WONG Wing-Cheong

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

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

dissectHMMER: a HMMER-based score dissection framework that statistically evaluates fold-critical sequence segments for domain fold similarity

Background: Annotation transfer for function and structure within the sequence homology concept essentially requires protein sequence similarity for the secondary structural blocks forming the fold of a protein. A simplistic similarity approach in the case of non-globular segments (coiled coils, low complexity regions, transmembrane regions, long loops, etc.) is not justified and a pertinent source for mistaken homologies.

type: 
Journal Paper
journal: 
Biology Direct (2015) 10:39, doi: 10.1186/s13062-015-0068-3
Impact Factor: 
4.66
Date of acceptance: 
2015-07-20

On the necessity of dissecting sequence similarity scores into segment-specific contributions for inferring protein homology, function prediction and annotation

Background

type: 
Journal Paper
journal: 
BMC Bioinformatics 2014, 15:66, doi:10.1186/1471-2105-15-166
Url: 
http://www.biomedcentral.com/1471-2105/15/166/abstract
Impact Factor: 
3.02
Date of acceptance: 
2014-05-27

A simple shortcut to unsupervised alignment-free phylogenetic genome groupings, even from unassembled sequencing reads

We propose an extension to alignment-free approaches that can produce reasonably accurate phylogenetic groupings starting from unaligned genomes, for example, as fast as 1 min on a standard desktop computer for 25 bacterial genomes. A 6-fold speed-up and 11-fold reduction in memory requirements compared to previous alignment-free methods is achieved by reducing the comparison space to a representative sample of k-mers of optimal length and with specific tag motifs.

type: 
Journal Paper
journal: 
Journal of Bioinformatics and Computational Biology, Vol. 11, No. 6 (2013), doi: 10.1142/S0219720013430051
Url: 
http://www.worldscientific.com/doi/abs/10.1142/S0219720013430051
Date of acceptance: 
2013-10-10

Peramivir and laninamivir susceptibility of circulating influenza A and B viruses

Influenza viruses collected from regions of Asia, Africa and Oceania between 2009 and 2012 were tested for their susceptibility to two new neuraminidase inhibitors, peramivir and laninamivir. All viruses tested had normal laninamivir inhibition. However, 3·2% (19/599) of A(H1N1)pdm09 viruses had highly reduced peramivir inhibition (due to H275Y NA mutation) and <1% (6/1238) of influenza B viruses had reduced or highly reduced peramivir inhibition, with single occurrence of variants containing I221T, A245T, K360E, A395E, D432G and a combined G145R+Y142H mutation.

type: 
Journal Paper
journal: 
Influenza and Other Respiratory Viruses, 2013, doi : 10.1111/irv.12187
Url: 
http://onlinelibrary.wiley.com/doi/10.1111/irv.12187/abstract
Impact Factor: 
1.471
Date of acceptance: 
2013-09-08

Combination Therapy with Gossypol Reveals Synergism against Gemcitabine Resistance in Cancer Cells with High BCL-2 Expression

Although gemcitabine is highly active in several cancer types, intrinsic and acquired drug resistance remains a major challenge. Overexpression of Bcl-2 has been associated with gemcitabine resistance. The aim of this study is to determine whether gossypol can overcome gemcitabine resistance in cell lines with high level of Bcl-2 expression in combination drug therapy. Our study demonstrated that in 10 cell lines derived from different cancers, high Bcl-2 baseline expression was observed in cell lines that were resistant to gemcitabine (GEM-R).

type: 
Journal Paper
journal: 
PLoS One 2012, 7(12): e50786. doi:10.1371/journal.pone.0050786
pubmed: 
23226540
Url: 
http://www.ncbi.nlm.nih.gov/pubmed/23226540
Impact Factor: 
4.411
Date of acceptance: 
2012-10-24

Transmembrane helix: simple or complex

Transmembrane helical segments (TMs) can be classified into two groups of so-called ‘simple’ and ‘complex’ TMs. Whereas the first group represents mere hydrophobic anchors with an overrepresentation of aliphatic hydrophobic residues that are likely attributed to convergent evolution in many cases, the complex ones embody ancestral information and tend to have structural and functional roles beyond just membrane immersion. Hence, the sequence homology concept is not applicable on simple TMs.

type: 
Journal Paper
journal: 
Nuclei Acids Research, 2012, Pg 1-6, doi:10.1093/NAR/GKS379
Url: 
http://nar.oxfordjournals.org/content/early/2012/05/07/nar.gks379
Date of acceptance: 
2012-04-12

Not all transmembrane helices are born equal: Towards the extension of the sequence homology concept to membrane proteins

type: 
Journal Paper
journal: 
Biology Direct 2011, Vol. 6, Issue 57, doi:10.1186/1745-6150-6-57
Date of acceptance: 
2011-10-25

Macrophages in Human Colorectal Cancer are Pro-inflammatory and Prime T cells towards an Anti-Tumour Type-1 Inflammatory Response

High macrophage infiltration into tumours often correlates with poor prognoses; in colorectal, stomach and skin cancers however, the opposite is observed but the mechanisms behind this phenomenon remain unclear. Here, we sought to understand how tumour-associated macrophages (TAMs) in colorectal cancer execute tumour-suppressive roles. We found that TAMs in a colorectal cancer model were pro-inflammatory and inhibited the proliferation of tumour cells.

type: 
Journal Paper
journal: 
European Journal of Immunology, 2011 Oct 18, doi: 10.1002/eji.201141825
pubmed: 
22009685
Url: 
http://www.ncbi.nlm.nih.gov/pubmed?term=22009685
Date of acceptance: 
2011-10-18
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