CHARMM36m: an improved force field for folded and intrinsically disordered proteins

J Huang, S Rauscher, G Nawrocki, T Ran, M Feig… - Nature …, 2017 - nature.com
The all-atom additive CHARMM36 protein force field is widely used in molecular modeling
and simulations. We present its refinement, CHARMM36m (http://mackerell. umaryland …

CHARMM36 all‐atom additive protein force field: Validation based on comparison to NMR data

J Huang, AD MacKerell Jr - Journal of computational chemistry, 2013 - Wiley Online Library
Protein structure and dynamics can be characterized on the atomistic level with both nuclear
magnetic resonance (NMR) experiments and molecular dynamics (MD) simulations. Here …

Nature and strength of sulfur-centred hydrogen bonds: laser spectroscopic investigations in the gas phase and quantum-chemical calculations

HS Biswal, S Bhattacharyya… - … Reviews in Physical …, 2015 - Taylor & Francis
The importance of Sulfur centred hydrogen bonds (SCHBs) cannot be underestimated given
the current day knowledge of its non-covalent interactions prevalent in many biopolymers as …

Covalent Organic Framework Cladding on Peptide-Amphiphile-Based Biomimetic Catalysts

A Kumar Mahato, S Pal, K Dey, A Reja… - Journal of the …, 2023 - ACS Publications
Peptide-based biomimetic catalysts are promising materials for efficient catalytic activity in
various biochemical transformations. However, their lack of operational stability and fragile …

pH-dependent random coil 1H, 13C, and 15N chemical shifts of the ionizable amino acids: a guide for protein pK a measurements

G Platzer, M Okon, LP McIntosh - Journal of biomolecular NMR, 2014 - Springer
The p K a values and charge states of ionizable residues in polypeptides and proteins are
frequently determined via NMR-monitored pH titrations. To aid the interpretation of the …

A spectroscopic overview of intramolecular hydrogen bonds of NH… O, S, N type

PE Hansen - Molecules, 2021 - mdpi.com
Intramolecular NH… O, S, N interactions in non-tautomeric systems are reviewed in a broad
range of compounds covering a variety of NH donors and hydrogen bond acceptors. 1H …

Comparison of structure determination methods for intrinsically disordered amyloid-β peptides

KA Ball, DE Wemmer… - The Journal of Physical …, 2014 - ACS Publications
Intrinsically disordered proteins (IDPs) represent a new frontier in structural biology since the
primary characteristic of IDPs is that structures need to be characterized as diverse …

Direct observation of the ion-pair dynamics at a protein–DNA interface by NMR spectroscopy

KM Anderson, A Esadze, M Manoharan… - Journal of the …, 2013 - ACS Publications
Ion pairing is one of the most fundamental chemical interactions and is essential for
molecular recognition by biological macromolecules. From an experimental standpoint, very …

Entropic enhancement of protein-DNA affinity by oxygen-to-sulfur substitution in DNA phosphate

L Zandarashvili, D Nguyen, KM Anderson, MA White… - Biophysical journal, 2015 - cell.com
Dithioation of DNA phosphate is known to enhance binding affinities, at least for some
proteins. We mechanistically characterized this phenomenon for the Antennapedia …

Physicochemical properties of ion pairs of biological macromolecules

J Iwahara, A Esadze, L Zandarashvili - Biomolecules, 2015 - mdpi.com
Ion pairs (also known as salt bridges) of electrostatically interacting cationic and anionic
moieties are important for proteins and nucleic acids to perform their function. Although …