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Backbone‐Only Protein Solution Structures with a Combination of Classical and Paramagnetism‐Based Constraints: A Method that Can Be Scaled to Large Molecules
Author(s) -
Barbieri Renato,
Luchinat Claudio,
Parigi Giacomo
Publication year - 2004
Publication title -
chemphyschem
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.016
H-Index - 140
eISSN - 1439-7641
pISSN - 1439-4235
DOI - 10.1002/cphc.200301058
Subject(s) - paramagnetism , chemistry , lanthanide , dihedral angle , relaxation (psychology) , crystallography , dipole , molecule , ion , computational chemistry , hydrogen bond , condensed matter physics , physics , social psychology , psychology , organic chemistry
Abstract Herein, it is shown that a medium‐resolution solution structure of a protein can be obtained with the sole assignment of the protein backbone and backbone‐related constraints if a derivative with a firmly bound paramagnetic metal is available. The proof‐of‐concept is provided on calbindin D 9k , a calcium binding protein in which one of the two calcium ions can be selectively substituted by a paramagnetic lanthanide ion. The constraints used are H N (and H α ) nuclear Overhauser effects (NOEs), hydrogen bonds, dihedral angle constraints from chemical shifts, and the following paramagnetism‐based constraints: 1) pseudocontact shifts, acquired by substituting one (or more) lanthanide(s) in the C‐terminal calcium binding site; 2) NH N residual dipolar couplings due to self‐orientation induced by the paramagnetic lanthanide(s); 3) cross‐correlations between the Curie and internuclear dipole–dipole interactions; and 4) paramagnetism‐induced relaxation rate enhancements. An upper distance limit for internuclear distances between any two backbone atoms was also given according to the molecular weight of the protein. For this purpose, the paramagnetism‐based constraints were collectively implemented in the program CYANA for solution structure determinations, similarly to what was previously done for the program DYANA. The method is intrinsically suitable for large molecular weight proteins.