Cross-reactive dengue human monoclonal antibody prevents severe pathologies and death from Zika virus infections

Zika virus (ZIKV) infections have been linked with neurological complications and congenital Zika syndrome. Given the high level of homology between ZIKV and the related flavivirus dengue virus (DENV), we investigated the level of cross-reactivity with ZIKV using a panel of DENV human mAbs. A majority of the mAbs showed binding to ZIKV virions, with several exhibiting neutralizing capacities against ZIKV in vitro. Three of the best ZIKV-neutralizing mAbs were found to recognize diverse epitopes on the envelope (E) glycoprotein: the highly conserved fusion-loop peptide, a

type: 
Journal Paper
journal: 
JCI Insight. 2017 Apr 20;2(8). pii: 92428. doi: 10.1172/jci.insight.92428
Url: 
https://insight.jci.org/articles/view/92428
Date of acceptance: 
2017-04-21

A novel toolbox to investigate tissue spatial organization applied to the study of the islets of Langerhans

Thanks to the development of new 3D Imaging techniques, volumetric data of thick samples, especially tissues, are commonly available. Several algorithms were proposed to analyze cells or nuclei in tissues, however these tools are limited to two dimensions. Within any given tissue, cells are not likely to be organized randomly and as such have specific patterns of cell-cell interaction forming complex communication networks. In this paper, we propose a new set of tools as an approach to segment and analyze tissues in 3D with single cell resolution.

type: 
Journal Paper
journal: 
Scientific Reports 7, Article number: 44261 (2017), doi:10.1038/srep44261
Url: 
http://www.nature.com/articles/srep44261
Impact Factor: 
5.228
Date of acceptance: 
2017-02-07

Molecular Environment Modulates Conformational Differences between Crystal and Solution States of Human beta-defensin 2

Human β-defensin 2 is a cysteine-rich antimicrobial peptide. In the crystal state, the N-terminal segment (residues 1−11) exhibits a helical conformation. However, a truncated form, with four amino acids removed from the N-terminus, adopts nonhelical conformations in solution, as shown by NMR. To explore the molecular origins of these different conformations, we performed Hamiltonian replica exchange molecular dynamics simulations of the peptide in solution and in the crystal state.

type: 
Journal Paper
journal: 
The Journal of Physical Chemistry Part B, 2017, doi : 10.1021/acs.jpcb.7b00083
Impact Factor: 
3.187
Date of acceptance: 
2017-03-15

APD SpectBT: Arduino-based mobile vis-Spectrophotometer

Quantification of samples is an integral step in numerous biological and chemical experiments. Spectrophotometers are often used together with colorimetric assays that react with the compound of interest in the samples. However, spectrophotometers are often costly, bulky and immobile. To increase the convenience and ease the process of spectrophotometry, the APD SpectBT was developed using the Arduino-based platform to create a smartphone dependent mobile spectrophotometer.

type: 
Journal Paper
journal: 
Nature Methods Application Notes 2017

Early spatiotemporal-specific changes in intermediate signals are predictive of cytotoxic sensitivity to TNFα and co-treatments

Signaling pathways can generate different cellular responses to the same cytotoxic agents. Current quantitative models for predicting these differential responses are usually based on large numbers of intracellular gene products or signals at different levels of signaling cascades. Here, we report a study to predict cellular sensitivity to tumor necrosis factor alpha (TNFα) using high-throughput cellular imaging and machine-learning methods.

type: 
Journal Paper
journal: 
Scientific Reports 7, Article 43541 (2017), doi:10.1038/srep43541
Url: 
http://www.nature.com/articles/srep43541
Impact Factor: 
5.228
Date of acceptance: 
2017-01-27

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

Membrane Active Antimicrobial Peptides: Translating Mechanistic Insights to Design

Antimicrobial peptides (AMPs) are promising next generation antibiotics that hold great potential for combating bacterial resistance. AMPs can be both bacteriostatic and bactericidal, induce rapid killing and display a lower propensity to develop resistance than do conventional antibiotics. Despite significant progress in the past 30 years, no peptide antibiotic has reached the clinic yet. Poor understanding of the action mechanisms and lack of rational design principles have been the two major obstacles that have slowed progress.

type: 
Journal Paper
journal: 
Frontiers in Neuroscience, Feb 2017, Vol. 11, Article 73, doi: 10.3389/fnins.2017.00073
Url: 
http://journal.frontiersin.org/article/10.3389/fnins.2017.00073/full
Impact Factor: 
3.398
Date of acceptance: 
2017-01-31

Hierarchical Assembly of Tough Bioelastomeric Egg Capsules is Mediated by a Bundling Protein

Marine snail egg capsules are shock-absorbing bioelastomers made from precursor "egg case proteins" (ECPs) that initially lack long-range order. During capsule formation, these proteins self-assemble into coiled-coil filaments that subsequently align into microscopic layers, a multiscale process which is crucial to the capsules' shock-absorbing properties.

type: 
Journal Paper
journal: 
Biomacromolecules, 2017, 18 (3), pg 931-942, doi: 10.1021/acs.biomac.6b01810
Url: 
https://www.ncbi.nlm.nih.gov/pubmed/28196415
Impact Factor: 
5.583
Date of acceptance: 
2017-03-16

Stabilization of Peptides against Proteolysis through Disulfide-Bridged Conjugation with Synthetic Aromatics

Peptides have been promising molecular scaffolds for the development of potential therapeutics with high affinity and specificity to biomacromolecules. However, their inherent proteolytic instability significantly hampers their biological applications. Strategies that can stabilize peptides against proteolytic digestion on the basis of noncovalent interactions—without extensive manipulation of the sequence or use of unnatural residues—are greatly desired.

type: 
Journal Paper
journal: 
Organic & Biomolecular Chemistry, 2017, Issue 15, Pg 1921-1929, doi: 10.1039/C6OB02786E
Url: 
http://pubs.rsc.org/en/content/articlelanding/2017/ob/c6ob02786e#!divAbstract
Impact Factor: 
3.559
Date of acceptance: 
2017-02-01

Discovery of Rab1 binding sites using an ensemble of clustering methods

Targeting non-native-ligand binding sites for potential investigative and therapeutic applications is an attractive strategy in proteins that share common native ligands, as in Rab1 protein. Rab1 is a subfamily member of Rab proteins, which are members of Ras GTPase superfamily. All Ras GTPase superfamily members bind to native ligands GTP and GDP, that switch on and off the proteins, respectively. Rab1 is physiologically essential for autophagy and transport between endoplasmic reticulum and Golgi apparatus.

type: 
Journal Paper
journal: 
PROTEINS: Structure, Function, and Bioinformatics, doi: 10.1002/prot.25254
Url: 
http://onlinelibrary.wiley.com/doi/10.1002/prot.25254/abstract
Impact Factor: 
2.499
Date of acceptance: 
2017-01-19
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