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Volumn 16, Issue 4, 2006, Pages 508-513

Knowledge-based potentials in protein design

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN;

EID: 33746592898     PISSN: 0959440X     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.sbi.2006.06.013     Document Type: Review
Times cited : (76)

References (54)
  • 1
    • 0036667733 scopus 로고    scopus 로고
    • Knowledge-based potential functions in protein design
    • Russ W.P., and Ranganathan R. Knowledge-based potential functions in protein design. Curr Opin Struct Biol 12 (2002) 447-452
    • (2002) Curr Opin Struct Biol , vol.12 , pp. 447-452
    • Russ, W.P.1    Ranganathan, R.2
  • 2
    • 0022596727 scopus 로고
    • Solvation energy in protein folding and binding
    • Eisenberg D., and McLachlan A.D. Solvation energy in protein folding and binding. Nature 319 (1986) 199-203
    • (1986) Nature , vol.319 , pp. 199-203
    • Eisenberg, D.1    McLachlan, A.D.2
  • 3
    • 0031844416 scopus 로고    scopus 로고
    • Pairwise calculation of protein solvent-accessible surface areas
    • Street A.G., and Mayo S.L. Pairwise calculation of protein solvent-accessible surface areas. Fold Des 3 (1998) 253-258
    • (1998) Fold Des , vol.3 , pp. 253-258
    • Street, A.G.1    Mayo, S.L.2
  • 4
    • 6344260488 scopus 로고    scopus 로고
    • Fast accurate evaluation of protein solvent exposure
    • Zhang N., Zeng C., and Wingreen N.S. Fast accurate evaluation of protein solvent exposure. Proteins 57 (2004) 565-576
    • (2004) Proteins , vol.57 , pp. 565-576
    • Zhang, N.1    Zeng, C.2    Wingreen, N.S.3
  • 5
    • 23444436172 scopus 로고
    • Protein design by binary patterning of polar and nonpolar amino acids
    • Kamtekar S., Schiffer J.M., Xiong H., Babik J.M., and Hecht M.H. Protein design by binary patterning of polar and nonpolar amino acids. Science 262 (1993) 1680-1685
    • (1993) Science , vol.262 , pp. 1680-1685
    • Kamtekar, S.1    Schiffer, J.M.2    Xiong, H.3    Babik, J.M.4    Hecht, M.H.5
  • 6
    • 0035910266 scopus 로고    scopus 로고
    • Achieving stability and conformational specificity in designed proteins via binary patterning
    • Marshall S.A., and Mayo S.L. Achieving stability and conformational specificity in designed proteins via binary patterning. J Mol Biol 305 (2001) 619-631
    • (2001) J Mol Biol , vol.305 , pp. 619-631
    • Marshall, S.A.1    Mayo, S.L.2
  • 7
    • 0036667731 scopus 로고    scopus 로고
    • Rotamer libraries in the 21st century
    • Dunbrack Jr. R.L. Rotamer libraries in the 21st century. Curr Opin Struct Biol 12 (2002) 431-440
    • (2002) Curr Opin Struct Biol , vol.12 , pp. 431-440
    • Dunbrack Jr., R.L.1
  • 9
    • 0037470581 scopus 로고    scopus 로고
    • An orientation-dependent hydrogen bonding potential improves prediction of specificity and structure for proteins and protein-protein complexes
    • Kortemme T., Morozov A.V., and Baker D. An orientation-dependent hydrogen bonding potential improves prediction of specificity and structure for proteins and protein-protein complexes. J Mol Biol 326 (2003) 1239-1259
    • (2003) J Mol Biol , vol.326 , pp. 1239-1259
    • Kortemme, T.1    Morozov, A.V.2    Baker, D.3
  • 10
    • 0032929780 scopus 로고    scopus 로고
    • Improved recognition of native-like protein structures using a combination of sequence-dependent and sequence-independent features of proteins
