EISENHABER Birgit

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

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

A Reversible Association between Smc Coiled Coils is Regulated by Lysine acetylation and Is Required for Cohesin Association with the DNA

Cohesin is a ring-shaped protein complex that is capable of embracing DNA. Most of the ring circumference is comprised of the anti-parallel intramolecular coiled coils of the Smc1 and Smc3 proteins, which connect globular head and hinge domains. Smc coiled coil arms contain multiple acetylated and ubiquitylated lysines. To investigate the role of these modifications, we substituted lysines for arginines to mimic the unmodified state and uncovered genetic interaction between the Smc arms.

type: 
Journal Paper
journal: 
Molecular Cell, Volume 63, Issue 6, p1044–1054, 15 September 2016, doi: 10.1016/j.molcel.2016.08.008
pubmed: 
27618487
Url: 
https://www.ncbi.nlm.nih.gov/pubmed/27618487
Impact Factor: 
13.958
Date of acceptance: 
2016-08-05

The Recipe for Protein-Based Function Predition and its implementation in the ANNOTATOR Software Environment

As biomolecular sequencing is becoming the main technique in life sciences, functional interpretation of sequences in terms of biomolecular mechanisms with in silico approaches is getting increasingly significant. Function prediction tools are most powerful for protein-coding sequences; yet, the concepts and technologies used for this purpose are not well reflected in bioinformatics textbooks. Notably, protein sequences typically consist of globular domains and non-globular segments. The two types of regions require cardinally different approaches for function prediction.

type: 
Book/Book Chapter
journal: 
Data Mining Techniques for the Life Sciences, Vol. 1415, pg 477-506,2016, ISBN: 978-1-4939-3570-3
Url: 
http://link.springer.com/protocol/10.1007%2F978-1-4939-3572-7_25

Low resolution solution structure of an enzymatic active AhpC10:AhpF2 ensemble of the Escherichia coli Alkyl hydroperoxide Reductase

The ability of bacteria to combat oxidative stress is imperative for their survival. The Alkyl hydroperoxide Reductase (AhpR) system, composed of the AhpC and AhpF proteins, is one of the dominant antioxidant defense systems required for scavenging hydrogen peroxide and organic peroxide. Therefore, it is necessary to understand the mechanism of the AhpR ensemble formation. In previous studies, we were able to elucidate conformational flexibility of Escherichia coli AhpF during the catalytic cycle and its binding site, the N-terminal domain (NTD), to AhpC.

type: 
Journal Paper
journal: 
Journal of Structural Biology, Jan;193 (2016), Pg 13-22, doi: 10.1016/j.jsb.2015.11.004
pubmed: 
26402142
Url: 
http://www.sciencedirect.com/science/article/pii/S1047847715301015
Impact Factor: 
3.231
Date of acceptance: 
2015-11-11

HPMV : Human protein mutation viewer - relating sequence mutations to protein sequence architecture and function changes

Next-generation sequencing advances are rapidly expanding the number of human mutations to be analyzed for causative roles in genetic disorders. Our Human Protein Mutation Viewer (HPMV) is intended to explore the biomolecular mechanistic significance of non-synonymous human mutations in protein-coding genomic regions. The tool helps to assess whether protein mutations affect the occurrence of sequence-architectural features (globular domains, targeting signals, post-translational modification sites, etc.). As input, HPMV accepts protein mutations - as UniProt accessions with mutations (e.g.

type: 
Journal Paper
journal: 
Journal of Bioinformatics and Computational Biology, Vol. 13, No. 5 (2015), doi: 10.1142/S0219720015500286
pubmed: 
26503432,
Url: 
http://www.ncbi.nlm.nih.gov/pubmed/26503432
Impact Factor: 
0.783
Date of acceptance: 
2015-08-21
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