Recognition between flexible protein molecules: Induced and assisted folding

Journal of Molecular Recognition

Volumn 14, Issue 1, 2001, Pages 42-61

  Demchenko, Alexander P ^a,b  

^a INSTITUTE OF HYDROBIOLOGY   (Ukraine)

^b MATERIALS INSTITUTE   (Turkey)

Author keywords

Flexible molecules; Folding diseases; Molecular chaperones; Molecular recognition; Protein folding; Protein ligand interaction

Indexed keywords

CHAPERONE; CONFORMATIONAL TRANSITION; MOLECULAR RECOGNITION; NUCLEIC ACID; PROTEIN FOLDING; PROTEIN PROTEIN INTERACTION; SIGNAL TRANSDUCTION;

ANIMALS; HUMANS; KINETICS; LIGANDS; MODELS, MOLECULAR; MOLECULAR CHAPERONES; NUCLEIC ACIDS; PROTEIN FOLDING; PROTEINS; THERMODYNAMICS;

EID: 0035096292     PISSN: 09523499     EISSN: None     Source Type: Journal    
DOI: 10.1002/1099-1352(200101/02)14:1<42::AID-JMR518>3.0.CO;2-8     Document Type: Review

References (245)

1. Specificity of ribonucleoprotein interaction determined by RNA folding during complex formulation
2. Spindle assembly and the art of regulating microtubule dynamics by MAPs and Stathmin/Op18
3. The specific binding of three fragments of staphylococcal nuclease
4. Principles that govern the folding of protein chains
5. Acetylcholinesterase: Role of the enzyme's charge distribution in steering charged ligands toward the active site
6. GroEL binds artificial proteins with random sequences
7. Dissecting the energetics of a protein-protein interaction: The binding of ovomucoid third domain to elastase
8. Thermodynamic analysis of unfolding and dissociation in lactose repressor protein
9. Protein-directed DNA structure II. Raman spectroscopy of a leucine zipper bZIP complex
10. Orientation constraints in diffusion-limited macromolecular association. The role of surface diffusion as a rate-enhancing mechanism
11. Coupled folding and site-specific binding of the GCN4-bZIP transcription factor to the AP-1 and ATF/CREB DNA sites studied by microcalorimetry
12. Diffusion-controlled DNA recognition by an unfolded, monomeric bZIP transcription factor
13. Antigen recognition by conformational selection
14. Crystal structure of the cell cycle-regulatory protein suc1 reveals a β-hinge conformational switch
15. Equilibrium dissociation and unfolding of the Arc repressor dimer
16. Conformational variability in the refined structure of the chaperonin GroEL at 2.8 A resolution
17. The base of the proteasome regulatory particle exhibits chaperone-like activity
18. Funnels, pathways, and the energy landscape of protein folding: A synthesis
19. Hsp90 & Co. - A holding for folding
20. A structural model for GroEL-polypeptide recognition
21. Monte Carlo docking of oligopeptides to proteins
22. Free energy landscapes of encounter complexes in protein-protein association
23. Kinetics of desolvation-mediated protein-protein binding
24. Hsp90's secrets unfold: New insights from structural and functional studies
25. SKN-1 domain folding and basic region monomer stabilization upon DNA binding
26. Identification by 1H NMR spectroscopy of flexible C-terminal extensions in bovine lens alpha-crystallin
27. On the interaction of alpha-crystallin with unfolded proteins
28. Recognition between disordered states: Kinetics of the self-assembly of thioredoxin fragments
29. GroEL recognizes sequential and non-sequential linear structural motifs compatible with extended beta-strands and alpha-helices
30. The crystal structure of a GroEL/peptide complex: Plasticity as a basis for substrate diversity
31. The DNA binding arm of lambda repressor: Critical contacts from a flexible region
32. Non-cooperative binding of the MAP-2 microtubule-binding region to microtubules
33. Protein misfolding and prion diseases
34. Pathologic conformations of prion proteins
35. Binding affinity of proteins to hsp90 correlates with both hydrophobicity and positive charges. A surface plasmon resonance study
36. The 90-kDa molecular chaperone family: Structure, function, and clinical applications. A comprehensive review
37. On the substrate specificity of alphacrystallin as a molecular chaperone
38. Conformational properties of substrate proteins bound to a molecular chaperone alpha-crystallin
39. Insight into the secondary structure of non-native proteins bound to a molecular chaperone alpha-crystallin. An isotope-edited infrared spectroscopic study
40. The C-terminal half of the anti-sigma factor, FlgM, becomes structured when bound to its target, sigma 28
41. Protein folding with molecular chaperones
42. Protein folding with molecular chaperones: Stochastic process under control
43. Concepts and misconcepts in the science of protein folding