    • Simons K.T., Ruczinski I., Kooperberg C., Fox B.A., Bystroff C., and Baker D. Improved recognition of native-like protein structures using a combination of sequence-dependent and sequence-independent features of proteins. Proteins 34 (1999) 82-95
    • (1999) Proteins , vol.34 , pp. 82-95
    • Simons, K.T.1    Ruczinski, I.2    Kooperberg, C.3    Fox, B.A.4    Bystroff, C.5    Baker, D.6
  • 11
    • 0041387567 scopus 로고    scopus 로고
    • A large scale test of computational protein design: folding and stability of nine completely redesigned globular proteins
    • Dantas G., Kuhlman B., Callender D., Wong M., and Baker D. A large scale test of computational protein design: folding and stability of nine completely redesigned globular proteins. J Mol Biol 332 (2003) 449-460
    • (2003) J Mol Biol , vol.332 , pp. 449-460
    • Dantas, G.1    Kuhlman, B.2    Callender, D.3    Wong, M.4    Baker, D.5
  • 12
    • 3042577367 scopus 로고    scopus 로고
    • De novo proteins from designed combinatorial libraries
    • Hecht M.H., Das A., Go A., Bradley L.H., and Wei Y. De novo proteins from designed combinatorial libraries. Protein Sci 13 (2004) 1711-1723
    • (2004) Protein Sci , vol.13 , pp. 1711-1723
    • Hecht, M.H.1    Das, A.2    Go, A.3    Bradley, L.H.4    Wei, Y.5
  • 13
    • 0842270116 scopus 로고    scopus 로고
    • Enzyme-like proteins from an unselected library of designed amino acid sequences
    • Wei Y., and Hecht M.H. Enzyme-like proteins from an unselected library of designed amino acid sequences. Protein Eng Des Sel 17 (2004) 67-75
    • (2004) Protein Eng Des Sel , vol.17 , pp. 67-75
    • Wei, Y.1    Hecht, M.H.2
  • 14
    • 0037305504 scopus 로고    scopus 로고
    • Computational design of a water-soluble analog of phospholamban
    • Slovic A.M., Summa C.M., Lear J.D., and DeGrado W.F. Computational design of a water-soluble analog of phospholamban. Protein Sci 12 (2003) 337-348
    • (2003) Protein Sci , vol.12 , pp. 337-348
    • Slovic, A.M.1    Summa, C.M.2    Lear, J.D.3    DeGrado, W.F.4
  • 15
    • 1242274445 scopus 로고    scopus 로고
    • Computational design of water-soluble analogues of the potassium channel KcsA
    • Slovic A.M., Kono H., Lear J.D., Saven J.G., and DeGrado W.F. Computational design of water-soluble analogues of the potassium channel KcsA. Proc Natl Acad Sci USA 101 (2004) 1828-1833
    • (2004) Proc Natl Acad Sci USA , vol.101 , pp. 1828-1833
    • Slovic, A.M.1    Kono, H.2    Lear, J.D.3    Saven, J.G.4    DeGrado, W.F.5
  • 16
    • 17444433002 scopus 로고    scopus 로고
    • The design of coiled-coil structures and assemblies
    • Woolfson D.N. The design of coiled-coil structures and assemblies. Adv Protein Chem 70 (2005) 79-112
    • (2005) Adv Protein Chem , vol.70 , pp. 79-112
    • Woolfson, D.N.1
  • 17
    • 0037217406 scopus 로고    scopus 로고
    • Automated design of specificity in molecular recognition
    • Havranek J.J., and Harbury P.B. Automated design of specificity in molecular recognition. Nat Struct Biol 10 (2003) 45-52
    • (2003) Nat Struct Biol , vol.10 , pp. 45-52
    • Havranek, J.J.1    Harbury, P.B.2
  • 18
    • 3042655537 scopus 로고    scopus 로고
    • Computational design of a biologically active enzyme
    • This work is noteworthy because it demonstrates that significant alteration or acquisition of protein function can be accomplished through the redesign of a relatively small proportion of a protein.
