Backbone‐Only Protein Solution Structures with a Combination of Classical and Paramagnetism‐Based Constraints: A Method that Can Be Scaled to Large Molecules

ChemPhysChem - Tập 5 Số 6 - Trang 797-806 - 2004
Renato Barbieri1, Claudio Luchinat2, Giacomo Parigi2
1CERM and Department of Chemistry, University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino (Italy).
2CERM and Department of Agricultural Biotechnology, University of Florence via L. Sacconi, 6, 50019 Sesto Fiorentino, Italy, Fax: (+39) 055‐457‐4253

Tóm tắt

AbstractHerein, 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 D9k, 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 HN (and Hα) 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) NHN 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.

Từ khóa


Tài liệu tham khảo

10.1021/bi00336a009

10.1016/0022-2836(91)90389-N

10.1023/A:1012422402545

10.1021/ja993691b

10.1021/ja0028626

10.1006/jmre.2000.2218

10.1021/ja025528d

10.1023/A:1016341507527

10.1002/1439-7633(20010803)2:7/8<550::AID-CBIC550>3.0.CO;2-T

10.1016/S0014-5793(99)01410-6

10.1007/s00775-003-0511-2

10.1016/S0079-6565(02)00002-X

10.1002/cmr.10027

10.1038/756

10.1016/S0969-2126(99)80167-1

10.1021/bi9905213

10.1006/jmbi.2000.3842

10.1021/ja002500y

10.1021/ja011806h

10.1021/ja003979x

10.1023/A:1013334513610

10.1021/ja0268783

10.1016/S0079-6565(01)00042-5

10.1073/pnas.92.20.9279

10.1002/pro.5560040216

10.1021/bi961354z

10.1007/s007750050030

10.1002/(SICI)1097-0134(199711)29:3<348::AID-PROT8>3.0.CO;2-6

10.1021/bi963025c

10.1021/bi971022

10.1038/nsb0497-254

10.1007/s002490050144

10.1021/ja9742592

10.1021/bi971896w

10.1021/ja981791w

10.1021/ja991228t

10.1021/bi982785f

10.1021/ja9904540

10.1006/jmbi.2000.3714

10.1023/A:1014214015858

10.1110/ps.0300203

10.1016/S0959-440X(00)00100-7

10.1038/80768

10.1038/80700

10.1110/ps.4570102

10.1021/ja005590f

10.1023/A:1024047103398

10.1021/ja0261123

10.1021/ja010002z

10.1021/ja028893d

Baig I., Biochemistry

10.1016/S0022-2836(02)00241-3

10.1021/ja9909024

10.1021/ja9902221

10.1021/ja983945d

10.1016/0022-2364(70)90100-9

Bertini I., 2001, Solution NMR of Paramagnetic Molecules

10.1021/ja960106n

10.1006/jmrb.1996.0187

10.1023/A:1018308717741

10.1080/00268978900100621

10.1016/0009-2614(93)85290-5

10.1023/B:JNMR.0000013703.30623.f7

10.1023/A:1008388614638

10.1016/S0969-2126(00)00065-4

Bertini I., 1993, J. Phys. Chem., 101, 198

10.1016/0022-2364(72)90027-3

10.1023/A:1008378624590

10.1007/BF00228148

10.1016/S1090-7807(03)00149-6

10.1023/A:1022225711122

10.1023/A:1023008719248

10.1021/ja037676p

Thông tin
Thông tin xuất bản

ChemPhysChem

Tập 5 Số 6

797-806

Thông tin tác giả