- IRE1 couples endoplasmic reticulum load to secretory capacity by processing the XBP-1 mRNA
Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY 10016, USA
Nature 415:92-6. 2002
..Our findings suggest that physiological ER load regulates a developmental decision in higher eukaryotes...
- Intrinsically disordered proteins in human diseases: introducing the D2 concept
Vladimir N Uversky
Center for Computational Biology and Bioinformatics, Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana 46202, USA
Annu Rev Biophys 37:215-46. 2008
..From these and other examples, novel strategies for drug discovery based on IDPs have been developed. To summarize work in this area, we are introducing the D2 (disorder in disorders) concept...
- Protein disaggregation mediated by heat-shock protein Hsp104
D A Parsell
Department of Molecular Genetics and Cell Biology, Howard Hughes Medical Institute, University of Chicago, Illinois 60637
Nature 372:475-8. 1994
..Rather, Hsp104 functions in a manner not previously described for other heat-shock proteins: it mediates the resolubilization of heat-inactivated luciferase from insoluble aggregates...
- Regulated translation initiation controls stress-induced gene expression in mammalian cells
H P Harding
Skirball Institute of Biomolecular Medicine The Department of Medicine, Kaplan Cancer Center New York University School of Medicine, New York, NY 10016, USA
Mol Cell 6:1099-108. 2000
..Mammalian cells thus utilize an ancient pathway to regulate gene expression in response to diverse stress signals...
- Feedback inhibition of the unfolded protein response by GADD34-mediated dephosphorylation of eIF2alpha
Skirball Institute of Biomolecular Medicine, Department of Medicine, New York University School of Medicine, New York, NY 10016, USA
J Cell Biol 153:1011-22. 2001
- Protein kinetic stability
Jose M Sanchez-Ruiz
Departamento de Quimica Fisica, Universidad de Granada, 18071 Granada, Spain
Biophys Chem 148:1-15. 2010
- Conformational constraints for amyloid fibrillation: the importance of being unfolded
Vladimir N Uversky
Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, USA
Biochim Biophys Acta 1698:131-53. 2004
..The inherent flexibility of such an intermediate is essential in allowing the conformational rearrangements necessary to form the core cross-beta structure of the amyloid fibril...
- Chemical screening methods to identify ligands that promote protein stability, protein crystallization, and structure determination
Structural Genomics Consortium, University of Toronto, 100 College Street, Toronto, ON, Canada M5G 1L5
Proc Natl Acad Sci U S A 103:15835-40. 2006
..The methods are cost-effective, can be implemented in any laboratory, promise to increase the success rates of purifying and crystallizing human proteins significantly, and identify new ligands for these proteins...
- Conformational thermostabilization of the beta1-adrenergic receptor in a detergent-resistant form
Maria J Serrano-Vega
Laboratory of Molecular Biology, Medical Research Council, Hills Road, Cambridge CB2 0QH, United Kingdom
Proc Natl Acad Sci U S A 105:877-82. 2008
..In addition, betaAR-m23 was significantly more stable in a wide range of detergents ideal for crystallization and was preferentially in an antagonist conformation in the absence of ligand...
- Protein stability and surface electrostatics: a charged relationship
Samantha S Strickler
Department of Biochemistry and Molecular Biology, Pennsylvania State University College of Medicine, Hershey, Pennsylvania 17033, USA
Biochemistry 45:2761-6. 2006
- Evaluation of fluorescence-based thermal shift assays for hit identification in drug discovery
Mei Chu Lo
Biophysics Enzymology Chemical and Screening Sciences, Wyeth Research, Pearl River, NY 10965, USA
Anal Biochem 332:153-9. 2004
..The potential pitfalls in the data analysis of thermal shift assays are also discussed...
- Effect of environmental factors on the kinetics of insulin fibril formation: elucidation of the molecular mechanism
Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, USA
Biochemistry 40:6036-46. 2001
..A kinetic model, involving the association of monomeric partially folded intermediates, whose concentration is stimulated by the air-water interface, leading to formation of the critical nucleus and thence fibrils, is proposed...
- Protein folding and misfolding
Christopher M Dobson
University of Cambridge, Department of Chemistry, Lensfield Road, Cambridge CB2 1EW, UK
Nature 426:884-90. 2003
..Aggregation of misfolded proteins that escape the cellular quality-control mechanisms is a common feature of a wide range of highly debilitating and increasingly prevalent diseases...