    • Dwyer M.A., Looger L.L., and Hellinga H.W. Computational design of a biologically active enzyme. Science 304 (2004) 1967-1971. This work is noteworthy because it demonstrates that significant alteration or acquisition of protein function can be accomplished through the redesign of a relatively small proportion of a protein.
    • (2004) Science , vol.304 , pp. 1967-1971
    • Dwyer, M.A.1    Looger, L.L.2    Hellinga, H.W.3
  • 20
    • 2542523113 scopus 로고    scopus 로고
    • Computational design of receptors for an organophosphate surrogate of the nerve agent soman
    • Allert M., Rizk S.S., Looger L.L., and Hellinga H.W. Computational design of receptors for an organophosphate surrogate of the nerve agent soman. Proc Natl Acad Sci USA 101 (2004) 7907-7912
    • (2004) Proc Natl Acad Sci USA , vol.101 , pp. 7907-7912
    • Allert, M.1    Rizk, S.S.2    Looger, L.L.3    Hellinga, H.W.4
  • 21
    • 0038752617 scopus 로고    scopus 로고
    • Computational design of receptor and sensor proteins with novel functions
    • Looger L.L., Dwyer M.A., Smith J.J., and Hellinga H.W. Computational design of receptor and sensor proteins with novel functions. Nature 423 (2003) 185-190
    • (2003) Nature , vol.423 , pp. 185-190
    • Looger, L.L.1    Dwyer, M.A.2    Smith, J.J.3    Hellinga, H.W.4
  • 22
    • 0344392711 scopus 로고    scopus 로고
    • Exploring the origins of binding specificity through the computational redesign of calmodulin
    • Shifman J.M., and Mayo S.L. Exploring the origins of binding specificity through the computational redesign of calmodulin. Proc Natl Acad Sci USA 100 (2003) 13274-13279
    • (2003) Proc Natl Acad Sci USA , vol.100 , pp. 13274-13279
    • Shifman, J.M.1    Mayo, S.L.2
  • 23
    • 0036407643 scopus 로고    scopus 로고
    • Modulating calmodulin binding specificity through computational protein design
    • Shifman J.M., and Mayo S.L. Modulating calmodulin binding specificity through computational protein design. J Mol Biol 323 (2002) 417-423
    • (2002) J Mol Biol , vol.323 , pp. 417-423
    • Shifman, J.M.1    Mayo, S.L.2
  • 24
    • 0035936702 scopus 로고    scopus 로고
    • Statistical theory for protein combinatorial libraries. Packing interactions, backbone flexibility, and the sequence variability of a main-chain structure
    • Kono H., and Saven J.G. Statistical theory for protein combinatorial libraries. Packing interactions, backbone flexibility, and the sequence variability of a main-chain structure. J Mol Biol 306 (2001) 607-628
    • (2001) J Mol Biol , vol.306 , pp. 607-628
    • Kono, H.1    Saven, J.G.2
  • 26
    • 0345304457 scopus 로고    scopus 로고
    • Computational design and characterization of a monomeric helical dinuclear metalloprotein
    • Calhoun J.R., Kono H., Lahr S., Wang W., DeGrado W.F., and Saven J.G. Computational design and characterization of a monomeric helical dinuclear metalloprotein. J Mol Biol 334 (2003) 1101-1115
    • (2003) J Mol Biol , vol.334 , pp. 1101-1115
    • Calhoun, J.R.1    Kono, H.2    Lahr, S.3    Wang, W.4    DeGrado, W.F.5    Saven, J.G.6
  • 29
    • 28444491969 scopus 로고    scopus 로고
    • Design of lambda Cro fold: solution structure of a monomeric variant of the de novo protein
    • Isogai Y., Ito Y., Ikeya T., Shiro Y., and Ota M. Design of lambda Cro fold: solution structure of a monomeric variant of the de novo protein. J Mol Biol 354 (2005) 801-814