44. Tolerance of protein structures to the changes of amino acid sequences and their interactions. The nature of the folding code
45. Computation of the binding of fully flexible peptides to proteins with flexible side chains
46. Molecular dynamics simulation of the docking of substrates to proteins
47. Protein-RNA recognition
48. Themes in RNA-protein recognition
49. Dynamic contributions to the DNA binding entropy of the EcoRI and EcoRV restriction nucleases
50. Inherent flexibility in a potent inhibitor of blood coagulation, recombinant nematode anticoagulant protein c2
51. The energetics and dynamics of molecular recognition by calmodulin
52. Binding of non-native protein to Hsp25 during heat shock creates a reservoir of folding intermediates for reactivation
53. The GCN4 basic region leucine zipper binds DNA as a dimer of uninterrupted alpha helices: Crystal structure of the protein-DNA complex
54. The crystal structure of p13-suc1, a p34-cdc2-interacting cell cycle control protein
55. Alzheimer's disease amyloid propagation by template-dependent dock-lock mechanism
56. Interaction of alpha-crystallin with spin-labeled peptides
57. Refinement of 3D structure of bovine lens alpha A-crystallin
58. Visualization of a slow, ATP-induced structural transition in the bacterial molecular chaperone DnaK
59. Multivalent binding of nonnative substrate proteins by the chaperonin GroEL
60. Chaperone SecB: Conformational changes demonstrated by circular dichroism
61. SH2 domains exhibit high-affinity binding to tyrosine-phosphorylated peptides yet also exhibit rapid dissociation and exchange
62. Conformational isomerism and the diversity of antibodies
63. The 'dynamics' in the thermodynamics of binding
64. Common and divergent peptide binding specificities of Hsp70 molecular chaperones
65. Induced folding in RNA-protein recognition: More than a simple molecular handshake
66. Structure of tau protein and assembly into paired helical filaments
67. Predicting molecular interactions and inducible complementarity: Fragment docking of Fab-peptide complexes
68. Brownian dynamics simulation of protein-protein diffusional encounter
69. On the protein-protein diffusional encounter complex
70. ATP hydrolysis induces an intermediate conformational state in GroEL
71. Prothymosin alpha: A biologically active protein with random coil conformation
72. Role of multiple CytR binding sites on cooperativity, competition and induction at the Escherichia coli udp promoter
73. Molecular recognition of the inhibitor AG-1343 by HIV-1 protease: Conformationally flexible docking by evolutionary programming
74. Thermodynamic and kinetic analysis of the Escherichia coli thioredoxin-C′ fragment complementation system
75. Catapult mechanism renders the chaperone action of Hsp70 unidirectional
76. Mechanism of folding of the dimeric core domain of Escherichia coli trp repressor: A nearly diffusion-limited reaction leads to the formation of an on-pathway dimeric intermediate
77. A specific transition state for S-peptide combining with folded S-protein and then refolding
78. Specificity of DnaK-peptide binding
79. Solution dynamics of the trp repressor: A study of amide proton exchange by T1 relaxation
80. Flexibility of DNA binding domain of trp repressor required for recognition of different operator sequences
81. Small heat-shock protein structures reveal a continuum from symmetric to variable assemblies
82. Protein fragments as probes in the study of protein folding mechanisms: Differential effects of dihydrofolate reductase fragments on the refolding of the intact protein
83. Protein substrate binding induces conformational changes in the chaperonin GroEL. A suggested mechanism for unfoldase activity
84. The core Alzheimer's peptide NAC forms amyloid fibrils which seed and are seeded by beta-amyloid: Is NAC a common trigger or target in neurodegenerative disease?
85. Formation of a biologically active, ordered complex from two overlapping fragments of cytochrome c
86. NMR studies of protein-nucleic acid complexes: Structures, solvation, dynamics and coupled protein folding
87. Molecular chaperone functions of heat-shock proteins
88. Physicochemical characterization of the heat-stable microtubule-associated protein MAP2
89. Kinetic proofreading: A new mechanism for reducing errors in biosynthetic processes requiring high specificity
90. Specific binding of normal prion protein to the scarpie form via a localized domain initiates its conversion to a protease-resistant state
91. Role of protein-induced bending in the specificity of DNA recognition: Crystal structure of EcoRV endonuclease complexed with d(AAAGAT)+ d(ATCTT)