- The mammalian unfolded protein response
School of Biological and Biomedical Sciences, University of Durham, Durham DH1 3LE, United Kingdom
Annu Rev Biochem 74:739-89. 2005
..Finally, we summarize data that demonstrate that UPR signaling feeds into decision making in other processes previously thought to be unrelated to ER function, e.g., eukaryotic starvation responses and differentiation programs...
- A regulatory link between ER-associated protein degradation and the unfolded-protein response
Max Delbruck Centrum fur Molekulare Medizin, Berlin, Germany
Nat Cell Biol 2:379-84. 2000
..However, when stress is applied, the UPR is required to increase ERAD activity. We thus demonstrate, for the first time, a regulatory loop between ERAD and the UPR, which is essential for normal growth of yeast cells...
- Strain-specified relative conformational stability of the scrapie prion protein
Institute for Neurodegenerative Diseases, University of California, San Francisco, California 94143, USA
Protein Sci 10:854-63. 2001
..Based on these results, the eight prion strains segregated into four distinct groups. Our results support the unorthodox proposal that distinct PrP(Sc) conformers encipher the biological properties of prion strains...
- Identification of thermolabile Escherichia coli proteins: prevention and reversion of aggregation by DnaK and ClpB
Institut fur Biochemie und Molekularbiologie, Universitat Freiburg, Hermann Herder Strasse 7, 79104 D Freiburg, Germany
EMBO J 18:6934-49. 1999
- Effects of common cancer mutations on stability and DNA binding of full-length p53 compared with isolated core domains
Hwee Ching Ang
Centre for Protein Engineering, Medical Research Council Centre, Hills Road, Cambridge CB2 2QH, United Kingdom
J Biol Chem 281:21934-41. 2006
..Many mutants that have lowered melting temperatures should be good drug targets, although the common R273H mutant binds response elements too weakly for simple rescue...
- Evidence for an unfolding/threading mechanism for protein disaggregation by Saccharomyces cerevisiae Hsp104
Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
J Biol Chem 279:29139-46. 2004
- Therapeutic approaches to protein-misfolding diseases
Fred E Cohen
University of California at San Francisco, Department of Cellular and Molecular Pharmacology, Genentech Hall, 600 16th Street N472J, San Francisco, California 94107, USA
Nature 426:905-9. 2003
..Molecules are now emerging that link our biophysical insights with our therapeutic aspirations...
- Role of solvation effects in protein denaturation: from thermodynamics to single molecules and back
Jeremy L England
Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, USA
Annu Rev Phys Chem 62:257-77. 2011
..Finally, we present recent single-molecule fluorescence studies of denatured proteins, the analysis of which corroborates the role of denaturants in shifting the equilibrium of the coil-globule transition...
- Amyloid-like properties of bacterial inclusion bodies
Institut de Biotecnologia i de Biomedicina, Universitat Autonoma de Barcelona, 08193 Bellaterra Barcelona, Spain
J Mol Biol 347:1025-37. 2005
- Sequential mechanism of solubilization and refolding of stable protein aggregates by a bichaperone network
Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, 91904 Jerusalem, Israel
Proc Natl Acad Sci U S A 96:13732-7. 1999
- Probing the free-energy surface for protein folding with single-molecule fluorescence spectroscopy
Laboratory of Chemical Physics, Building 5, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892 0520, USA
Nature 419:743-7. 2002
..Unlike the activation energy, the free-energy barrier includes the activation entropy and thus has been elusive to experimental determination for any kinetic process in solution...
- Sequence complexity of disordered protein
School of Electrical Engineering and Computer Science, Washington State University, Pullman, Washington 99164 4660, USA
Proteins 42:38-48. 2001
- Hsp104, Hsp70, and Hsp40: a novel chaperone system that rescues previously aggregated proteins
J R Glover
Howard Hughes Medical Institute and Department of Molecular Genetics and Cell Biology, The University of Chicago, Illinois 60637, USA
Cell 94:73-82. 1998
..coli. We conclude that Hsp104 has a protein remodeling activity that acts on trapped, aggregated proteins and requires specific interactions with conventional chaperones to promote refolding of the intermediates it produces...
