NMR structures of two designed proteins with high sequence identity but different fold and function.
How protein sequence codes for 3D structure remains a fundamental question in biology. One approach to understanding the folding code is to design a pair of proteins with maximal sequence identity but retaining different folds. Therefore, the nonidentities must be responsible for determining which fold topology prevails and constitute a fold-specific folding code. We recently designed two proteins, G(A)88 and G(B)88, with 88% sequence identity but different folds and functions [Alexander et al. (2007) Proc Natl Acad Sci USA 104:11963-11968]. Here, we describe the detailed 3D structures of these proteins determined in solution by NMR spectroscopy. Despite a large number of mutations taking the sequence identity level from 16 to 88%, G(A)88 and G(B)88 maintain their distinct wild-type 3-alpha and alpha/beta folds, respectively. To our knowledge, the 3D-structure determination of two monomeric proteins with such high sequence identity but different fold topology is unprecedented. The geometries of the seven nonidentical residues (of 56 total) provide insights into the structural basis for switching between 3-alpha and alpha/beta conformations. Further mutation of a subset of these nonidentities, guided by the G(A)88 and G(B)88 structures, leads to proteins with even higher levels of sequence identity (95%) and different folds. Thus, conformational switching to an alternative monomeric fold of comparable stability can be effected with just a handful of mutations in a small protein. This result has implications for understanding not only the folding code but also the evolution of new folds.
He
Yanan
Y
Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute, 9600 Gudelsky Drive, Rockville, MD 20850, USA.
Chen
Yihong
Y
Alexander
Patrick
P
Bryan
Philip N
PN
Orban
John
J
D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000737:chemistry* / Q000378:metabolism; D006801:Humans; D008958:Models, Molecular; D008969:Molecular Sequence Data; D050505:Mutant Proteins / Q000737:chemistry* / Q000378:metabolism; D019906:Nuclear Magnetic Resonance, Biomolecular; D017510:Protein Folding; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D017386:Sequence Homology, Amino Acid; D012997:Solvents / Q000737:chemistry; D013291:Streptococcus / Q000737:chemistry; D013329:Structure-Activity Relationship
D001426:Bacterial Proteins; C034284:IgG Fc-binding protein, Streptococcus; D050505:Mutant Proteins; D012997:Solvents
Proc Natl Acad Sci U S A. 1993 Jan 15;90(2):439-41
8421673
Nat Struct Biol. 1997 Jul;4(7):548-52
9228947
J Biomol NMR. 1999 Mar;13(3):289-302
10212987
J Biol Chem. 1996 Oct 25;271(43):26609-15
8900134
Acta Crystallogr D Biol Crystallogr. 1998 Sep 1;54(Pt 5):905-21
9757107
Proc Natl Acad Sci U S A. 1992 Sep 15;89(18):8532-6
1528858
Proc Natl Acad Sci U S A. 2007 Jul 17;104(29):11963-8
17609385
Science. 1973 Jul 20;181(4096):223-30
4124164
Science. 1999 Apr 9;284(5412):325-8
10195898
Proc Natl Acad Sci U S A. 1997 Sep 16;94(19):10172-7
9294182
Biochemistry. 1992 Feb 11;31(5):1451-7
1737003
Biochemistry. 1994 Apr 19;33(15):4721-9
8161530
J Biomol NMR. 1996 Dec;8(4):477-86
9008363
Proteins. 1996 Apr;24(4):502-13
8859998
J Biomol NMR. 1994 Mar;4(2):171-80
8019132
Biochemistry. 2004 Nov 23;43(46):14539-46
15544324
Fold Des. 1997;2(5):R71-9
9377709
J Immunol. 1984 Jun;132(6):3098-102
6233368
Proteins. 1994 Dec;20(4):301-11
7731949
J Biol Chem. 1994 Apr 22;269(16):12147-51
8163519
J Mol Graph. 1996 Feb;14(1):51-5, 29-32
8744573
Biochemistry. 2006 Mar 14;45(10):3263-71
16519521
Infect Immun. 1977 Sep;17(3):475-82
409673
Nature. 1992 Apr 2;356(6368):453-5
1557131
J Biomol NMR. 1995 Nov;6(3):277-93
8520220
Nat Struct Biol. 2002 Nov;9(11):877-85
12379842
Proc Natl Acad Sci U S A. 1999 Aug 3;96(16):9074-6
10430897
J Biol Chem. 2002 May 17;277(20):17863-70
11889129
J Mol Biol. 1999 Jan 15;285(2):741-53
9878441
Proteins. 1994 May;19(1):1-3
8066081
Protein Sci. 2000 Sep;9(9):1651-9
11045612
Cell. 2005 Jul 29;122(2):165-8
16051142
Proteins. 1998 Feb 1;30(2):136-43
9489921
J Bacteriol. 1986 Sep;167(3):870-80
3745123
Biochemistry. 2006 Aug 22;45(33):10102-9
16906768
Biochemistry. 1992 Apr 14;31(14):3597-603
1567818