title: Maximum occurrence analysis of protein conformations for different distributions of paramagnetic metal ions within flexible two-domain proteins.
abstract: Multidomain proteins are composed of rigid domains connected by (flexible) linkers. Therefore, the domains may experience a large degree of reciprocal reorientation. Pseudocontact shifts and residual dipolar couplings arising from one or more paramagnetic metals successively placed in a single metal binding site in the protein can be used as restraints to assess the degree of mobility of the different domains. They can be used to determine the maximum occurrence (MO) of each possible protein conformation, i.e. the maximum weight that such conformations can have independently of the real structural ensemble, in agreement with the provided restraints. In the case of two-domain proteins, the metal ions can be placed all in the same domain, or distributed between the two domains. It has been demonstrated that the quantity of independent information for the characterization of the system is larger when all metals are bound in the same domain. At the same time, it has been shown that there are practical advantages in placing the metals in different domains. Here, it is shown that distributing the metals between the domains provides a tool for defining a coefficient of compatibility among the restraints obtained from different metals, without a significant decrease of the capability of the MO values to discriminate among conformations with different weights.
authors.affiliation: Magnetic Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy. luchinat@cerm.unifi.it
authors.forename: Claudio
authors.initials: C
authors.lastname: Luchinat
authors.forename: Malini
authors.initials: M
authors.lastname: Nagulapalli
authors.forename: Giacomo
authors.initials: G
authors.lastname: Parigi
authors.forename: Luca
authors.initials: L
authors.lastname: Sgheri
mesh_terms: D000465:Algorithms; D016880:Anisotropy; D002147:Calmodulin / Q000737:chemistry; D003627:Data Interpretation, Statistical; D004574:Electromagnetic Fields; D004578:Electron Spin Resonance Spectroscopy; D028581:Lanthanoid Series Elements; D008670:Metals / Q000737:chemistry*; D008958:Models, Molecular; D011487:Protein Conformation; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry*
chemical_list: D002147:Calmodulin; D028581:Lanthanoid Series Elements; D008670:Metals; D011506:Proteins