- Correlation of levels of folded recombinant p53 in escherichia coli with thermodynamic stability in vitro
Cambridge University Chemical Laboratory and Cambridge Centre for Protein Engineering, MRC Centre, Hills Road, Cambridge CB2 0QH, UK
J Mol Biol 372:268-76. 2007
..coli, and provide insights into the correlation between protein instability and disease at the cellular level...
- Distinct roles of activating transcription factor 6 (ATF6) and double-stranded RNA-activated protein kinase-like endoplasmic reticulum kinase (PERK) in transcription during the mammalian unfolded protein response
Graduate School of Biostudies, Kyoto University, 46 29 Yoshida Shimoadachi, Sakyo ku, Kyoto 606 8304, Japan
Biochem J 366:585-94. 2002
..Thus we propose that mammalian cells have evolved a strategy to cope with ER stress different from that of yeast cells...
- Why is trehalose an exceptional protein stabilizer? An analysis of the thermal stability of proteins in the presence of the compatible osmolyte trehalose
Jai K Kaushik
Centre for Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India
J Biol Chem 278:26458-65. 2003
..8 kcal mol-1 at pH 2.5. There is a decrease in the heat capacity of protein denaturation (DeltaCp) in trehalose solutions for all the studied proteins...
- Unfolding of proteins and long transient conformations detected by single nanopore recording
Laboratoire de Recherche sur les Polymeres, Equipe Matériaux Polymères aux Interfaces, CNRS UMR 7581, Université d Evry, 91025 Evry, France
Phys Rev Lett 98:158101. 2007
..Long blockades reveal partially folded conformations. Their duration increases as the proteins are more folded. The observation of a Vogel-Fulcher law suggests a glassy behavior...
- In vitro unfolding, refolding, and polymerization of human gammaD crystallin, a protein involved in cataract formation
Melissa S Kosinski-Collins
Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
Protein Sci 12:480-90. 2003
..The mechanism of HgammaD-Crys aggregation may provide clues to understanding age-onset cataract formation in vivo...
- Thermal stability of alpha-amylase in aqueous cosolvent systems
Jay Kant Yadav
Department of Protein Chemistry and Technology, Central Food Technological Research Institute, Mysore 570020, India
J Biosci 34:377-87. 2009
..Preferential interaction parameters indicated extensive hydration of the enzyme in the presence of cosolvents...
- Heat shock protein coinducers with no effect on protein denaturation specifically modulate the membrane lipid phase
Institute of Biochemistry, Biological Research Centre, Hungarian Academy of Sciences, P O Box 521, H 6701 Szeged, Hungary
Proc Natl Acad Sci U S A 100:3131-6. 2003
..We show here that the presence of BM does not influence protein denaturation in the cells...
- Immunolocalisation of PrPSc in scrapie-infected N2a mouse neuroblastoma cells by light and electron microscopy
Nathalie M Veith
Molecular Toxicology, Department of Biology, University of Konstanz, Box X911, D 78457 Konstanz, Germany
Eur J Cell Biol 88:45-63. 2009
..Finally, we observed the release of PrPC/PrPSc via exocytotic pathways, i.e. via exosomes and as an opaque electron-dense mass which may represent a mechanism of intercellular spreading of infectious prions...
- A hydrogen bond surrogate approach for stabilization of short peptide sequences in alpha-helical conformation
Department of Chemistry, New York University, New York, New York 10003, USA
Acc Chem Res 41:1289-300. 2008
..Notably, our preliminary studies illustrate that HBS helices can target their expected protein receptors with high affinity...
- Interaction of urea with amino acids: implications for urea-induced protein denaturation
Martin C Stumpe
Department of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Gottingen, Germany
J Am Chem Soc 129:16126-31. 2007
The molecular mechanism of urea-induced protein denaturation is not yet fully understood...
- A functional single-molecule binding assay via force spectroscopy
Department of Chemistry, University of British Columbia, Vancouver, BC, Canada V6T 1Z1
Proc Natl Acad Sci U S A 104:15677-81. 2007
..This methodology opens up avenues for studying protein-ligand interactions in a functional context, and we anticipate that it will find broad application in diverse protein-ligand systems...
- Atypical AAA+ subunit packing creates an expanded cavity for disaggregation by the protein-remodeling factor Hsp104
Department of Crystallography, Birkbeck College, Malet Street, London WC1E 7HX, UK
Cell 131:1366-77. 2007
..The large cavity could enable the uptake of polypeptide loops without a requirement for exposed N or C termini...