92. Identification of in vivo substrates of the chaperonin GroEL
93. Transcriptional activator-coactivator recognition: Nascent folding of a kinase-inducible transactivation domain predicts its structure on coactivator binding
94. Functional significance of flexibility in proteins
95. Resonance assignments, solution structure and backbone dynamics of the DNA- and RPA-binding domain of human repair factor XPA
96. X-ray diffraction analysis of scarpie priorn: Intermediate and folded structures in a peptide containing two putative α-helices
97. Nature and consequences of GroEL-protein interactions
98. Rapid refinement of protein interfaces incorporating solvation: Application to the docking problem
99. A folded monomeric intermediate in the formation of lambda Cro dimer-DNA complexes
100. Protein-protein recognition
101. X-ray diffraction studies of fibrils formed from peptide fragments of transthyretin
102. Protein-DNA recognition complexes: Conservation of structure and binding energy in the transition state
103. Principles of protein-protein interactions
104. DNA-binding characteristics of the Escherichia coli CytR regulator: A relaxed spacing requirement between operator half-sites is provided by a flexible, unstructured interdomain linker
105. Conformational dynamics of a biologically active three fragment complex of horse cytochrome c
106. A biologically active, three-fragment complex of horse heart cytochrome c
107. Effect of caldesmon on the assembly of smooth muscle myosin
108. Correlation between dynamics and high affinity binding in an SH2 domain interaction
109. Correlation between binding and dynamics at SH2 domain interfaces
110. Crystal structure of a small heat-shock protein
111. Thermolabile folding intermediates: Inclusion body precursors and chaperonin substrates
112. Analysis of the mechanism of assembly of cleaved barnase from two peptide fragments and its relevance to the folding pathway of uncleaved barnase
113. Substrate specificity of the SecB chaperone
114. One nanosecond molecular dynamics simulation of the N-terminal domain of the lambda repressor protein
115. The X-ray structure of the GCN4-bZlP bound to ATF/CREB site DNA shows the complex depends on DNA flexibility
116. The SKN-1 amino-terminal arm is a DNA specificity segment
117. The catalytic and regulatory properties of enzymes
118. Alzheimer's disease: A cell biological perspective
119. Structural studies of p21Waf1/Cip1/Sdi1 in the free and Cdk2-bound state: Conformational disorder mediates binding diversity
120. Folding and binding cascades: Dynamic landscapes and population shifts
121. Secondary structure in ribonuclease. I. Equilibrium folding transitions seen by amide circular dichroism
122. Kinetic circular dichroism shows that the S-peptide alpha-helix of ribonuclease S unfolds fast and refolds slowly
123. The chaperonin GroEL binds a polypeptide in an alpha-helical conformation
124. Different conformations for the same polypeptide bound to chaperones DnaK and GroEL
125. Op18/stathmin mediates multiple region-specific tubulin and microtubule-regulating activities
126. Binding of polylysine to GroEL. Inhibition of the refolding of mMDH
127. Spectroscopic, calorimetric, and kinetic demonstration of conformational adaptation in peptide-antibody recognition
128. A small heat shock protein stably binds heat-denatured model substrates and can maintain a substrate in a folding-competent state
129. The aspartic proteinase from Saccharomyces cerevisiae folds its own inhibitor into a helix
130. A kinetic study of the complementation of fragments of staphylococcal nuclease
131. The hydrophobic nature of GroEL-substrate binding
132. Structural alterations of alpha-crystallin during its chaperone action
133. Conformational changes affect binding and catalysis by ester-hydrolysing antibodies
134. The atomic structure of protein-protein recognition sites
135. Bivalency as a principle for proteasome inhibition
136. Flexible ligand docking using conformational ensembles
137. Manganese stabilizing protein of photosystem II is a thermostable, natively unfolded polypeptide
138. Smooth muscle caldesmon is an extended flexible monomeric protein in solution that can readily undergo reversible intra- and intermolecular sulfhydryl cross-linking. A mechanism for caldesmon's F-actin bundling activity
139. Folding funnels and binding mechanisms
140. Docking of flexible ligands to flexible receptors in solution by molecular dynamics simulation
141. High resolution solution structure of ribosomal protein L11-C76, a helical protein with a flexible loop that becomes structured upon binding to RNA
