Proteins
-
LINUS is an ab initio method for the prediction of protein structure based on simple physical principles. Here we report the performance of LINUS at CASP4, a community wide experiment to predict protein structure in which participants are blinded to the structures they seek to predict. ⋯ Coordinates for all predictions are available from the CASP web site (http://predictioncenter.llnl.gov). It should be emphasized that our use of the descriptor "ab initio" is unequivocal: the sole input into these simulations is the amino acid sequence.
-
Comparative Study
Molecular modelling of Trematomus newnesi Hb 1: insights for a lowered oxygen affinity and lack of root effect.
Three-dimensional structural models of the hemoglobin (Hb 1) of the Antarctic fish Trematomus newnesi were built by homology modelling, using as template the X-ray crystallographic structures of Trematomus (previously named Pagothenia) bernacchii Hb 1, both in R and T state. The Hbs of these two fishes, although showing remarkably different oxygen binding properties, differ only by 4 residues in the alpha chain (142 aa) and 10 residues in the beta chain (146 aa). T. newnesi Hb1 R-state model, essentially performed as a quality control of the adopted modelling procedure, showed a good correspondence with the crystallographic one. ⋯ Similar modifications are also found in T. bernacchii Hb 1 modelled in the T state with the single substitution Thr-->Ile in 41alpha. These models also suggest that the lower oxygen affinity observed in T. newnesi Hb1 is related to structural differences at the alpha(1)beta(2) interface leading to a more stable low-affinity T state. Proteins 2000;39:155-165.
-
Comparative Study
Molecular dynamics study of secondary structure motions in proteins: application to myohemerythrin.
The concept of secondary structure motions is examined in a molecular dynamics simulation of the protein myohemerythrin. We extracted from the simulation a corresponding trajectory of helices and demonstrated that the fluctuations of the protein are dominated by a rigid shift of these secondary structure elements. The relative motions of the helices are irregular, with no clear periodicity. ⋯ It is shown that the one-dimensional mean force potentials are close to quadratic for most of the helices coordinates. The anharmonicity is reflected by changes in the direction of the normal modes as a function of the energy and by the existence of multiple free energy minima for the helices packing. The multiple conformations are associated with a single type of secondary structure coordinate: the angle that describes the relative orientation of the helices in a plane perpendicular to the line connecting their center of mass.