[HTML][HTML] Geometry of nonbonded interactions involving planar groups in proteins

P Chakrabarti, R Bhattacharyya - Progress in biophysics and molecular …, 2007 - Elsevier
Although hydrophobic interaction is the main contributing factor to the stability of the protein
fold, the specificity of the folding process depends on many directional interactions. An …

Histidine in Proteins: pH-Dependent Interplay between π–π, Cation–π, and CH–π Interactions

R Calinsky, Y Levy - Journal of Chemical Theory and …, 2024 - ACS Publications
Histidine (His) stands out as the most versatile natural amino acid due to its side chain's
facile propensity to protonate at physiological pH, leading to a transition from aromatic to …

Molecular interactions between graphene and biological molecules

X Zou, S Wei, J Jasensky, M Xiao, Q Wang… - Journal of the …, 2017 - ACS Publications
Applications of graphene have extended into areas of nanobio-technology such as nanobio-
medicine, nanobio-sensing, as well as nanoelectronics with biomolecules. These …

Ordered packing of β-sheet nanofibrils into nanotubes: Multi-hierarchical assembly of designed short peptides

X Ma, Y Zhao, C He, X Zhou, H Qi, Y Wang, C Chen… - Nano …, 2021 - ACS Publications
Although it is well-known proteins and their complexes are hierarchically organized and
highly ordered structures, it remains a major challenge to replicate their hierarchical self …

De novo design of a pH-triggered self-assembled β-hairpin nanopeptide with the dual biological functions for antibacterial and entrapment

Q Li, J Li, W Yu, Z Wang, J Li, X Feng, J Wang… - Journal of …, 2021 - Springer
Background Acid-tolerant enteric pathogens can evade small intestinal acid barriers,
colonize and infect the intestinal tract. However, broad-spectrum antibiotics are not the best …

Stereospecific interactions of proline residues in protein structures and complexes

R Bhattacharyya, P Chakrabarti - Journal of molecular biology, 2003 - Elsevier
The constrained backbone torsion angle of a proline (Pro) residue has usually been invoked
to explain its three-dimensional context in proteins. Here we show that specific interactions …

Stochastic sensing of TNT with a genetically engineered pore

X Guan, LQ Gu, S Cheley, O Braha, H Bayley - ChemBioChem, 2005 - Wiley Online Library
Engineered versions of the transmembrane protein pore α‐hemolysin (αHL) can be used as
stochastic sensing elements for the identification and quantification of a wide variety of …

Disulfide bonds, their stereospecific environment and conservation in protein structures

R Bhattacharyya, D Pal… - … Engineering Design and …, 2004 - academic.oup.com
We studied the specificity of the non-bonded interaction in the environment of 572 disulfide
bonds in 247 polypeptide chains selected from the Protein Data Bank. The preferred …

Aromatic Residues in Proteins: Re-Evaluating the Geometry and Energetics of π–π, Cation− π, and CH− π Interactions

R Calinsky, Y Levy - The Journal of Physical Chemistry B, 2024 - ACS Publications
Aromatic residues can participate in various biomolecular interactions, such as π–π, cation−
π, and CH− π interactions, which are essential for protein structure and function. Here, we re …

Structural studies of adeno-associated virus serotype 8 capsid transitions associated with endosomal trafficking

HJ Nam, BL Gurda, R McKenna, M Potter… - Journal of …, 2011 - Am Soc Microbiol
The single-stranded DNA (ssDNA) parvoviruses enter host cells through receptor-mediated
endocytosis, and infection depends on processing in the early to late endosome as well as …