SAMPLEX: Automatic mapping of perturbed and unperturbed regions of proteins and complexes

Abstract

BackgroundThe activity of proteins within the cell is characterized by their motions, flexibility, interactions or even the particularly intriguing case of partially unfolded states. In the last two cases, a part of the protein is affected either by binding or unfolding and the detection of the respective perturbed and unperturbed region(s) is a fundamental part of the structural characterization of these states. This can be achieved by comparing experimental data of the same protein in two different states (bound/unbound, folded/unfolded). For instance, measurements of chemical shift perturbations (CSPs) from NMR 1H-15N HSQC experiments gives an excellent opportunity to discriminate both moieties.ResultsWe describe an innovative, automatic and unbiased method to distinguish perturbed and unperturbed regions in a protein existing in two distinct states (folded/partially unfolded, bound/unbound). The SAMPLEX program takes as input a set of data and the corresponding three-dimensional structure and returns the confidence for each residue to be in a perturbed or unperturbed state. Its performance is demonstrated for different applications including the prediction of disordered regions in partially unfolded proteins and of interacting regions in protein complexes.ConclusionsThe proposed approach is suitable for partially unfolded states of proteins, local perturbations due to small ligands and protein-protein interfaces. The method is not restricted to NMR data, but is generic and can be applied to a wide variety of information.

Refined solution structure and backbone dynamics of the archaeal MC1 protein

“…An antiparallel b-bulge (B1), composed of Leu8, His16, and Gly17, is present in seven structures, and another antiparallel b-bulge (B2), composed of Val57, Glu87, and Arg88, is observed for all the structures. The secondary structure elements are connected by loops LP1 (10)(11)(12)(13)(14), LP2 (22)(23)(24), LP3 (35)(36)(37)(38)(39)(40)(41)(42), LP4 (50-53), and LP5 (67-77), referred to as 'arm' in the text. The latter now appears to be remote from the protein core, whereas it was previously described as pulled down on the a-helix.…”

“…The lack of stable hydrogen bonds in loop LP3 (35)(36)(37)(38)(39)(40)(41)(42) corresponds with large motions of the N)H vectors for Gly35, Ser36, and Gly37. However, this nonstructured loop is probably not important in the DNA binding, because the number of residues between Gly35 and Ile45 (MC1-CHTI55 numbering) varies from 3 to 14 in different species of Halobacteria and Methanomicrobia [15].…”

“…One water molecule bridging NH(Glu87) and CO(Val57) through hydrogen bonding contributed to these dynamics. Nanosecond slow motions observed in loops LP3 (35)(36)(37)(38)(39)(40)(41)(42) and LP5 (67-77) reflected the lack of stable hydrogen bonds, whereas the other loops, LP1 (10)(11)(12)(13)(14), LP2 (22)(23)(24), and LP4 (50-53), were stabilized by several hydrogen bonds. Dynamics are often directly related to function.…”

The NMR2 Method to Determine Rapidly the Structure of the Binding Pocket of a Protein–Ligand Complex with High Accuracy

“…The most popular program used in NMR is CSP-HADDOCK [40,47,60], which can make use of a large set of additional experimental restraints such as residual dipolar couplings or pseudocontact shifts [41,61,62]. Other docking programs are BiGGER [63], AutoDockFilter [64], SAMPLEX [65], and LIGDOCK [47].…”

Gentamicin Binds to the Megalin Receptor as a Competitive Inhibitor Using the Common Ligand Binding Motif of Complement Type Repeats

“…No significant chemical shift changes were observed for residues outside this region. Active and passive residues were analyzed using the program SAMPLEX (49). Active ambiguous interaction restraints (AIRs) included residues Gln-1120 -Ile-1122, Lys-1124 -Val-1127, Asp-1129 -Asn-1132, and Asp-1139.…”