- Thermal adaptation of viruses and bacteria
Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts Department of Physics, Harvard University, Cambridge, Massachusetts, USA
Biophys J 98:1109-18. 2010
- More stable structure of wheat germ lipase at low pH than its native state
Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, India
Biochimie 92:885-93. 2010
..Although enzymatically inactive, acid-induced state at pH 0.8 was found to be structurally more stable than native lipase, as shown by chemical and thermal denaturation profiles...
- First-order rate-determining aggregation mechanism of p53 and its implications
MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
Proc Natl Acad Sci U S A 109:13590-5. 2012
- Rapid and selective characterization of influenza virus constituents in monovalent and multivalent preparations using non-porous reversed-phase high performance liquid chromatography columns
Centre for Biologics Research, Health Canada, Banting Bldg, Tunney s Pasture, Ottawa, Ont, Canada K1A 0L2
J Chromatogr A 1123:225-32. 2006
..Several influenza constituents were detected including nucleoprotein, the highly hydrophobic matrix protein and the primary surface antigen, haemagglutinin (HA)...
- Tracking mutant huntingtin aggregation kinetics in cells reveals three major populations that include an invariant oligomer pool
Maya A Olshina
Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, 30 Flemington Road, Parkville, Victoria 3010, Australia
J Biol Chem 285:21807-16. 2010
- The cold denatured state of the C-terminal domain of protein L9 is compact and contains both native and non-native structure
Department of Chemistry, State University of New York at Stony Brook, Stony Brook, New York 11794 3400, USA
J Am Chem Soc 132:4669-77. 2010
..8 unfolded state of wild type CTL9 at 25 degrees C, suggesting that it is a robust feature of the denatured state ensemble of this protein. The implications for protein folding and for studies of cold denatured states are discussed...
- Understanding cold denaturation: the case study of Yfh1
MRC National Institute for Medical Research, The Ridgeway, London NW7 1AA, United Kingdom
J Am Chem Soc 132:16240-6. 2010
..We discuss the implications of our findings for understanding cold denatured states...
- Microscale fluorescent thermal stability assay for membrane proteins
Alexander I Alexandrov
Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
Structure 16:351-9. 2008
..To evaluate the method, three different protein families were analyzed, including the Apelin G protein-coupled receptor (APJ)...
- Structure and folding of a designed knotted protein
Neil P King
Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095 1569, USA
Proc Natl Acad Sci U S A 107:20732-7. 2010
..The success of the design strategy--connecting two monomers of an intertwined homodimer into a single protein chain--supports a model for evolution of knotted structures via gene duplication...
- Protein folding and unfolding at atomic resolution
Alan R Fersht
Department of Chemistry, MRC Centre for Protein Engineering, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
Cell 108:573-82. 2002
..We are on the threshold of predicting those protein folding events using simulation that has been carefully benchmarked by experiment...
- Electrostatic interactions across the dimer-dimer interface contribute to the pH-dependent stability of a tetrameric malate dehydrogenase
Department of Biology, University of Oslo, Box 1031 Blindern, N 0316 Oslo, Norway
FEBS Lett 553:423-6. 2003
..8 degrees C, and depended strongly on pH. Gel-filtration experiments indicated that the 26.8 degrees C loss in stability observed for the D56K mutant at low pH was accompanied by a shift towards a lower oligomerization state...
- Amyloid fibril formation can proceed from different conformations of a partially unfolded protein
Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
Biophys J 89:4201-10. 2005
..In addition, the structures of the resulting aggregates are largely independent of the conformational properties of their soluble precursors...
- Thermally induced fibrillar aggregation of hen egg white lysozyme
Luben N Arnaudov
Laboratory of Physical Chemistry and Colloid Science, Wageningen University, Wageningen, The Netherlands
Biophys J 88:515-26. 2005
..These fibrils have a coiled structure with a periodicity of approximately 30 nm and show characteristic defects after every four or five turns...
- A network representation of protein structures: implications for protein stability
K V Brinda
Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
Biophys J 89:4159-70. 2005
..Based on these results, we also predict a few residues in the thermophilic and mesophilic proteins that can be mutated to alter their thermal stability...
- Comparative studies on the structure and stability of fluorescent proteins EGFP, zFP506, mRFP1, "dimer2", and DsRed1
Olesia V Stepanenko
Institute of Cytology, Russian Academy of Sciences, St Petersburg 194064, Russia
Biochemistry 43:14913-23. 2004
..This means that the quaternary structure, being an important stabilizing factor, does not represent the only circumstance dictating the dramatic variations between fluorescent proteins in their conformational stabilities...
