De novo design of proteins

Can we design and produce novel proteins with desired structures and functions using amino acid sequences not found in nature? The design principles, abstracted from observation of natural proteins, are simplest for α-helical bundles, more complicated for β-sheet or mixed structures, and most subtle for the design of catalytic function. The simplest designs have been the most successful so far, but we have yet to encounter an experimentally determined three-dimensional structure for any de novo designed protein that folded as expected. The field is still in its infancy, but its ultimate potential for applications is enormous.

[1]  M Mutter,et al.  Nature's rules and chemist's tools: a way for creating novel proteins. , 1988, Trends in biochemical sciences.

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

[3]  W. DeGrado,et al.  Synthetic amphiphilic peptide models for protein ion channels. , 1988, Science.

[4]  S. McKnight,et al.  The leucine zipper: a hypothetical structure common to a new class of DNA binding proteins. , 1988, Science.

[5]  R. Hodges,et al.  Synthetic model proteins: contribution of hydrophobic residues and disulfide bonds to protein stability. , 1990, Peptide research.

[6]  D. Ringe.  Designing the enzyme of the nineties , 1991, Current Biology.

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

[8]  C. Sander,et al.  Database algorithm for generating protein backbone and side-chain co-ordinates from a C alpha trace application to model building and detection of co-ordinate errors. , 1991, Journal of molecular biology.

[9]  B. W. Erickson,et al.  Designed coiled-coil proteins: synthesis and spectroscopy of two 78-residue alpha-helical dimers. , 1991, Biochemistry.

[10]  D Eisenberg,et al.  Crystal structure of alpha 1: implications for protein design. , 1990, Science.

[11]  R. Hodges,et al.  Tropomyosin: Amino Acid Sequence and Coiled-Coil Structure , 1973 .

[12]  R. Hodges,et al.  Synthetic model for two-stranded alpha-helical coiled-coils. Design, synthesis, and characterization of an 86-residue analog of tropomyosin. , 1981, The Journal of biological chemistry.

[13]  A. D. McLachlan,et al.  Solvation energy in protein folding and binding , 1986, Nature.

[14]  R. Lerner,et al.  Antibody remodeling: a general solution to the design of a metal-coordination site in an antibody binding pocket. , 1990, Proceedings of the National Academy of Sciences of the United States of America.

[15]  B. Gutte,et al.  Design, synthesis and characterisation of a 34-residue polypeptide that interacts with nucleic acids , 1979, Nature.

[16]  L. Regan,et al.  Characterization of a helical protein designed from first principles. , 1988, Science.

[17]  E. Kaiser,et al.  Helichrome: synthesis and enzymic activity of a designed hemeprotein , 1989 .

[18]  G Vriend,et al.  WHAT IF: a molecular modeling and drug design program. , 1990, Journal of molecular graphics.

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

[20]  J. Martial,et al.  Synthesis, purification and initial structural characterization of octarellin, a de novo polypeptide modelled on the alpha/beta-barrel proteins. , 1990, Protein engineering.

[21]  D Eisenberg,et al.  The design, synthesis, and crystallization of an alpha‐helical peptide , 1986, Proteins.

[22]  W. DeGrado.  Design of peptides and proteins. , 1988, Advances in protein chemistry.

[23]  F E Cohen,et al.  Novel method for the rapid evaluation of packing in protein structures. , 1990, Journal of molecular biology.

[24]  O. Ptitsyn,et al.  Why do globular proteins fit the limited set of folding patterns? , 1987, Progress in biophysics and molecular biology.

[25]  E. Kaiser,et al.  Syntehsis and structural stability of helichrome as an artificial hemeproteins , 1990, Biopolymers.

[26]  W. DeGrado,et al.  Conformationally constrained α‐helical peptide models for protein ion channels , 1990 .

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

[28]  D. Parry,et al.  α‐Helical coiled coils and bundles: How to design an α‐helical protein , 1990 .

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

[30]  Bernd Gutte,et al.  An artificial crystalline DDT‐binding polypeptide , 1983 .

[31]  C Sander,et al.  Polarity as a criterion in protein design. , 1989, Protein engineering.

[32]  D C Richardson,et al.  The de novo design of protein structures. , 1989, Trends in biochemical sciences.