    • (2005) J Mol Biol , vol.354 , pp. 801-814
    • Isogai, Y.1    Ito, Y.2    Ikeya, T.3    Shiro, Y.4    Ota, M.5
  • 31
    • 0344255687 scopus 로고    scopus 로고
    • Optimization of the antibody C(H)3 domain by residue frequency analysis of IgG sequences
    • Demarest S.J., Rogers J., and Hansen G. Optimization of the antibody C(H)3 domain by residue frequency analysis of IgG sequences. J Mol Biol 335 (2004) 41-48
    • (2004) J Mol Biol , vol.335 , pp. 41-48
    • Demarest, S.J.1    Rogers, J.2    Hansen, G.3
  • 32
    • 19244366496 scopus 로고    scopus 로고
    • Evolution of coral pigments recreated
    • Ugalde J.A., Chang B.S., and Matz M.V. Evolution of coral pigments recreated. Science 305 (2004) 1433
    • (2004) Science , vol.305 , pp. 1433
    • Ugalde, J.A.1    Chang, B.S.2    Matz, M.V.3
  • 33
    • 0141957399 scopus 로고    scopus 로고
    • A despecialization step underlying evolution of a family of serine proteases
    • Wouters M.A., Liu K., Riek P., and Husain A. A despecialization step underlying evolution of a family of serine proteases. Mol Cell 12 (2003) 343-354
    • (2003) Mol Cell , vol.12 , pp. 343-354
    • Wouters, M.A.1    Liu, K.2    Riek, P.3    Husain, A.4
  • 34
    • 0141431993 scopus 로고    scopus 로고
    • Resurrecting the ancestral steroid receptor: ancient origin of estrogen signaling
    • Thornton J.W., Need E., and Crews D. Resurrecting the ancestral steroid receptor: ancient origin of estrogen signaling. Science 301 (2003) 1714-1717
    • (2003) Science , vol.301 , pp. 1714-1717
    • Thornton, J.W.1    Need, E.2    Crews, D.3
  • 35
    • 0141828152 scopus 로고    scopus 로고
    • Inferring the palaeoenvironment of ancient bacteria on the basis of resurrected proteins
    • Gaucher E.A., Thomson J.M., Burgan M.F., and Benner S.A. Inferring the palaeoenvironment of ancient bacteria on the basis of resurrected proteins. Nature 425 (2003) 285-288
    • (2003) Nature , vol.425 , pp. 285-288
    • Gaucher, E.A.1    Thomson, J.M.2    Burgan, M.F.3    Benner, S.A.4
  • 37
    • 0015859467 scopus 로고
    • Principles that govern the folding of protein chains
    • Anfinsen C.B. Principles that govern the folding of protein chains. Science 181 (1973) 223-230
    • (1973) Science , vol.181 , pp. 223-230
    • Anfinsen, C.B.1
  • 38
    • 0033536602 scopus 로고    scopus 로고
    • Evolutionarily conserved pathways of energetic connectivity in protein families
    • Lockless S.W., and Ranganathan R. Evolutionarily conserved pathways of energetic connectivity in protein families. Science 286 (1999) 295-299
    • (1999) Science , vol.286 , pp. 295-299
    • Lockless, S.W.1    Ranganathan, R.2
  • 39
    • 0035823119 scopus 로고    scopus 로고
    • Understanding hierarchical protein evolution from first principles
    • Dokholyan N.V., and Shakhnovich E.I. Understanding hierarchical protein evolution from first principles. J Mol Biol 312 (2001) 289-307
    • (2001) J Mol Biol , vol.312 , pp. 289-307
    • Dokholyan, N.V.1    Shakhnovich, E.I.2
  • 40
    • 0029913807 scopus 로고    scopus 로고
    • An evolutionary trace method defines binding surfaces common to protein families
    • Lichtarge O., Bourne H.R., and Cohen F.E. An evolutionary trace method defines binding surfaces common to protein families. J Mol Biol 257 (1996) 342-358
    • (1996) J Mol Biol , vol.257 , pp. 342-358
