De novo design of helical bundles as models for understanding protein folding and function

Accounts of Chemical Research

Volumn 33, Issue 11, 2000, Pages 745-754

  Hill, R B ^a   Raleigh, D P ^b   Lombardi, A ^c   Degrado, W F ^a  

^a UNIVERSITY OF PENNSYLVANIA   (United States)

^b STONY BROOK UNIVERSITY   (United States)

^c UNIVERSITY OF NAPLES FEDERICO II   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

BINDING PROTEIN; PROTEIN;

ARTICLE; ENERGY; LABORATORY; METAL BINDING; PHYSICAL CHEMISTRY; PROTEIN ANALYSIS; PROTEIN BINDING; PROTEIN FOLDING; PROTEIN SECONDARY STRUCTURE; PROTEIN STRUCTURE; STRUCTURE ANALYSIS;

CHEMISTRY, PHYSICAL; PROTEIN FOLDING; PROTEIN STRUCTURE, SECONDARY; PROTEINS;

EID: 0033694923     PISSN: 00014842     EISSN: None     Source Type: Journal    
DOI: 10.1021/ar970004h     Document Type: Article

References (120)

1. Protein folding
2. Sequence space, folding and protein design
3. Dominant forces in protein folding
4. Characterization of protein folding intermediates
5. Fast events in protein folding
6. Optimization of rates of protein folding: The nucleation-condensation mechanism and its implications
7. Free energy balance in protein folding
8. Probing the determinants of protein folding and stability with amino acid substitutions
9. Protein design: A hierarchic approach
10. De novo design and structural characterization of proteins and metalloproteins
11. De novo designed polypeptide catalysts with adopted folded structures
12. Three-dimensional solution structure of the B domain of staphylococcal protein A: Comparisons of the solution and crystal structures
13. Solution structure and dynamics of a de novo designed three helix bundle protein
14. How different amino acid sequences determine similar protein structures: The structure and evolutionary dynamics of the globins
15. Bayesian statistical analysis of protein side-chain rotamer preferences
16. Conformational analysis of the backbone-dependent rotamer preferences of protein sidechains
17. Backbone-dependent rotamer library for proteins. Application to side-chain prediction
18. Analysis of the relationship between side-chain conformation and secondary structure in globular proteins
19. Rotamers: To be or not to be?
20. Metal ion-dependent modulation of the dynamics of a designed protein
21. De novo protein design: From molten globules to native-like states
22. The molten globule state as a clue for understanding the folding and cooperativity of globular-protein structure
23. Evidence for a molten globule state as a general intermediates in protein folding
24. Reaction paths and free energy profiles for conformational transitions: An internal coordinate approach
25. Universality and diversity of the protein folding scenarios: A comprehensive analysis with the aid of a lattice model
26. Towards an outline of the topography of a realistic protein folding funnel
27. Gene mutation in human hemoglobin: The chemical difference between normal and sickle cell hemoglobin
28. Sickle cell anemia: A molecular disease
29. Instability, unfolding and aggregation of human lysozyme variants underlying amyloid fibrillogenesis
30. Protein misfolding, evolution and disease
31. The alternative conformations of amyloidogenic proteins and their multistep assembly patterns
32. Rational design of potent human transthyretic amyloid disease inhibitors
33. Design of peptides undergoing self-catalytic α-to-β transition and amyloidogenesis
34. Mad cows meet psi-chotic yeast: The expansion of the prion hypotheses
35. Novel proteinaceous infectious particles cause scrapie
36. The de novo design of protein structures
37. NMR structure of a de novo designed, peptide 33mer with two distinct, compact β-sheet folds
38. A recipe for designing water-soluble, β-sheet-forming peptides
39. Design of a unique protein scaffold for maquettes
40. Solution structure of a designed four α-helix bundle maquette scaffold
41. Effect of four helix bundle topology on heine binding and redox properties
42. Functionalization of designed folded polypeptides
43. Cooperative nucleophilic and general-acid catalysis by the HisH-(+)-His pair and arginine transition state binding in catalysis of ester hydrolysis reactions by designed helix-loop-helix motifs
44. A noncovalent peptide complex as a model for an early folding intermediate of cytochrome c
45. Defining the core structure of the α-lactalbumin molten globule
46. Design and NMR analyses of compact, independently folded BBA motifs
47. Economy in protein design: Evolution of a metal-independent β β α motif based on the zinc finger domains
48. Design of a monomeric 23-residue polypeptide with defined tertiary structure
49. De novo protein design: Fully automated sequence selection
50. De novo protein design: Towards fully automated sequence selection
51. Use of a designed triple-stranded antiparallel β-sheet to probe β-sheet cooperativity in aqueous solution
52. Design of a 20-amino acid, three-stranded β-sheet protein
53. Cooperative interaction between the three strands of a designed antiparallel β-sheet
