Metal ion-dependent modulation of the dynamics of a designed protein.

The peptide alpha 4 is a designed four-helix bundle that contains a highly simplified hydrophobic core composed exclusively of leucine residues; its tertiary structure is therefore largely dictated by hydrophobic forces. This small protein adopts a structure with properties intermediate between those of the native and molten globule states of proteins: it is compact, globular, and has very stable helices, but its apolar side chains are mobile and not as well packed as in many natural proteins. To induce a more native-like state, two Zn(2+)-binding sites were introduced into the protein, thereby replacing some of the non-specific hydrophobic interactions with more geometrically restrictive metal-ligand interactions. In the metal-bound state, this protein has properties that approach those of native proteins. Thus, hydrophobic interactions alone are sufficient to drive polypeptide chain folding nearly to completion, but specific interactions are required for a unique structure.

[1]  M. Akke,et al.  Three-dimensional solution structure of Ca(2+)-loaded porcine calbindin D9k determined by nuclear magnetic resonance spectroscopy. , 1992, Biochemistry.

[2]  F. Dahlquist,et al.  Detection and characterization of an early folding intermediate of T4 lysozyme using pulsed hydrogen exchange and two-dimensional NMR. , 1992, Biochemistry.

[3]  K. Moffat,et al.  The refined structure of vitamin D-dependent calcium-binding protein from bovine intestine. Molecular details, ion binding, and implications for the structure of other calcium-binding proteins. , 1986, The Journal of biological chemistry.

[4]  A. Fersht,et al.  Detection and characterization of a folding intermediate in barnase by NMR , 1990, Nature.

[5]  H. Roder,et al.  Early hydrogen-bonding events in the folding reaction of ubiquitin. , 1992, Proceedings of the National Academy of Sciences of the United States of America.

[6]  L Regan,et al.  A tetrahedral zinc(II)-binding site introduced into a designed protein. , 1990, Biochemistry.

[7]  Robert L. Baldwin,et al.  NMR evidence for an early framework intermediate on the folding pathway of ribonuclease A , 1988, Nature.

[8]  P E Wright,et al.  Structural characterization of a partly folded apomyoglobin intermediate. , 1990, Science.

[9]  A. Fink,et al.  Conformational states of beta-lactamase: molten-globule states at acidic and alkaline pH with high salt. , 1989, Biochemistry.

[10]  R. L. Baldwin,et al.  Characterizing protein folding intermediates , 1991, Current Biology.

[11]  A. Fersht,et al.  The folding of an enzyme. V. H/2H exchange-nuclear magnetic resonance studies on the folding pathway of barnase: complementarity to and agreement with protein engineering studies. , 1992, Journal of molecular biology.

[12]  M. Akke,et al.  Molecular basis for co-operativity in Ca2+ binding to calbindin D9k. 1H nuclear magnetic resonance studies of (Cd2+)1-bovine calbindin D9k. , 1991, Journal of molecular biology.

[13]  S. Walter Englander,et al.  Structural characterization of folding intermediates in cytochrome c by H-exchange labelling and proton NMR , 1988, Nature.

[14]  C. Bugg,et al.  Structure of calmodulin refined at 2.2 A resolution. , 1988, Journal of molecular biology.

[15]  N. A. Rodionova,et al.  Study of the “molten globule” intermediate state in protein folding by a hydrophobic fluorescent probe , 1991, Biopolymers.

[16]  William F. DeGrado,et al.  De novo protein design: what are we learning? , 1991 .

[17]  P. S. Kim,et al.  X-ray structure of the GCN4 leucine zipper, a two-stranded, parallel coiled coil. , 1991, Science.

[18]  K. Dill,et al.  Denatured states of proteins. , 1991, Annual review of biochemistry.

[19]  E. Kaiser,et al.  Amphiphilic secondary structure: design of peptide hormones. , 1984, Science.

