Protein refolding versus aggregation: Computer simulations on an intermediate-resolution protein model

Journal of Molecular Biology

Volumn 312, Issue 1, 2001, Pages 187-202

  Smith, Anne Voegler ^a   Hall, Carol K ^a  

^a North Carolina State University   (United States)

Author keywords

Aggregation; Discontinuous molecular dynamics; Four helix bundle; Protein folding; Protein misfolding

Indexed keywords

PROTEIN;

ALGORITHM; ARTICLE; COMPUTER SIMULATION; CONFORMATIONAL TRANSITION; HYDROGEN BOND; MOLECULAR DYNAMICS; PRIORITY JOURNAL; PROTEIN ASSEMBLY; PROTEIN FOLDING; TEMPERATURE DEPENDENCE;

EID: 0035823222     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.2001.4845     Document Type: Article

References (77)

1. Protein mis-assembly in vitro
2. Translating cell biology into therapeutic advances in Alzheimer's disease
3. Pathologic conformations of prion proteins
4. Stability of protein pharmaceuticals
5. Aggregation of lyophilized pharmaceutical protein, recombinant human albumin: Effect of moisture and stabilization by excipients
6. A green light for protein folding
7. Design of a 4-helix bundle protein: Synthesis of peptides which self-associate into a helical protein
8. Characterization of a helical protein designed from first principles
9. 1: Implications for protein design
10. Native-like and structurally characterized designed α-helical bundles
11. A de novo designed protein mimics the native state of natural proteins
12. Assembly of a tetrameric α-helical bundle: Computer simulations on an intermediate-resolution protein model
13. Effect of denaturant and protein concentrations upon protein refolding and aggregation: A simple lattice model
14. AMBER - Assisted model-building with energy refinement - A general program for modeling molecules and their interactions
15. CHARMM - A program for macromolecular energy, minimization, and dynamics calculations
16. Potential energy function and parameters for simulations of the molecular dynamics of proteins and nucleic acids in solution
17. Acid and thermal-denaturation of barnase investigated by molecular-dynamics simulations
18. "New view" of protein folding reconciled with the old through multiple unfolding simulations
19. Analysis methods for comparison of multiple molecular dynamics trajectories: Applications to protein unfolding pathways and denatured ensembles
20. Simulations of the structural and dynamical properties of denatured proteins: The "molten coil" state of bovine pancreatic trypsin inhibitor
21. Towards a complete description of the structural and dynamic properties of the denatured state of barnase and the role of residual structure in folding
22. Computer simulation of protein-protein association kinetics: Acetylcholin-esterase-fasciculin
23. A lattice statistical mechanics model of the conformational and sequence spaces of proteins
24. Engineering of stable and fast-folding sequences of model proteins
25. Folding kinetics of protein-like heteropolymers
26. Phase diagram of a semiflexible polymer chain in a θ solvent: Application to protein folding
27. First-order disorder-to-order transition in an isolated homopolymer model
28. Equilibrium thermodynamics of homopolymers and clusters: Molecular dynamics and Monte Carlo simulations of systems with square-well interactions
29. Structural transformation in the collapse transition of the single flexible homopolymer model
30. Globule-to-coil transition of a single homopolymer chain in solution
31. Statistical mechanics of heteropolymer folding
32. Kinetics and thermodynamics of folding in model proteins
33. The structure of a random heteropolymer in a disordered medium: Ensemble growth simulation
34. Local interactions and protein folding: A three-dimensional off-lattice approach
35. Monte Carlo simulation of protein folding with orientation-dependent monomer-monomer interactions
36. Folding funnels and frustraction in off-lattice minimalist protein landscapes
37. The thermodynamics and kinetics of protein folding: A lattice model analysis of multiple pathways with intermediates
38. Discretized model of proteins. I. Monte Carlo study of cooperativity in homopolypeptides
39. Monte Carlo simulations of protein folding. I. Lattice model and interaction scheme
40. Monte Carlo simulations of protein folding. I. Application to Protein A, ROP, and crambin
41. Computer simulations of de novo designed helical proteins
42. 2D de novo designed helical proteins
43. A simplified amino acid potential for use in structure predictions of proteins
44. Reduced representation model of protein structure prediction: Statistical potential and genetic algorithms
45. Folding dynamics with nonadditive forces: A simulation study of a designed helical protein and a random heteropolymer
46. Kinetics and thermodynamics of folding of a de novo designed four-helix bundle protein
47. Simulations of kinetically irreversible protein aggregate structure
48. Simulations of reversible protein aggregate and crystal structure
49. Lattice simulations of aggregation funnels for protein folding
50. Folding and aggregation of designed proteins
51. Compactness, aggregation, and prionlike behavior of protein: A lattice model study
52. Thermodynamics of model prions and its implications for the problem of prion protein folding
53. Bridging the gap between homopolymer and protein models: A discontinuous molecular dynamics study
54. α-Helix formation: Discontinuous molecular dynamics on an intermediate-resolution protein model
55. Hydrogen bonding in globular proteins
56. Virtual atom representation of hydrogen bonds in minimal off-lattice models of α helices: Effect on stability, cooperativity and kinetics
57. Studies in molecular dynamics I. General method
58. Molecular dynamics simulation of polymer chains with excluded volume
59. Molecular dynamics of rigid and non-rigid necklaces of hard discs
60. Molecular dynamics for polymeric fluids using discontinuous potentials
61. Molecular dynamics simulations at constant temperature and/or pressure
62. The packing of α-helices: Simple coiled-coils
63. The four-helix bundle: What determines a fold?
64. Molecular dynamics simulation of a synthetic ion channel
65. Brownian dynamics simulations of protein folding: Access to milliseconds time scale and beyond
66. Protein folding in the landscape prespective: Chevron plots and non-Arrhenius kinetics
67. Matching speed and locality
68. Alternative explanations for multistate kinetics in protein folding: Transient aggregation and changing transition-state ensembles
69. X-ray diffraction from intraneuronal paired helical filaments and extraneuronal amyloid fibers in Alzheimer disease indicates cross-β conformation
70. The alternative conformations of amyloidogenic proteins and their multi-step assembly pathways
71. Nativelike secondary structure in interleukin-1-beta inclusion bodies by attenuated total relectance FT-IR
72. Multimeric intermediates in the pathway to the aggregated inclusion body state for P22 tailspike polypeptide chains
73. For protein misassembly, it's the "I" decade
74. Thermolabile folding intermediates: Inclusion body precursors and chaperonin substrates
75. Protein aggregation: Folding aggregates, inclusion bodies and amyloid
76. RasMol: Biomolecular graphics for all