1YYJ

The NMR solution structure of a redesigned apocytochrome b562:Rd-apocyt b562

Summary for 1YYJ

• Entry DOI: 10.2210/pdb1yyj/pdb
• Related: 1RAC 1YYX
• NMR Information: BMRB: 6560
• Descriptor: redesigned apocytochrome B562 (1 entity in total)
• Functional Keywords: four helix protein, structural genomics, psi, protein structure initiative, berkeley structural genomics center, bsgc, de novo protein
• Biological source: Homo sapiens (human)
• Total number of polymer chains: 1
• Total formula weight: 11729.12

Authors

Feng, H.,Takei, J.,Lipsitz, R.,Tjandra, N.,Bai, Y.,Berkeley Structural Genomics Center (BSGC) (deposition date: 2005-02-25, release date: 2005-08-25, Last modification date: 2023-09-27)

Primary citation

Feng, H.,Takei, J.,Lipsitz, R.,Tjandra, N.,Bai, Y.
Specific non-native hydrophobic interactions in a hidden folding intermediate: implications for protein folding
Biochemistry, 42:12461-12465, 2003

PubMed Abstract: Structures of intermediates and transition states in protein folding are usually characterized by amide hydrogen exchange and protein engineering methods and interpreted on the basis of the assumption that they have native-like conformations. We were able to stabilize and determine the high-resolution structure of a partially unfolded intermediate that exists after the rate-limiting step of a four-helix bundle protein, Rd-apocyt b(562), by multidimensional NMR methods. The intermediate has partial native-like secondary structure and backbone topology, consistent with our earlier native state hydrogen exchange results. However, non-native hydrophobic interactions exist throughout the structure. These and other results in the literature suggest that non-native hydrophobic interactions may occur generally in partially folded states. This can alter the interpretation of mutational protein engineering results in terms of native-like side chain interactions. In addition, since the intermediate exists after the rate-limiting step and Rd-apocyt b(562) folds very rapidly (k(f) approximately 10(4) s(-1)), these results suggest that non-native hydrophobic interactions, in the absence of topological misfolding, are repaired too rapidly to slow folding and cause the accumulation of folding intermediates. More generally, these results illustrate an approach for determining the high-resolution structure of folding intermediates.

PubMed: 14580191
DOI: 10.1021/bi035561s

Experimental method

SOLUTION NMR