Conformational dynamics of intrinsically disordered proteins regulate biomolecular condensate chemistry
Motions in biomolecules are critical for biochemical reactions. In cells, many biochemical
reactions are executed inside of biomolecular condensates formed by ultradynamic …
reactions are executed inside of biomolecular condensates formed by ultradynamic …
Integrated modeling program, applied chemical theory (IMPACT)
JL Banks, HS Beard, Y Cao, AE Cho… - Journal of …, 2005 - Wiley Online Library
We provide an overview of the IMPACT molecular mechanics program with an emphasis on
recent developments and a description of its current functionality. With respect to core …
recent developments and a description of its current functionality. With respect to core …
Optimization of the Additive CHARMM All-Atom Protein Force Field Targeting Improved Sampling of the Backbone ϕ, ψ and Side-Chain χ1 and χ2 Dihedral Angles
While the quality of the current CHARMM22/CMAP additive force field for proteins has been
demonstrated in a large number of applications, limitations in the model with respect to the …
demonstrated in a large number of applications, limitations in the model with respect to the …
Balanced protein–water interactions improve properties of disordered proteins and non-specific protein association
Some frequently encountered deficiencies in all-atom molecular simulations, such as
nonspecific protein–protein interactions being too strong, and unfolded or disordered states …
nonspecific protein–protein interactions being too strong, and unfolded or disordered states …
Polarizable force field for peptides and proteins based on the classical drude oscillator
Presented is a polarizable force field based on a classical Drude oscillator framework,
currently implemented in the programs CHARMM and NAMD, for modeling and molecular …
currently implemented in the programs CHARMM and NAMD, for modeling and molecular …
Responsive hydrogels from the intramolecular folding and self-assembly of a designed peptide
A general peptide design is presented that links the pH-dependent intramolecular folding of
β-hairpin peptides to their propensity to self-assemble, affording hydrogels rich in β-sheet …
β-hairpin peptides to their propensity to self-assemble, affording hydrogels rich in β-sheet …
The protein folding 'speed limit'
How fast can a protein possibly fold? This question has stimulated experimentalists to seek
fast folding proteins and to engineer them to fold even faster. Proteins folding at or near the …
fast folding proteins and to engineer them to fold even faster. Proteins folding at or near the …
Tryptophan zippers: Stable, monomeric β-hairpins
AG Cochran, NJ Skelton… - Proceedings of the …, 2001 - National Acad Sciences
A structural motif, the tryptophan zipper (trpzip), greatly stabilizes the β-hairpin conformation
in short peptides. Peptides (12 or 16 aa in length) with four different turn sequences are …
in short peptides. Peptides (12 or 16 aa in length) with four different turn sequences are …
Free-energy landscape for β hairpin folding from combined parallel tempering and metadynamics
We develope a new free-energy method, based on the combination of parallel tempering
and metadynamics, and apply this method to the calculation of the free-energy landscape of …
and metadynamics, and apply this method to the calculation of the free-energy landscape of …
[HTML][HTML] Unfolding of titin immunoglobulin domains by steered molecular dynamics simulation
H Lu, B Isralewitz, A Krammer, V Vogel, K Schulten - Biophysical journal, 1998 - cell.com
Abstract Titin, a 1-μm-long protein found in striated muscle myofibrils, possesses unique
elastic and extensibility properties in its I-band region, which is largely composed of a PEVK …
elastic and extensibility properties in its I-band region, which is largely composed of a PEVK …