Large scale ab initio modelling of structurally uncharacterized antimicrobial peptides reveals known and novel folds

Published date : 18 Feb 2018

Antimicrobial resistance within a wide range of infectious agents is a severe and growing public health threat. Antimicrobial peptides (AMPs) are among the leading alternatives to current antibiotics, exhibiting broad spectrum activity. Their activity is determined by numerous properties such as cationic charge, amphipathicity, size, and amino acid composition. Currently, only around 10% of known AMP sequences have experimentally solved structures.

type
Journal Paper
journal
Proteins: Structure, Function, and Bioinformatics, 2018, doi: 10.1002/prot.25473
Impact Factor
2.499

Large scale ab initio modeling of structurally uncharacterized antimicrobial peptides reveals known and novel folds

Published date : 18 Feb 2018

Antimicrobial resistance within a wide range of infectious agents is a severe and growing public health threat. Antimicrobial peptides (AMPs) are among the leading alternatives to current antibiotics, exhibiting broad spectrum activity. Their activity is determined by numerous properties such as cationic charge, amphipathicity, size, and amino acid composition. Currently, only around 10% of known AMP sequences have experimentally solved structures.

type
Journal Paper
journal
Proteins: Structure, Function, and Bioinformatics, Vol. 86, Issue 5, May 2018, Pg 548-565, doi: 10.1002/prot.25473
Impact Factor
2.289

Identification of a biosynthetic gene cluster for the polyene macrolactam sceliphrolactam in a Streptomyces strain isolated from mangrove sediment

Published date : 25 Jan 2018

Streptomyces are a genus of Actinobacteria capable of producing structurally diverse natural products. Here we report the isolation and characterization of a biosynthetically talented Streptomyces (Streptomyces sp. SD85) from tropical mangrove sediments. Whole-genome sequencing revealed that Streptomyces sp. SD85 harbors at least 52 biosynthetic gene clusters (BGCs), which constitute 21.2% of the 8.6-Mb genome. When cultivated under lab conditions, Streptomyces sp. SD85 produces sceliphrolactam, a 26-membered polyene macrolactam with unknown biosynthetic origin.

type
Journal Paper
journal
Scientific Reports 8, Article no. 1594 (2018), doi:10.1038/s41598-018-20018-8
Impact Factor
4.259

The effects of Antibody Engineering CH and CL in Trastuzumab and Pertuzumab recombinant models: Impact on antibody production and antigen-binding

Published date : 15 Jan 2018

Current therapeutic antibodies such as Trastuzumab, are typically of the blood circulatory IgG1 class (Cκ/ CHγ1). Due to the binding to Her2 also present on normal cell surfaces, side effects such as cardiac failure can sometimes be associated with such targeted therapy. Using antibody isotype swapping, it may be possible to reduce systemic circulation through increased tissue localization, thereby minimising unwanted side effects. However, the effects of such modifications have yet to be fully characterized, particularly with regards to their biophysical properties in antigen binding.

type
Journal Paper
journal
Scientific Reports 8, Article no 718, 2018, doi:10.1038/s41598-017-18892-9
Impact Factor
4.259

Cytoplasmic polyadenylation-mediated translational control of maternal mRNAs directs maternal-to-zygotic transition

Published date : 08 Jan 2018

In the earliest stages of animal development following fertilization, maternally deposited mRNAs direct biological processes to the point of zygotic genome activation (ZGA). These maternal mRNAs undergo cytoplasmic polyadenylation (CPA), suggesting translational control of their activation. To elucidate the biological role of CPA during embryogenesis, we performed genome-wide polysome profiling at several stages of zebrafish development. Our analysis revealed a correlation between CPA and polysome-association dynamics, demonstrating a coupling of translation to the CPA of maternal mRNAs.

type
Journal Paper
journal
Development, 8 Jan 2018, Vol 145, Issue 1, doi: 10.1242/dev.159566
Impact Factor
5.843

Multivariate Regression with Gross Errors on Manifold-valued Data

Published date : 04 Jan 2018

We consider the topic of multivariate regression on manifold-valued output, that is, for a multivariate observation, its output response lies on a manifold. Moreover, we propose a new regression model to deal with the presence of grossly corrupted manifold-valued responses, a bottleneck issue commonly encountered in practical scenarios. Our model first takes a correction step on the grossly corrupted responses via geodesic curves on the manifold, then performs multivariate linear regression on the corrected data.

type
Journal Paper
journal
IEEE Transactions on Pattern Analysis and Machine Intelligence, 2018, doi: 10.1109/TPAMI.2017.2776260
Impact Factor
8.329

Role of the N-terminal lid in regulating the interaction of phosphorylated MDMX with p53

Published date : 19 Dec 2017

Murine double minute 4 protein (MDMX) is crucial for the regulation of the tumor suppressor protein p53. Phosphorylation of the N-terminal domain of MDMX is thought to affect its binding with the transactivation domain of p53, thus playing a role in p53 regulation. In this study, the effects of MDMX phosphorylation on the binding of p53 were investigated using molecular dynamics simulations.

type
Journal Paper
journal
Oncotarget, 2017, Vol. 8, No. 68, Pg 112825-112840, doi.org/10.18632/oncotarget.22829
Impact Factor
5.168

Covariant Conservation Laws and the Spin Hall Effect in Dirac-Rashba Systems

Published date : 14 Dec 2017

We present a theoretical analysis of two-dimensional Dirac-Rashba systems in the presence of disorder and external perturbations. We unveil a set of exact symmetry relations (Ward identities) that impose strong constraints on the spin dynamics of Dirac fermions subject to proximity-induced interactions. This allows us to demonstrate that an arbitrary dilute concentration of scalar impurities results in the total suppression of nonequilibrium spin Hall currents when only Rashba spin-orbit coupling is present.

type
Journal Paper
journal
Physical Review Letters, Vol. 119, Issue 24, 14 Dec 2017, doi: 10.1103/PhysRevLett.119.246801
Impact Factor
8.462