54. A designed three-stranded β-sheet peptide as a multiple β-hairpin model
55. A four stranded β-sheet in a designed, synthetic polypeptide
56. Solution structure of α t α, a helical hairpin peptide of de novo design
57. 2D, a native-like de novo designed protein
58. A designed four helix bundle with native-like structure
59. Structure of ColE1 rop protein at 1.7 Å resolution
60. Controlling topology and native-like behavior of de novo-designed peptides: Design and characterization of antiparallel four-stranded coiled coils
61. Patterns of loop regions in proteins
62. The hydrophobic-staple motif and a role for loop-residues in α-helix stability and protein folding
63. Amino-acid substitutions in a surface turn modulate protein stability
64. Using loop length variants to dissect the folding pathway of a four-helix-bundle protein
65. In vitro evolution of thermodynamically stable turns
66. Protein plasticity to the extreme: Changing the topology of a four α-helical bundle with a single amino acid substitution
67. Design of a 4-helix bundle protein: Synthesis of peptides which self-associate into a helical protein
68. A de novo designed protein shows a thermally induced transition from a native to a molten globule-like state
69. A de novo designed protein mimics the native state of natural proteins
70. Active barnase variants with completely random hydrophobic cores
71. A test of the 'jigsaw puzzle' model for protein folding by multiple methionine substitutions within the core of T4 lysozyme
72. Studies on protein stability with T4 lysozyme
73. The crystal structure of a mutant protein with altered but improved hydorphobic core packing
74. Structural and energetic consequences of disruptive mutations in a protein core
75. The role of internal packing interaction in determining the structure and stability of a protein
76. A polar, solvent-exposed residue can be essential for native protein structure
77. Hydrogen bonded cluster can specify the native state of a protein
78. A switch between two-, three-, and four-stranded coiled coils
79. Protein folding from a combinatorial perspective
80. The response of T4 lysozyme to large-to-small substitutions within the core and its relation to the hydrophobic effect
81. Probing the role of packing specificity in protein design
82. Solution structure and dynamics of a designed hydrophob c core variant of ubiquitin
83. Protein design by binary patterning of polar and nonpolar amino acids
84. Detecting native-like properties in combinatorial libraries of de novo proteins
85. Cooperative thermal denaturation of proteins designed by binary patterning of polar and nonpolar amino acids
86. The construction of metal centers in proteins by rational design
87. Computer search algorithms in protein modification and design
88. Design and creation of a Cu(II)-binding site in cytochrome c peroxidase that mimics the Cu(B)-heme center in terminal oxidases
89. Selective recognition and cleavage of RNA loop structures by Ni(II). Xaa-Gly-His metallopeptides
90. Kinetic and thermodynamic studies of the copper (II) and nickel (II) complexes of glycylglycyl-L-histidine
91. The sal-XH motif for metal-mediated oxidative DNA-peptide cross-linking
92. Exploiting polypeptide motifs for the design of selective Cu(II) ion chemosensors
93. Ferredoxin and ferredoxin-heme maquettes
94. The rational design and construction of a cuboidal iron-sulfur protein
95. Miniaturized metalloproteins. Application to iron-sulfur proteins
96. Looking at proteins: Representations, folding, packing, and design. Biophysical Society National Lecture
97. Tertiary templates for the design of diiron proteins
98. De-novo design of a novel heterodinuclear 3-helix bundle metalloprotein
99. De novo design of protein function: Predictable structure-function relationships in synthetic redox proteins
100. De novo heme proteins from designed combinatorial libraries
101. Design of a heme-binding four-helix bundle
102. Histidine placement in de novo-designed heme proteins
103. A tetrahedal zinc(II)-binding site introduced into a designed protein
104. Hemoprotein models based on a covalent helix-heme-helix sandwich. 2. Structural characterization of Co-III mimochrome I Delta and Delta isomers
105. Miniaturized hemoproteins
106. Synthesis of novel proteins
107. Design and synthesis of multi-haem proteins
108. Retrostructural analysis of metalloproteins: Application to the design of a minimal model for diiron proteins
109. Hydrophobic core packing and protein design
110. Computational protein design
111. De novo design of native proteins: Characterization of proteins intended to fold into antiparallel, rop-like, four-helix bundles
112. Three-dimensional structure of the E. coli DNA-binding protein FIS
113. NMR structure and mutagenesis of the Fas (APO-1/CD95) death domain
114. Solution structure of the N-terminal domain of the delta subunit of the E. coli ATP synthase
115. Structural evidence for induced fit as a mechanism for antigen-antibody recognition
116. Solution structure of the tetrameric minimum transforming domain of p53