Gene Function Prediction/Annotator Group

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

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
pubmed: 
28935609
Url: 
https://www.ncbi.nlm.nih.gov/pubmed/28935609
Impact Factor: 
4.702
Date of acceptance: 
2017-09-15

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

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
pubmed: 
28885709
Url: 
https://www.ncbi.nlm.nih.gov/pubmed/28885709
Impact Factor: 
4.441

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

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
pubmed: 
28738801
Url: 
https://bmcbiol.biomedcentral.com/articles/10.1186/s12915-017-0404-4
Impact Factor: 
6.779
Date of acceptance: 
2017-08-07

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

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
Url: 
http://www.jbc.org/content/early/2017/03/07/jbc.M117.775858
Impact Factor: 
4.258
Date of acceptance: 
2017-03-07

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

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
Url: 
http://www.tandfonline.com/doi/full/10.1080/15384101.2017.1281480?scroll=top&needAccess=true
Impact Factor: 
3.952
Date of acceptance: 
2017-01-05

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

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
Url: 
http://pubs.acs.org/doi/abs/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

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
pubmed: 
27894340
Url: 
https://biologydirect.biomedcentral.com/articles/10.1186/s13062-016-0163-0
Impact Factor: 
3.016
Date of acceptance: 
2016-10-24

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

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
Url: 
http://www.nature.com/articles/srep37610
Impact Factor: 
5.228
Date of acceptance: 
2016-10-31

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

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
pubmed: 
27865209
Url: 
http://www.sciencedirect.com/science/article/pii/S0959440X1630183X
Impact Factor: 
6.7

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

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
pubmed: 
27733306
Url: 
https://www.ncbi.nlm.nih.gov/pubmed/27733306
Impact Factor: 
1.883
Date of acceptance: 
2016-10-03
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