- Protein aggregation in crowded environments
R John Ellis
Department of Biological Sciences, University of Warwick, Coventry CV4 7AL, UK
Biol Chem 387:485-97. 2006
..This review discusses the quantitative effects of crowding on protein aggregation and the role of molecular chaperones in combating this problem...
- Fibrillar aggregates of the tumor suppressor p53 core domain
Departamento de Bioquímica Médica and Centro Nacional de Ressonância Magnética Nuclear, Universidade Federal do Rio de Janeiro, 21941 590 Rio de Janeiro, RJ, Brazil
Biochemistry 42:9022-7. 2003
..Fibrillar aggregates of p53C contribute to the loss of function of p53 and seed the accumulation of conformationally altered protein in some cancerous cells...
- Probing structural heterogeneities and fluctuations of nucleic acids and denatured proteins
Ted A Laurence
Physical Biosciences Institute, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
Proc Natl Acad Sci U S A 102:17348-53. 2005
..We propose that the larger fluctuations may indicate transient residual structure in the unfolded state...
- Random-coil behavior and the dimensions of chemically unfolded proteins
Jonathan E Kohn
Interdepartmental Program in Biomolecular Science and Engineering, University of California Santa Barbara, Santa Barbara, CA 93106, USA
Proc Natl Acad Sci U S A 101:12491-6. 2004
..588 predicted for an excluded volume random coil. Therefore, it appears that the mean dimensions of the large majority of chemically denatured proteins are effectively indistinguishable from the mean dimensions of a random-coil ensemble...
- The unfolded protein response is involved in the pathology of Alzheimer's disease
Department of Psychiatry and Behavioral Science, Osaka University Graduate School of Medicine, 2 2 Yamadaoka, Suita, Osaka 565 0871, Japan
Ann N Y Acad Sci 977:349-55. 2002
..Experimental manipulation of IRE1, PERK, or eIF2alpha phosphorylation or GRP78 expression might allow the development of therapeutic strategies for FAD...
- Identifying unfolding intermediates of FN-III(10) by steered molecular dynamics
Department of Physics and Beckman Institute, University of Illinois, Urbana 61801, USA
J Mol Biol 323:939-50. 2002
..The simulations revealed three forced unfolding pathways of FN-III(10), one of which is preferentially selected under physiological conditions. Implications for fibronectin fibrillogenesis are discussed...
- Protease-sensitive scrapie prion protein in aggregates of heterogeneous sizes
Department of Molecular Biology, The Hebrew University Hadassah Medical School, and Hadassah University Hospital, Jerusalem 91120, Israel
Biochemistry 41:12868-75. 2002
..Whether these new PrP(Sc) species play a role in the biogenesis or the pathogenesis of prions remains to be established...
- Increasing temperature accelerates protein unfolding without changing the pathway of unfolding
Department of Medicinal Chemistry, University of Washington, Seattle, WA 98195 7610, USA
J Mol Biol 322:189-203. 2002
..We conclude that 498K simulations are suitable for elucidating the details of protein unfolding at a minimum of computational expense...
- Universal antibodies and their applications to the quantitative determination of virtually all subtypes of the influenza A viral hemagglutinins
Centre for Biologics Research, Biologics and Genetic Therapies Directorate, HPFB, Health Canada, Ottawa, Ontario, Canada
Vaccine 26:6068-76. 2008
..To our knowledge, this is the first report on the quantitative determination of virtually all influenza vaccines using a single universal antibody...
- Ageing and vision: structure, stability and function of lens crystallins
Department of Biochemistry, University of Nijmegen, 6500HB, The Netherlands
Prog Biophys Mol Biol 86:407-85. 2004
..Understanding the structural basis of protein stability and interactions in the healthy eye lens is the route to solve the enormous medical and economical problem of cataract...
- Genetic dissection of the roles of chaperones and proteases in protein folding and degradation in the Escherichia coli cytosol
Institut fur Biochemie und Molekularbiologie, Universitat Freiburg, Hermann Herder Str 7, D 79104 Freiburg, Germany
Mol Microbiol 40:397-413. 2001
..At 42 degrees C, ClpXP and Lon became essential for viability of cells with low DnaK levels, indicating synergistic action of proteases and the DnaK system, which is essential for cell growth at 42 degrees C...