142. Tubulin folding cofactor D is a microtubule destabilizing protein
143. Mechanism of folding and assembly of a small tetrameric protein domain from tumor suppressor p53
144. Recognizing misfolded proteins in the endoplasmic reticulum
145. Multistep mechanism of substrate binding determines chaperone activity of Hsp70
146. The role of ATP in the functional cycle of the DnaK chaperone system
147. Ligand-induced conformational changes of GroEL are dependent on the bound substrate polypeptide
148. Structural and functional similarities of bovine alpha-crystallin and mouse small heat-shock protein. A family of chaperones
149. Ligand binding to proteins: The binding landscape model
150. Protein folding in the absence of chemical denaturants. Reversible pressure denaturation of the noncovalent complex formed by the association of two protein fragments
151. OP18/stathmin binds near the C-terminus of tubulin and facilitates GTP binding
152. An epitope structure for the C-terminal domain of dystrophin and utrophin
153. High-resolution solution structure of the 18 kDa substrate-binding domain of the mammalian chaperone protein Hsc70
154. Intermolecular forces and energies between ligands and receptors
155. Structural energetics of peptide recognition: Angiotensin II/antibody binding
156. Side-chain flexibility in proteins upon ligand binding
157. Structure of the double-stranded RNA-binding domain of the protein kinase PKR reveals the molecular basis of its dsRNA-mediated activation
158. Electrostatic complementarity in molecular associations
159. Analysis of molecular recognition: Steric, electrostatic and hydrophobic complementarity
160. Dynamics of molecular recognition in enzyme-catalyzed reactions
161. Conformational changes of small molecules binding to proteins
162. Stopped-flow kinetic analysis of the ligand-induced coil-helix transition in glutathione S-transferase A1-1: Evidence for a persistent denatured state
163. Kinetic amplification of enzyme discrimination
164. Are further kinetic amplification schemes possible?
165. Kinetics of protein-protein association explained by Brownian dynamics computer simulation
166. Fluorescence properties of calmodulin-binding peptides reflect alpha-helical periodicity
167. DNA-induced increase in the alpha-helical content of C/EBP and GCN4
168. Enthalpy of captopril-angiotensin I - Converting enzyme binding
169. Structural and energetic aspects of protein-protein recognition
170. The NMR solution conformation of unligated human cyclophilin A
171. BiGGER: A new (soft) docking algorithm for predicting protein interactions
172. Structural insights into substrate binding by the molecular chaperone DnaK
173. Importance of electrostatic interactions in the rapid binding of polypeptides to GroEL
174. Modulation of transcription factor Ets-1 DNA binding: DNA-induced unfolding of an alpha helix
175. The power stroke of the DnaK/DnaJ/GrpE molecular chaperone system
176. Effects of site-directed mutations on the chaperone-like activity of αB-crystallin
177. Association of complementary fragments and the elucidation of protein folding pathways
178. Interaction with GroEL destabilises non-amphiphilic secondary structure in a peptide
179. Identification and structural characterization of the ATP/ADP-binding site in the Hsp90 molecular chaperone
180. Structure of a pancreatic alpha-amylase bound to a substrate analogue at 2.03 A resolution
181. Temperature dependent chaperone-like activity of alpha-crystallin
182. Peptide binding by chaperone SecB: Implications for recognition of nonnative structure
183. High selectivity with low specificity: How SecB has solved the paradox of chaperone binding
184. The interaction between the chaperone SecB and its ligands: Evidence for multiple subsites for binding
185. Folding of protein fragments: Conformational and biological studies on thioredoxin and its fragments
186. Recognition of local glycoprotein misfolding by the ER folding sensor UDP-Glucose: Glycoprotein glucosyltransferase
187. A study of hydrogen exchange of monoclonal antibodies: Specificity of the antigen-binding induced conformational stabilization
188. Flexible docking and design
189. Substrate specificity of the DnaK chaperone determined by screening cellulose-bound peptide libraries
190. Interaction of Hsp70 chaperones with substrates
191. In vivo folding of inclusion bodies proteins
192. Protein fragments as models for events in protein folding pathways: Protein engineering analysis of the association of two complementary fragments of the barley chymotrypsin inhibitor 2 (Cl-2)
193. A method for biomolecular structural recognition and docking allowing conformational flexibility
