An automated approach for defining core atoms and domains in an ensemble of NMR-derived protein structures

Abstract

A single NMR-derived protein structure is usually deposited as an ensemble containing many structures, each consistent with the restraint set used. The number of NMR-derived structures deposited in the Protein Data Bank (PDB) is increasing rapidly. In addition, many of the structures deposited in an ensemble exhibit variation in only some regions of the structure, often with the majority of the structure remaining largely invariant across the family of structures. Therefore it is useful to determine the set of atoms whose positions are 'well defined' across an ensemble (also known as the 'core' atoms). We have developed a computer program, NMRCORE, which automatically defines (i) the core atoms, and (ii) the rigid body(ies), or domain(s), in which they occur. The program uses a sorted list of the variances in individual dihedral angles across the ensemble to define the core, followed by the automatic clustering of the variances in pairwise inter-atom distances across the ensemble to define the rigid body(ies) which comprise the core. The program is freely available via the World Wide Web (http://neon.chem.le.ac.uk/nmrcore/).

Structural and Functional Characterization of Transmembrane Segment IV of the NHE1 Isoform of the Na+/H+ Exchanger

“…Three sections of four to nine residues of the TM IV segment converge structurally and were defined as core regions by NMRCORE (23) and confirmed by analysis of r.m.s.d. values (Table III).…”

Strain analysis of protein structures and low dimensionality of mechanical allosteric couplings

“…Other methods have been applied to analyze large-scale protein deformations, usually based on some variant of global alignment of the structures to be compared (17)(18)(19)(20)(21). These global and semilocal methods for comparing protein structures are useful in some circumstances, such as estimating structural similarity of two different proteins.…”

BAX-Induced Apoptosis Can Be Initiated through a Conformational Selection Mechanism

“…a The SD of the averaged distances when the side-chain disordering is considered in the MtsslWizard. The MtsslWizard simulations were based on the most representative structural model (i.e., model 3 in the 20 available NMR models) determined in the Olderado analysis (Kelley et al, 1997). This Olderado program automatically clusters ensemble members of NMR results into conformationally related subfamilies.…”