- Rebuilt AAA + motors reveal operating principles for ATP-fuelled machines
Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
Nature 437:1115-20. 2005
..Energy-dependent machines with highly diverse quaternary architectures and molecular functions could operate by similar asymmetric mechanisms...
- Stabilization of an immunoglobulin fold domain by an engineered disulfide bond at the buried hydrophobic region
Research Institute for Cell Engineering, National Institute of Advanced Industrial Science and Technology AIST, Ikeda, Osaka 563 8577, Japan
J Biol Chem 282:36489-95. 2007
..The introduction of a hydrophobic cystine into the hydrophobic region maintains the hydrophobicity of the protein and is expected to minimize the unfavorable mutational effects...
- The density and refractive index of adsorbing protein layers
BioInterface Group, Laboratory for Surface Science and Technology, ETH Zurich, Schlieren, Switzerland
Biophys J 87:553-61. 2004
..Our measurements indicated that water and solvent molecules not only influence the 3D structure of proteins in solution but also play a crucial role in their adsorption onto surfaces...
- Parkin suppresses unfolded protein stress-induced cell death through its E3 ubiquitin-protein ligase activity
Laboratory for Motor System Neurodegeneration, RIKEN Brain Science Institute BSI, Saitama 351 0198, Japan
J Biol Chem 275:35661-4. 2000
- Impact of the deltaF508 mutation in first nucleotide-binding domain of human cystic fibrosis transmembrane conductance regulator on domain folding and structure
Hal A Lewis
Structural GenomiX, Inc, San Diego, California 92121, USA
J Biol Chem 280:1346-53. 2005
- Invariant amino acids essential for decoding function of polypeptide release factor eRF1
Engelhardt Institute of Molecular Biology, The Russian Academy of Sciences, 119991 Moscow, Russia
Nucleic Acids Res 33:6418-25. 2005
..The data point to a pivotal role played by the YxCxxxF motif (positions 125-131) in purine discrimination of the stop codons. We speculate that eRF1 decoding site is formed by a 3D network of amino acids side chains...
- A backbone-based theory of protein folding
George D Rose
T C Jenkins Department of Biophysics, The Johns Hopkins University, Jenkins Hall, 3400 North Charles Street, Baltimore, MD 21218, USA
Proc Natl Acad Sci U S A 103:16623-33. 2006
..Then, under folding conditions, the resultant fold is selected from a limited repertoire of structural possibilities, each corresponding to a distinct hydrogen-bonded arrangement of alpha-helices and/or strands of beta-sheet...
- Rapid screening for improved solubility of small human proteins produced as fusion proteins in Escherichia coli
Department of Biotechnology, Royal Institute of Technology KTH Center for Physics, Astronomy and Biotechnology, S 106 91 Stockholm, Sweden
Protein Sci 11:313-21. 2002
- Structural basis of protein kinetic stability: resistance to sodium dodecyl sulfate suggests a central role for rigidity and a bias toward beta-sheet structure
Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, 110 8th Street, Troy, New York 12180, USA
Biochemistry 43:11248-54. 2004
..Remarkably, most of the kinetically stable SDS-resistant proteins in this study are oligomeric beta-sheet proteins, suggesting a bias of these types of structures toward kinetic stability...
- Eight prion strains have PrP(Sc) molecules with different conformations
Department of Neurology, University of California, San Francisco 94143 0518, USA
Nat Med 4:1157-65. 1998
- Type I collagen is thermally unstable at body temperature
National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
Proc Natl Acad Sci U S A 99:1314-8. 2002
..Apparently, Nature adjusts collagen hydroxyproline content to ensure that the melting temperature of triple helical monomers is several degrees below rather than above body temperature...
- Partially folded conformations in the folding pathway of bovine carbonic anhydrase II: a fluorescence spectroscopic analysis
N A Bushmarina
Institute of Cytology, Russian Academy of Sciences, Tikhoretsky Ave. 4, 194064 St. Petersburg, Russia
Chembiochem 2:813-21. 2001
- Rationalization of the effects of mutations on peptide and protein aggregation rates
Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
Nature 424:805-8. 2003
- BPPred: a Web-based computational tool for predicting biophysical parameters of proteins
Christian D Geierhaas
Department of Chemistry, University of Cambridge, UK
Protein Sci 16:125-34. 2007
..Taken together, these results suggest that BPPred should represent a valuable tool for interpreting experimental measurements, as well as the results of molecular dynamics simulations...
