establishing the basic structural and functional units of soluble proteins. We discuss how these elementary building blocks work in the hierarchy of protein domain structure, co-translational folding, as well as in enzymatic activity and molecular interactions.

type
Journal Paper
journal
Current Opinion in Structural Biology, Vol. 42, Feb 17, Pg 67-74, doi: 10.1016/j.sbi.2016.10.021
Impact Factor
6.7

Genome-wide comparative analysis of codon usage bias and codon context patterns among cyanobacterial genomes

Published date : 10 Oct 2016

With the increasing accumulation of genomic sequence information of prokaryotes, the study of codon usage bias has gained renewed attention. The purpose of this study was to examine codon selection pattern within and across cyanobacterial species belonging to diverse taxonomic orders and habitats. We performed detailed comparative analysis of cyanobacterial genomes with respect to codon bias. Our analysis reflects that in cyanobacterial genomes, A- and/or T-ending codons were used predominantly in the genes whereas G- and/or C-ending codons were largely avoided.

type
Journal Paper
journal
Marine Genomics 2016 Oct 9, doi: 10.1016/j.margen.2016.10.00
Impact Factor
1.883