    • Lichtarge, O.1    Bourne, H.R.2    Cohen, F.E.3
  • 41
    • 0034721944 scopus 로고    scopus 로고
    • Analysis of covariation in an SH3 domain sequence alignment: applications in tertiary contact prediction and the design of compensating hydrophobic core substitutions
    • Larson S.M., Di Nardo A.A., and Davidson A.R. Analysis of covariation in an SH3 domain sequence alignment: applications in tertiary contact prediction and the design of compensating hydrophobic core substitutions. J Mol Biol 303 (2000) 433-446
    • (2000) J Mol Biol , vol.303 , pp. 433-446
    • Larson, S.M.1    Di Nardo, A.A.2    Davidson, A.R.3
  • 42
    • 0033977832 scopus 로고    scopus 로고
    • Correlations among amino acid sites in bHLH protein domains: an information theoretic analysis
    • Atchley W.R., Wollenberg K.R., Fitch W.M., Terhalle W., and Dress A.W. Correlations among amino acid sites in bHLH protein domains: an information theoretic analysis. Mol Biol Evol 17 (2000) 164-178
    • (2000) Mol Biol Evol , vol.17 , pp. 164-178
    • Atchley, W.R.1    Wollenberg, K.R.2    Fitch, W.M.3    Terhalle, W.4    Dress, A.W.5
  • 43
    • 31344432159 scopus 로고    scopus 로고
    • Determination of network of residues that regulate allostery in protein families using sequence analysis
    • Dima R.I., and Thirumalai D. Determination of network of residues that regulate allostery in protein families using sequence analysis. Protein Sci 15 (2006) 258-268
    • (2006) Protein Sci , vol.15 , pp. 258-268
    • Dima, R.I.1    Thirumalai, D.2
  • 44
    • 0037219686 scopus 로고    scopus 로고
    • Evolutionarily conserved networks of residues mediate allosteric communication in proteins
    • Suel G.M., Lockless S.W., Wall M.A., and Ranganathan R. Evolutionarily conserved networks of residues mediate allosteric communication in proteins. Nat Struct Biol 10 (2003) 59-69
    • (2003) Nat Struct Biol , vol.10 , pp. 59-69
    • Suel, G.M.1    Lockless, S.W.2    Wall, M.A.3    Ranganathan, R.4
  • 45
    • 1642304065 scopus 로고    scopus 로고
    • Structural determinants of allosteric ligand activation in RXR heterodimers
    • Shulman A.I., Larson C., Mangelsdorf D.J., and Ranganathan R. Structural determinants of allosteric ligand activation in RXR heterodimers. Cell 116 (2004) 417-429
    • (2004) Cell , vol.116 , pp. 417-429
    • Shulman, A.I.1    Larson, C.2    Mangelsdorf, D.J.3    Ranganathan, R.4
  • 47
    • 25644452032 scopus 로고    scopus 로고
    • Evolutionary information for specifying a protein fold
    • A small set of sequence constraints derived from the conservation of residues and the co-evolution of pairs of residues in an MSA of WW domains were found to be sufficient to create a library of folded proteins. These proteins were shown to adopt the same fold and possess the same range of thermostability as natural WW domains.
    • Socolich M., Lockless S.W., Russ W.P., Lee H., Gardner K.H., and Ranganathan R. Evolutionary information for specifying a protein fold. Nature 437 (2005) 512-518. A small set of sequence constraints derived from the conservation of residues and the co-evolution of pairs of residues in an MSA of WW domains were found to be sufficient to create a library of folded proteins. These proteins were shown to adopt the same fold and possess the same range of thermostability as natural WW domains.