- Determination of the folding of proteins as a function of denaturants, osmolytes or ligands using circular dichroism
Norma J Greenfield
Department of Neuroscience and Cell Biology, Robert Wood Johnson Medical School, 675 Hoes Lane West, Piscataway, New Jersey 08854 8021, USA
Nat Protoc 1:2733-41. 2006
..The experiments require 2-5 h...
- Predicting the energetics of osmolyte-induced protein folding/unfolding
Department of Human Biological Chemistry, University of Texas Medical Branch, 301 University Boulevard, 5 154 Medical Research Building, Galveston, TX 77555 1052, USA
Proc Natl Acad Sci U S A 102:15065-8. 2005
..Moreover, the approach permits dissection of the folding/unfolding free-energy changes into individual contributions from the peptide backbone and residue side chains...
- Methylene blue inhibits amyloid Abeta oligomerization by promoting fibrillization
Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92697, USA
Biochemistry 46:8850-60. 2007
..If Abeta oligomers represent the primary pathogenic species, then inhibition of this highly toxic species via promotion of formation of less toxic aggregates may be therapeutically useful...
- Characterization of DLC1-SAM equilibrium unfolding at the amino acid residue level
Department of Chemistry, 3 Science Drive 3, Faculty of Science, National University of Singapore, Singapore 117543
Biochemistry 48:4040-9. 2009
..Analysis of the midpoints of the transitions shows that the unfolding of the native state and formation of the denatured state are not cooperative and the unfolding of only a few residues seems to follow a two-state mechanism...
- Stability and dynamics of the porcine odorant-binding protein
Institute of Protein Biochemistry, CNR, Naples, Italy
Biochemistry 46:11120-7. 2007
- A new method for determining the constant-pressure heat capacity change associated with the protein denaturation induced by guanidinium chloride (or urea)
Department of Biosciences, Jamia Millia Islamia, New Delhi 110 025, India
Biophys Chem 133:81-9. 2008
..DeltaC(p)(D) of the protein is also compared with that estimated using the known heat capacities of amino acid residues and their fractional area exposed on denaturation...
- Structural adaptations that modulate monosaccharide, disaccharide, and trisaccharide specificities in periplasmic maltose-binding proteins
Matthew J Cuneo
Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA
J Mol Biol 389:157-66. 2009
..We provide a model in which the energetics of long-range conformational equilibria controls subsite occupancy and ligand binding...
- The effect of engineered disulfide bonds on the stability of Drosophila melanogaster acetylcholinesterase
Omid Ranaei Siadat
IPBS CNRS 205 route de Narbonne, Toulouse, France
BMC Biochem 7:12. 2006
..Drosophila acetylcholinesterase is the most sensitive enzyme known and has been improved by in vitro mutagenesis. However, its stability has to be improved for extensive utilization...
- Protein denaturation and protein:drugs interactions from intrinsic protein fluorescence measurements at the nanolitre scale
Department of Biochemical Engineering, University College London, Torrington Place, London WC1E 7JE, United Kingdom
Protein Sci 19:1544-54. 2010
..The results show that 75% of the interaction energy between FKBP-12 and rapamycin originates from residue Phe99 in the binding site...
- Residue-specific description of non-native transient structures in the ensemble of acid-denatured structures of the all-beta protein c-src SH3
Heike I Rösner
Structure Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK 2200 Copenhagen N, Denmark
Biochemistry 49:3246-53. 2010
- Influence of substrate binding on the mechanical stability of mouse dihydrofolate reductase
J P Junker
Physik Department E22, Technische Universitat Munchen, D 85748 Garching, Germany
Biophys J 89:L46-8. 2005
..These experiments demonstrate that protein mechanics can be used to probe the substrate binding status of an enzyme...
- Ligand binding modulates the mechanical stability of dihydrofolate reductase
Sri Rama Koti Ainavarapu
Department of Biological Sciences, Columbia University, New York, NY, USA
Biophys J 89:3337-44. 2005
..Our observations support the view that the rate-limiting step in protein degradation by adenosine triphosphate-dependent proteases is the mechanical unfolding of the target protein...
