The Yin and Yang of protein folding

The study of protein aggregation saw a renaissance in the last decade, when it was discovered that aggregation is the cause of several human diseases, making this field of research one of the most exciting frontiers in science today. Building on knowledge about protein folding energy landscapes, determined using an array of biophysical methods, theory and simulation, new light is now being shed on some of the key questions in protein‐misfolding diseases. This review will focus on the mechanisms of protein folding and amyloid fibril formation, concentrating on the role of partially folded states in these processes, the complexity of the free energy landscape, and the potentials for the development of future therapeutic strategies based on a full biophysical description of the combined folding and aggregation free‐energy surface.

[1]  A. Fersht,et al.  Is there a unifying mechanism for protein folding? , 2003, Trends in biochemical sciences.

[2]  Mehmet Sarikaya,et al.  Hsp70 and Hsp40 attenuate formation of spherical and annular polyglutamine oligomers by partitioning monomer , 2004, Nature Structural &Molecular Biology.

[3]  S. Radford,et al.  GroEL accelerates the refolding of hen lysozyme without changing its folding mechanism , 1999, Nature Structural Biology.

[4]  C. Brooks,et al.  From folding theories to folding proteins: a review and assessment of simulation studies of protein folding and unfolding. , 2001, Annual review of physical chemistry.

[5]  C. Dobson Experimental investigation of protein folding and misfolding. , 2004, Methods.

[6]  I D Campbell,et al.  Amyloid fibril formation by an SH3 domain. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[7]  L. Serrano,et al.  Prediction of sequence-dependent and mutational effects on the aggregation of peptides and proteins , 2004, Nature Biotechnology.

[8]  A I Jewett,et al.  Accelerated folding in the weak hydrophobic environment of a chaperonin cavity: creation of an alternate fast folding pathway. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[9]  Christopher M. Dobson,et al.  Instability, unfolding and aggregation of human lysozyme variants underlying amyloid fibrillogenesis , 1997, Nature.

[10]  Patricia L Clark,et al.  Protein folding in the cell: reshaping the folding funnel. , 2004, Trends in biochemical sciences.

[11]  J. Kemp,et al.  Targeted pharmacological depletion of serum amyloid P component for treatment of human amyloidosis , 2002, Nature.

[12]  R. Tycko Progress towards a molecular-level structural understanding of amyloid fibrils. , 2004, Current opinion in structural biology.

[13]  John Q Trojanowski,et al.  Neurodegenerative diseases: a decade of discoveries paves the way for therapeutic breakthroughs , 2004, Nature Medicine.

[14]  Robert E. Cohen,et al.  Proteasomes and their kin: proteases in the machine age , 2004, Nature Reviews Molecular Cell Biology.

[15]  Petra Schwille,et al.  Single-molecule spectroscopic methods. , 2004, Current opinion in structural biology.

[16]  E. Appella,et al.  Beta 2-microglobulin. , 1984, Methods in enzymology.

[17]  A. Fersht,et al.  Transition-state structure as a unifying basis in protein-folding mechanisms: contact order, chain topology, stability, and the extended nucleus mechanism. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[18]  V. Uversky,et al.  Conformational constraints for amyloid fibrillation: the importance of being unfolded. , 2004, Biochimica et biophysica acta.

[19]  M. Stefani Protein misfolding and aggregation: new examples in medicine and biology of the dark side of the protein world. , 2004, Biochimica et biophysica acta.

[20]  M. Karplus,et al.  Structures and relative free energies of partially folded states of proteins , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[21]  C. Dobson,et al.  Rationalization of the effects of mutations on peptide andprotein aggregation rates , 2003, Nature.

[22]  C. Blake,et al.  The structure of amyloid fibrils by electron microscopy and X-ray diffraction. , 1997, Advances in protein chemistry.

[23]  N. Ban,et al.  A cradle for new proteins: trigger factor at the ribosome. , 2005, Current opinion in structural biology.

[24]  Zhanjiang Li,et al.  Novel glycosaminoglycan precursors as anti-amyloid agents, Part III , 2002, Journal of Molecular Neuroscience.

[25]  M. Sowa,et al.  The ClpB/Hsp104 molecular chaperone-a protein disaggregating machine. , 2004, Journal of structural biology.

[26]  J. Kelly,et al.  Prevention of Transthyretin Amyloid Disease by Changing Protein Misfolding Energetics , 2003, Science.

[27]  W. Szarek,et al.  Novel glycosaminoglycan precursors as anti-amyloid agents part II , 2002, Journal of Molecular Neuroscience.

[28]  J. Kelly,et al.  Sequence-dependent denaturation energetics: A major determinant in amyloid disease diversity , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[29]  C. Dobson,et al.  The folding of hen lysozyme involves partially structured intermediates and multiple pathways , 1992, Nature.

[30]  I. Braakman,et al.  Protein folding and quality control in the endoplasmic reticulum. , 2004, Current opinion in cell biology.

