Macromolecular modeling with rosetta

R Das, D Baker - Annu. Rev. Biochem., 2008 - annualreviews.org
Advances over the past few years have begun to enable prediction and design of
macromolecular structures at near-atomic accuracy. Progress has stemmed from the …

Biomolecules under mechanical force

S Kumar, MS Li - Physics Reports, 2010 - Elsevier
Recent advances in single molecule experiments have raised many challenges. These
challenges can be met by a proper understanding of the inter-and intra-molecular …

Socket: a program for identifying and analysing coiled-coil motifs within protein structures

J Walshaw, DN Woolfson - Journal of molecular biology, 2001 - Elsevier
The coiled coil is arguably the simplest protein-structure motif and probably the most
ubiquitous facilitator of protein-protein interactions. Coiled coils comprise two or more α …

Discrete molecular dynamics: an efficient and versatile simulation method for fine protein characterization

D Shirvanyants, F Ding, D Tsao… - The journal of …, 2012 - ACS Publications
Until now it has been impractical to observe protein folding in silico for proteins larger than
50 residues. Limitations of both force field accuracy and computational efficiency make the …

Unfolding proteins by external forces and temperature: the importance of topology and energetics

E Paci, M Karplus - Proceedings of the National Academy of Sciences, 2000 - pnas.org
Unfolding of proteins by forced stretching with atomic force microscopy or laser tweezer
experiments complements more classical techniques using chemical denaturants or …

Improved Gō-like models demonstrate the robustness of protein folding mechanisms towards non-native interactions

J Karanicolas, CL Brooks III - Journal of molecular biology, 2003 - Elsevier
The use of simple theoretical models has provided a considerable contribution to our
present understanding of the means by which proteins adopt their native fold from the …

Thermodynamics of ligand binding to acyl-coenzyme A binding protein studied by titration calorimetry

NJ Færgeman, BW Sigurskjold, BB Kragelund… - Biochemistry, 1996 - ACS Publications
Ligand binding to recombinant bovine acyl-CoA binding protein (ACBP) was examined
using isothermal microcalorimetry. Microcalorimetric measurements confirm that the binding …

The formation of a native-like structure containing eight conserved hydrophobic residues is rate limiting in two-state protein folding of ACBP

BB Kragelund, P Osmark, TB Neergaard… - nature structural …, 1999 - nature.com
The acyl-coenzyme A-binding proteins (ACBPs) contain 26 highly conserved sequence
positions. The majority of these have been mutated in the bovine protein, and their influence …

Features and possible applications of plant lipid-binding and transfer proteins

DN Melnikova, EI Finkina, IV Bogdanov, AA Tagaev… - Membranes, 2022 - mdpi.com
In plants, lipid trafficking within and inside the cell is carried out by lipid-binding and transfer
proteins. Ligands for these proteins are building and signaling lipid molecules, secondary …

Arabidopsis ACBP3 is an extracellularly targeted acyl-CoA-binding protein

KC Leung, HY Li, S **ao, MH Tse, ML Chye - Planta, 2006 - Springer
Abstract Cytosolic 10-kDa acyl-CoA-binding proteins (ACBPs) function in the storage and
intracellular transport of acyl-CoA esters in eukaryotes. Fatty acids synthesized de novo in …