    • (2005) Nature , vol.437 , pp. 512-518
    • Socolich, M.1    Lockless, S.W.2    Russ, W.P.3    Lee, H.4    Gardner, K.H.5    Ranganathan, R.6
  • 48
    • 25644442464 scopus 로고    scopus 로고
    • Natural-like function in artificial WW domains
    • In a companion paper to that of Socolich et al. [45], the functional properties (peptide-binding affinity and specificity) of artificial WW domains were found to be consistent with those of natural WW domains. This finding illustrates that a very small set of constraints are sufficient to encode function in a protein.
    • Russ W.P., Lowery D.M., Mishra P., Yaffe M.B., and Ranganathan R. Natural-like function in artificial WW domains. Nature 437 (2005) 579-583. In a companion paper to that of Socolich et al. [45], the functional properties (peptide-binding affinity and specificity) of artificial WW domains were found to be consistent with those of natural WW domains. This finding illustrates that a very small set of constraints are sufficient to encode function in a protein.
    • (2005) Nature , vol.437 , pp. 579-583
    • Russ, W.P.1    Lowery, D.M.2    Mishra, P.3    Yaffe, M.B.4    Ranganathan, R.5
  • 51
    • 2442668927 scopus 로고    scopus 로고
    • Discovery and directed evolution of a glyphosate tolerance gene
    • In a very successful venture, this group was able to blend the iterative incorporation of sequence diversity and functional selection to find a genetic variant of GAT with enzymatic efficiency four log orders higher than that of any of the parent sequences. The new enzyme was also effective in vivo and rescued plants from lethal doses of herbicide.
    • Castle L.A., Siehl D.L., Gorton R., Patten P.A., Chen Y.H., Bertain S., Cho H.J., Duck N., Wong J., Liu D., et al. Discovery and directed evolution of a glyphosate tolerance gene. Science 304 (2004) 1151-1154. In a very successful venture, this group was able to blend the iterative incorporation of sequence diversity and functional selection to find a genetic variant of GAT with enzymatic efficiency four log orders higher than that of any of the parent sequences. The new enzyme was also effective in vivo and rescued plants from lethal doses of herbicide.
    • (2004) Science , vol.304 , pp. 1151-1154
    • Castle, L.A.1    Siehl, D.L.2    Gorton, R.3    Patten, P.A.4    Chen, Y.H.5    Bertain, S.6    Cho, H.J.7    Duck, N.8    Wong, J.9    Liu, D.10
  • 53
    • 33646178621 scopus 로고    scopus 로고
    • Designed divergent evolution of enzyme function
    • Libraries containing degenerate codons at a single amino acid position were constructed and characterized based on their enzymatic products. The authors then demonstrated that the product profiles could be rationally combined to predict enzyme variants with specific activity profiles. This construction of a specialized functional database illustrates how functional information can be cleverly incorporated into protein design.
    • Yoshikuni Y., Ferrin T.E., and Keasling J.D. Designed divergent evolution of enzyme function. Nature 440 (2006) 1078-1082. Libraries containing degenerate codons at a single amino acid position were constructed and characterized based on their enzymatic products. The authors then demonstrated that the product profiles could be rationally combined to predict enzyme variants with specific activity profiles. This construction of a specialized functional database illustrates how functional information can be cleverly incorporated into protein design.
    • (2006) Nature , vol.440 , pp. 1078-1082
    • Yoshikuni, Y.1    Ferrin, T.E.2    Keasling, J.D.3
  • 54
    • 0346555269 scopus 로고    scopus 로고
    • Optimization of specificity in a cellular protein interaction network by negative selection
    • Zarrinpar A., Park S.H., and Lim W.A. Optimization of specificity in a cellular protein interaction network by negative selection. Nature 426 (2003) 676-680
    • (2003) Nature , vol.426 , pp. 676-680
    • Zarrinpar, A.1    Park, S.H.2    Lim, W.A.3


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