- From the Cover: Charge interactions can dominate the dimensions of intrinsically disordered proteins
Biochemisches Institut, Universitat Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
Proc Natl Acad Sci U S A 107:14609-14. 2010
..The pronounced effect of charges on the dimensions of unfolded proteins has important implications for the cellular functions of IDPs...
- Prion disease susceptibility is affected by beta-structure folding propensity and local side-chain interactions in PrP
M Qasim Khan
Campbell Family Institute for Cancer Research, Department of Biochemistry, University of Toronto, Toronto Medical Discovery Tower 4 307, 101 College Street, Toronto, ON, Canada M5G 1L7
Proc Natl Acad Sci U S A 107:19808-13. 2010
..Removal of this capping motif increases the β-structure folding propensity of rabbit PrP to match that of PrP from mouse, a species more susceptible to prion disease...
- The equilibrium unfolding intermediate observed at pH 4 and its relationship with the kinetic folding intermediates in green fluorescent protein
Department of Physics, Graduate School of Science, University of Tokyo, 7 3 1 Hongo, Tokyo 113 0033, Japan
J Mol Biol 361:969-82. 2006
..0. These results indicate that the equilibrium unfolding intermediate is composed of an ensemble of the folding intermediate species accumulated during the folding reaction, and thus support a hierarchical model of protein folding...
- The prominent conformational plasticity of lactoperoxidase: a chemical and pH stability analysis
Dipartimento di Chimica I F M, Universita di Torino, Torino, Italy
Biochim Biophys Acta 1794:1041-8. 2009
..Overall, LPO is characterised by a high degree of peripheral structural plasticity without perturbation of the core heme moiety. The possible physiological meaning of such features is discussed...
- Detection of initiation sites in protein folding of the four helix bundle ACBP by chemical shift analysis
Structural Biology and NMR Laboratory, Department of Molecular Biology, University of Copenhagen, Copenhagen Biocenter, Ole Maaløes Vej 5, DK 2200, Copenhagen, Denmark
FEBS Lett 581:4965-71. 2007
..These findings strongly suggest transient formation of short helix-like segments, and identify unique sequence segments important for protein folding...
- Formation of on- and off-pathway intermediates in the folding kinetics of Azotobacter vinelandii apoflavodoxin
Yves J M Bollen
Department of Agrotechnology and Food Sciences, Laboratory of Biochemistry, Wageningen University, Dreijenlaan 3, NL 6703 HA Wageningen, The Netherlands
Biochemistry 43:10475-89. 2004
..The presence of such on-pathway and off-pathway intermediates in the folding kinetics of alpha-beta parallel proteins is apparently governed by protein topology...
- Force-induced unfolding of fibronectin in the extracellular matrix of living cells
Michael L Smith
Laboratory for Biologically Oriented Materials, Department of Materials, Swiss Federal Institute of Technology Zurich, Zurich, Switzerland
PLoS Biol 5:e268. 2007
..This could imply that Fn might play a significant role in mechanotransduction processes...
- Differences in the pathways of proteins unfolding induced by urea and guanidine hydrochloride: molten globule state and aggregates
Olga I Povarova
Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology of the Russian Academy of Science, St Petersburg, Russia
PLoS ONE 5:e15035. 2010
..That is why the increase in ANS fluorescence intensity is often recorded in the pathway of protein denaturation by GdnHCl, but not by urea...
- The rate of polyQ-mediated aggregation is dramatically affected by the number and location of surrounding domains
Amy L Robertson
Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3800, Australia
J Mol Biol 413:879-87. 2011
..Our experimental data, together with a bioinformatic analysis of all human proteins possessing polyQ tracts, suggest that repeat location and protein domain architecture affect the disease susceptibility of human polyQ proteins...
- Adaptive evolution of p53 thermodynamic stability
Kian Hoe Khoo
MRC Centre for Protein Engineering, Hills Road, Cambridge CB2 0QH, UK
J Mol Biol 393:161-75. 2009
..p53 from vertebrates has evolved to have a low thermodynamic stability and similarly short spontaneous half-life at organismal body temperature, which is related to function...
- The denatured state dictates the topology of two proteins with almost identical sequence but different native structure and function
Istituto Pasteur Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche A Rossi Fanelli, Universita di Roma La Sapienza, 5 00185 Rome, Italy
J Biol Chem 286:3863-72. 2011
..Our results suggest a mechanism whereby protein topology is committed very early along the folding pathway, being imprinted in the residual structure of the denatured state...