Dissecting π‐helices: sequence, structure and function

P Kumar, M Bansal - The FEBS Journal, 2015‏ - Wiley Online Library
A new procedure for the identification of regular secondary structures using a Cα trace has
identified 659 π‐helices in 3582 protein chains, solved at high resolution. Taking advantage …

Frequent side chain methyl carbon‐oxygen hydrogen bonding in proteins revealed by computational and stereochemical analysis of neutron structures

JD Yesselman, S Horowitz… - Proteins: Structure …, 2015‏ - Wiley Online Library
The propensity of backbone Cα atoms to engage in carbon‐oxygen (CH··· O) hydrogen
bonding is well‐appreciated in protein structure, but side chain CH··· O hydrogen bonding …

Structural and functional analyses of PolyProline-II helices in globular proteins

P Kumar, M Bansal - Journal of Structural Biology, 2016‏ - Elsevier
PolyProline-II (PPII) helices are defined as a continuous stretch of a protein chain in which
the constituent residues have backbone torsion angle (φ, ψ) values of (− 75°, 145°) and take …

Role of synergistic π–π stacking and X–H⋯ Cl (X= C, N, O) H-bonding interactions in gelation and gel phase crystallization

S Bhattacharjee, S Bhattacharya - Chemical Communications, 2015‏ - pubs.rsc.org
The self-assembly of p-pyridyl-ended oligo-p-phenylenevinylenes (OPVs) in ethanol leads
to the formation of either hollow or solid microrods. The corresponding protonated OPVs with …

Mechanism of iron-dependent repressor (IdeR) activation and DNA binding: a molecular dynamics and protein structure network study

S Ghosh, N Chandra… - PLoS computational …, 2015‏ - journals.plos.org
Metalloproteins form a major class of enzymes in the living system that are involved in
crucial biological functions such as catalysis, redox reactions and as 'switches' in signal …

Identification of local variations within secondary structures of proteins

P Kumar, M Bansal - Biological Crystallography, 2015‏ - journals.iucr.org
Secondary-structure elements (SSEs) play an important role in the folding of proteins.
Identification of SSEs in proteins is a common problem in structural biology. A new method …

[HTML][HTML] Helix perturbations in membrane proteins assist in inter-helical interactions and optimal helix positioning in the bilayer

A Shelar, M Bansal - Biochimica et Biophysica Acta (BBA)-Biomembranes, 2016‏ - Elsevier
Transmembrane (TM) helices in integral membrane proteins are primarily α-helical in
structure. Here we analyze 1134 TM helices in 90 high resolution membrane proteins and …

Flexible aspartates propel iron to the ferroxidation sites along pathways stabilized by a conserved arginine in Dps proteins from Mycobacterium smegmatis

SM Williams, D Chatterji - Metallomics, 2017‏ - academic.oup.com
DNA-binding proteins under starvation (Dps) are dodecameric nano-compartments for iron
oxidation and storage in bacterial cells. These proteins have roughly spherical structures …

[HTML][HTML] PIF–A Java library for finding atomic interactions and extracting geometric features supporting the analysis of protein structures

W Jargieło, B Małysiak-Mrozek, D Mrozek - Methods, 2022‏ - Elsevier
Proteins play an essential role in the functioning of living organisms. The enormity of the
atomic interactions in proteins is essential in controlling their spatial structures and …

[PDF][PDF] A domain-resolution map of in vivo DNA binding reveals the regulatory consequences of somatic mutations in zinc finger transcription factors

B Dogan, S Kailasam, AH Corchado, N Nikpoor… - bioRxiv, 2020‏ - scholar.archive.org
Multi-zinc finger proteins constitute the largest class of human transcription factors. Their
DNA-binding specificity is usually encoded by a subset of their tandem Cys2His2 zinc finger …