OmpA: A Flexible Clamp for Bacterial Cell Wall Attachment

The envelope of Gram-negative bacteria is highly complex, containing separate outer and inner membranes and an intervening periplasmic space encompassing a peptidoglycan (PGN) cell wall. The PGN scaffold is anchored non-covalently to the outer membrane via globular OmpA-like domains of various proteins. We report atomically detailed simulations of PGN bound to OmpA in three different states, including the isolated C-terminal domain (CTD), the full-length monomer, or the complete full-length dimeric form.

type: 
Journal Paper
journal: 
Structure 2016, Vol. 24, Issue 12, 6 Dec 2016, Pg 2227-2235, doi: 10.1016/j.str.2016.10.009
pubmed: 
27866852
Url: 
http://www.cell.com/structure/abstract/S0969-2126(16)30317-3
Impact Factor: 
5.237
Date of acceptance: 
2016-10-14

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

Viral factors in influenza pandemic risk assessment

The threat of an influenza A virus pandemic stems from continual virus spillovers from reservoir species, a tiny fraction of which spark sustained transmission in humans. To date, no pandemic emergence of a new influenza strain has been preceded by detection of a closely related precursor in an animal or human. Nonetheless, influenza surveillance efforts are expanding, prompting a need for tools to assess the pandemic risk posed by a detected virus.

type: 
Journal Paper
journal: 
Elife, 2016 Nov 11;5. pii: e18491. doi: 10.7554/eLife.18491
pubmed: 
27834632
Url: 
https://www.ncbi.nlm.nih.gov/pubmed/27834632
Impact Factor: 
8.3

Big genomics and clinical data analytics strategies for precision cancer prognosis

The field of personalized and precise medicine in the era of big data analytics is growing rapidly. Previously, we proposed our model of patient classification termed Prognostic Signature Vector Matching (PSVM) and identified a 37 variable signature comprising 36 let-7b associated prognostic significant mRNAs and the age risk factor that stratified large high-grade serous ovarian cancer patient cohorts into three survival-significant risk groups.

type: 
Journal Paper
journal: 
Scientific Reports 6, 2016, Article no. 36493 (2016), doi:10.1038/srep36493
pubmed: 
27819294
Url: 
https://www.ncbi.nlm.nih.gov/pubmed/27819294
Date of acceptance: 
2016-10-12

Segment 2D and 3D Filaments by Learning Sructured and Contextual Features

We focus on the challenging problem of filamentary structure segmentation in both 2D and 3D images, including retinal vessels and neurons, among others. Despite the increasing amount of efforts in learning based methods to tackle this

type: 
Journal Paper
journal: 
IEEE Transactions on Medical Imaging, Issue 99, 2016, doi: 10.1109/TMI.2016.2623357
Impact Factor: 
2.536

A large common-source outbreak of norovirus gastroenteritis in a hotel in Singapore, 2012

An outbreak of gastroenteritis affected 453 attendees (attack rate 28·5%) of six separate events held at a hotel in Singapore. Active case detection, case-control studies, hygiene inspections and microbial analysis of food, environmental and stool samples were conducted to determine the aetiology of the outbreak and the modes of transmission. The only commonality was the food, crockery and cutlery provided and/or handled by the hotel's Chinese banquet kitchen. Stool specimens from 34 cases and 15 food handlers were positive for norovirus genogroup II.

type: 
Journal Paper
journal: 
Epidemiology & Infection 2016, Pg 1-10, DOI: 10.1017/S095026881600248X
pubmed: 
27788694
Url: 
https://www.ncbi.nlm.nih.gov/pubmed/27788694
Impact Factor: 
2.4
Date of acceptance: 
2017-01-09

Energetics and Dynamics Across the Bcl-2-Regulated Apoptotic Pathway Reveal Distinct Evolutionary Determinants of Specificity and Affinity

Critical regulatory pathways are replete with instances of intra- and interfamily protein-protein interactions due to the pervasiveness of gene duplication throughout evolution. Discerning the specificity determinants within these systems has proven a challenging task. Here, we present an energetic analysis of the specificity determinants within the Bcl-2 family of proteins (key regulators of the intrinsic apoptotic pathway) via a total of ∼20 μs of simulation of 60 distinct protein-protein complexes.

type: 
Journal Paper
journal: 
Structure, Vol 24, Issue 11, pg 2024-2033, 1 Nov 2016, doi: 10.1016/j.str.2016.09.006
pubmed: 
27773689
Url: 
https://www.ncbi.nlm.nih.gov/pubmed/27773689
Impact Factor: 
5.237
Date of acceptance: 
2016-09-28

Full-Length OmpA: Structure, Function, and Membrane Interactions Predicted by Molecular Dynamics Simulations

OmpA is a multidomain protein found in the outer membranes of most Gram-negative bacteria. Despite a wealth of reported structural and biophysical studies, the structure-function relationships of this protein remain unclear. For example, it is still debated whether it functions as a pore, and the precise molecular role it plays in attachment to the peptidoglycan of the periplasm is unknown. The absence of a consensus view is partly due to the lack of a complete structure of the full-length protein.

type: 
Journal Paper
journal: 
Biophysical Journal, Vol. 111, Issue 8, pg 1692-1702, 18 Oct 2016, doi: 10.1016/j.bpj.2016.09.009
pubmed: 
27760356
Url: 
https://www.ncbi.nlm.nih.gov/pubmed/27760356
Impact Factor: 
3.632
Date of acceptance: 
2016-09-06

Multiscale Molecular Dynamics Simulation Approaches to the Structure and Dynamics of Viruses

Viral pathogens are a significant source of human morbidity and mortality, and have a major impact on societies and economies around the world. One of the challenges inherent in targeting these pathogens with drugs is the tight integration of the viral life cycle with the host's cellular machinery. However, the reliance of the virus on the host cell replication machinery is also an opportunity for therapeutic targeting, as successful entry- and exit-inhibitors have demonstrated.

type: 
Journal Paper
journal: 
Progress in Biophysics and Molecular Biology, Oct 17 2016, doi: 10.1016/j.pbiomolbio.2016.09.010
pubmed: 
27765545
Url: 
https://www.ncbi.nlm.nih.gov/pubmed/27765545
Impact Factor: 
2.581
Date of acceptance: 
2016-09-27

Directed Evolution of a Fluorinase for Improved Fluorination Efficiency with a Non-native Substrate

Fluorinases offer an environmentally friendly alternative for selective fluorination under mild conditions. However, their diversity is limited in nature and they have yet to be engineered through directed evolution. Herein, we report the directed evolution of the fluorinase FlA1 for improved conversion of the non-native substrate 5′-chloro-5′-deoxyadenosine (5′-ClDA) into 5′-fluoro-5′-deoxyadenosine (5′-FDA).

type: 
Journal Paper
journal: 
Angewandte Chemie, 2016, Vol. 55, Issue 46, Nov 7 2016, pg 14277-14280, doi: 10.1002/anie.201606722
pubmed: 
27739177
Url: 
Angewandte Chemie, 2016, Vol. 55, Issue 46, Nov 7 2016, pg 14277-14280, doi: 10.1002/anie.201606722
Impact Factor: 
11.709
Date of acceptance: 
2016-08-24
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