[20]  William F. DeGrado,et al.  De novo design of a Zn2+-binding protein , 1990 .

[21]  B. L. Chen,et al.  Low-temperature unfolding of a mutant of phage T4 lysozyme. 1. Equilibrium studies. , 1989, Biochemistry.

[22]  D. W. Bolen,et al.  Unfolding free energy changes determined by the linear extrapolation method. 1. Unfolding of phenylmethanesulfonyl alpha-chymotrypsin using different denaturants. , 1988, Biochemistry.

[23]  Manfred Mutter,et al.  A Chemical Approach to Protein Design—Template‐Assembled Synthetic Proteins (TASP) , 1989 .

[24]  K. P. Murphy,et al.  Common features of protein unfolding and dissolution of hydrophobic compounds. , 1990, Science.

[25]  P. Privalov,et al.  Cold Denaturation of Protein , 1990 .

[26]  J. Richardson,et al.  The anatomy and taxonomy of protein structure. , 1981, Advances in protein chemistry.

[27]  W. DeGrado,et al.  Protein design, a minimalist approach. , 1989, Science.

[28]  M. Sternberg,et al.  Analysis of the relationship between side-chain conformation and secondary structure in globular proteins. , 1987, Journal of molecular biology.

[29]  S W Englander,et al.  Structural description of acid-denatured cytochrome c by hydrogen exchange and 2D NMR. , 1990, Biochemistry.

[30]  M. Kronman,et al.  Binding of naphthalene dyes to the N and A conformers of bovine α-lactalbumin , 1982 .

[31]  W. DeGrado,et al.  Design of a 4-helix bundle protein: synthesis of peptides which self-associate into a helical protein , 1987 .

[32]  R. L. Baldwin,et al.  Temperature dependence of the hydrophobic interaction in protein folding. , 1986, Proceedings of the National Academy of Sciences of the United States of America.

[33]  K. Kuwajima,et al.  Evidence for identity between the equilibrium unfolding intermediate and a transient folding intermediate: a comparative study of the folding reactions of alpha-lactalbumin and lysozyme. , 1986, Biochemistry.

[34]  O. Ptitsyn,et al.  Evidence for a molten globule state as a general intermediate in protein folding , 1990, FEBS letters.

[35]  K. Dill.  Dominant forces in protein folding. , 1990, Biochemistry.

[36]  L. Stryer,et al.  The interaction of a naphthalene dye with apomyoglobin and apohemoglobin. A fluorescent probe of non-polar binding sites. , 1965, Journal of molecular biology.

[37]  J. Richardson,et al.  De novo design, expression, and characterization of Felix: a four-helix bundle protein of native-like sequence. , 1990, Science.

[38]  K. Sharp,et al.  Linkage of thioredoxin stability to titration of ionizable groups with perturbed pKa. , 1991, Biochemistry.

[39]  P. Alexander,et al.  Thermodynamic analysis of the folding of the streptococcal protein G IgG-binding domains B1 and B2: why small proteins tend to have high denaturation temperatures. , 1992, Biochemistry.

[40]  C. Dobson,et al.  The folding of hen lysozyme involves partially structured intermediates and multiple pathways , 1992, Nature.

[41]  William F. DeGrado,et al.  A de novo designed protein shows a thermally induced transition from a native to a molten globule-like state , 1992 .

[42]  L. Regan,et al.  The design of a four-helix bundle protein. , 1987, Cold Spring Harbor symposia on quantitative biology.

[43]  J. Berg,et al.  Metal binding and folding properties of a minimalist Cys2His2 zinc finger peptide. , 1992, Proceedings of the National Academy of Sciences of the United States of America.

[44]  J. Hoch,et al.  Characterization of the structural properties of .alpha.1B, a peptide designed to form a four-helix bundle , 1992 .

[45]  J. Stewart,et al.  Design and synthesis of a peptide having chymotrypsin-like esterase activity. , 1990, Science.