[31]  M. Karplus,et al.  Three key residues form a critical contact network in a protein folding transition state , 2001, Nature.

[32]  Ralf Langen,et al.  Structural organization of alpha-synuclein fibrils studied by site-directed spin labeling. , 2003, The Journal of biological chemistry.

[33]  J. Richardson,et al.  Natural β-sheet proteins use negative design to avoid edge-to-edge aggregation , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[34]  Christopher M. Dobson,et al.  Kinetic partitioning of protein folding and aggregation , 2002, Nature Structural Biology.

[35]  J. Sipe Amyloid proteins : the beta sheet conformation and disease , 2005 .

[36]  J. Hofrichter,et al.  The protein folding 'speed limit'. , 2004, Current opinion in structural biology.

[37]  Zhanjiang Li,et al.  Novel glycosaminoglycan precursors as antiamyloid agents , 2004, Journal of Molecular Neuroscience.

[38]  L. Serpell,et al.  The Structure of Amyloid , 2004 .

[39]  Valerie Daggett,et al.  From conversion to aggregation: protofibril formation of the prion protein. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[40]  H. Dyson,et al.  Unfolded proteins and protein folding studied by NMR. , 2004, Chemical reviews.

[41]  Min Goo Lee,et al.  A protein sequence that can encode native structure by disfavoring alternate conformations , 2002, Nature Structural Biology.

[42]  A. Fersht,et al.  Phi-value analysis and the nature of protein-folding transition states. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[43]  C. Hall,et al.  Molecular dynamics simulations of spontaneous fibril formation by random-coil peptides. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[44]  P. Lansbury,et al.  Protofibrils, pores, fibrils, and neurodegeneration: separating the responsible protein aggregates from the innocent bystanders. , 2003, Annual review of neuroscience.

[45]  I. E. Sánchez,et al.  Formation of on- and off-pathway intermediates in the folding kinetics of Azotobacter vinelandii apoflavodoxin. , 2004, Biochemistry.

[46]  Christopher M. Dobson,et al.  A camelid antibody fragment inhibits the formation of amyloid fibrils by human lysozyme , 2003, Nature.

[47]  P. Lansbury,et al.  Amyloid fibrillogenesis: themes and variations. , 2000, Current opinion in structural biology.

[48]  S. Radford,et al.  Competing pathways determine fibril morphology in the self-assembly of beta2-microglobulin into amyloid. , 2005, Journal of molecular biology.

[49]  J. Buxbaum Diseases of protein conformation: what do in vitro experiments tell us about in vivo diseases? , 2003, Trends in biochemical sciences.

[50]  C. Anfinsen Principles that govern the folding of protein chains. , 1973, Science.

[51]  C. Dobson,et al.  Inherent toxicity of aggregates implies a common mechanism for protein misfolding diseases , 2002, Nature.

[52]  A. Yonath,et al.  From peptide‐bond formation to cotranslational folding: dynamic, regulatory and evolutionary aspects , 2005, FEBS letters.

[53]  Michele Vendruscolo,et al.  Towards complete descriptions of the free–energy landscapes of proteins , 2005, Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences.

[54]  A. Alexandrescu Amyloid accomplices and enforcers , 2005, Protein science : a publication of the Protein Society.

[55]  A. Fersht,et al.  Protein Folding and Unfolding at Atomic Resolution , 2002, Cell.

[56]  Jason C. Young,et al.  Pathways of chaperone-mediated protein folding in the cytosol , 2004, Nature Reviews Molecular Cell Biology.

[57]  D. J. Naylor,et al.  Dual Function of Protein Confinement in Chaperonin-Assisted Protein Folding , 2001, Cell.

[58]  P. Muchowski Protein Misfolding, Amyloid Formation, and Neurodegeneration A Critical Role for Molecular Chaperones? , 2002, Neuron.

[59]  Ralf Langen,et al.  Structural Organization of α-Synuclein Fibrils Studied by Site-directed Spin Labeling* , 2003, Journal of Biological Chemistry.

[60]  P. Wolynes Energy landscapes and solved protein–folding problems , 2004, Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences.

[61]  D. Selkoe Folding proteins in fatal ways , 2003, Nature.

[62]  J. Sipe,et al.  Review: history of the amyloid fibril. , 2000, Journal of structural biology.

[63]  J. Kelly,et al.  The Biological and Chemical Basis for Tissue-Selective Amyloid Disease , 2005, Cell.

[64]  F. Hartl,et al.  Roles of molecular chaperones in protein misfolding diseases. , 2004, Seminars in cell & developmental biology.

[65]  C. Dobson,et al.  Low-populated folding intermediates of Fyn SH3 characterized by relaxation dispersion NMR , 2004, Nature.

[66]  Kresten Lindorff-Larsen,et al.  Protein folding and the organization of the protein topology universe. , 2005, Trends in biochemical sciences.

[67]  Sheena E. Radford,et al.  Ultrarapid mixing experiments reveal that Im7 folds via an on-pathway intermediate , 2001, Nature Structural Biology.