194. Structural studies of tau protein a Alzheimer paired helical filaments show no evidence for beta-structure
195. Chaperonin function: Folding by forced unfolding
196. A comparison of structural relationships among alpha-crystallin, human Hsp27, gamma-crystallins and beta B2-crystallin
197. Peptide-induced conformational changes in the molecular chaperone DnaK
198. Immobilization of the C-terminal extension of bovine alpha A-crystallin reduces chaperone-like activity
199. Molecular docking using surface complementarity
200. Unfolded conformations of alpha-lytic protease are more stable than its native state
201. Functional specificity conferred by the unique plasticity of fully alpha-helical Ras and Rho GAPs
202. Dynamics of the GroEL-protein complex: Effects of nucleotides and folding mutants
203. Coupling of local folding to site-specific binding of proteins to DNA
204. Antigen-induced conformational changes in antibodies: A problem for structural prediction and design
205. Molecular dynamics simulations of human glutathione transferase P1-1: Conformational fluctuations of the apo-structure
206. The NMR structure of the 5S rRNA E-domain-protein L25 complex shows preformed and induced recognition
207. Catalysis of a protein folding reaction: Thermodynamic and kinetic analysis of subtilisin BPN' interactions with its propeptide fragment
208. Simultaneous formation of two alternative enzymology active structures by complementation of two overlapping fragments of staphylococcal nuclease
209. Study of equilibration of the system involving two alternative, enzymatically active complementing structures simultaneously formed from two overlapping fragments of staphylococcal nuclease
210. Complementation in folding and fragment exchange
211. Ordered self-assembly of polypeptide fragments to form nativelike dimeric trp repressor
212. Structure of Met30 variant of transthyretin and its amyloidogenic implications
213. Crystal structure of UvrB, a DNA helicase adapter for nucleotide excision repair
214. Folding and binding cascades: Shifts in energy landscapes
215. RNA-protein intermolecular recognition
216. Flexible structural comparison allowing hinge-bending, swiveling motions
217. Conformational changes generated in GroEL during ATP hydrolysis as seen by time-resolved infrared spectroscopy
218. Facilitated target location in biological systems
219. Species dependence of enzyme-substrate encounter rates for triose phosphate isomerases
220. Model for stathmin/OP18 binding to tubulin
221. New algorithm to model protein-protein recognition based on surface complementarity. Applications to antibody-antigen docking
222. Enzymes as chaperones and chaperones as enzymes
223. NMR solution structure of the 21 kDa chaperone protein DnaK substrate binding domain: A preview of chaperone-protein interaction
224. Basis of substrate binding by the chaperonin GroEL
225. Flexible ligand docking: A multistep strategy approach
226. An unstructured C-terminal region of the Hsp90 co-chaperone p23 is important for its chaperone function
227. NACP, a protein implicated in Alzheimer's disease and learning, is natively unfolded
228. Folding transition in the DNA-binding domain of GCN4 on specific binding to DNA
229. Very rapid, ionic strength-dependent association and folding of a heterodimeric leucine zipper
230. DNA-mediated folding and assembly of MyoD-E47 heterodimers
231. Folding of protein fragments
232. The crystal structure of EcoRV endonuclease and of its complexes with cognate and non-cognate DNA fragments
233. Energetics of target peptide recognition by calmodulin: A calorimetric study
234. Intrinsically unstructured proteins: Reassessing the protein structure-function paradigm
235. The Mycobacterium tuberculosis small heat shock protein Hsp 16.3 exposes hydrophobic surfaces at mild conditions: Conformational flexibility and molecular chaperone activity
236. pH- and Ca(2+)-induced conformational change and aggregation of chromogranin B. Comparison with chromogranin A and implication in secretory vesicle biogenesis
237. Destabilization of the complete protein secondary structure on binding to the chaperone GroEL
238. NMR solution structure of the human prion protein
239. The solution structures of the trp repressor-operator DNA complex
240. Protein-protein recognition: Exploring the energy funnels near the binding sites
241. Refined solution structures of the Escherichia coli trp holo- and aporepressor
242. Structural analysis of substrate binding by molecular chaperone DnaK
243. Increased protein backbone conformational entropy upon hydrophobic ligand binding