Rational coupled dynamics network manipulation rescues disease-relevant mutant cystic fibrosis transmembrane conductance regulator

A novel approach identifying networks of residues involved in trans-protein dynamic coupling is applied to rescue mutant CFTR.

[1]  Pradeep Kota,et al.  Regulatory insertion removal restores maturation, stability and function of DeltaF508 CFTR. , 2010, Journal of molecular biology.

[2]  Kevin Barraclough,et al.  I and i , 2001, BMJ : British Medical Journal.

[3]  W. P. Russ,et al.  Evolutionary information for specifying a protein fold , 2005, Nature.

[4]  J. Riordan,et al.  COPII-dependent export of cystic fibrosis transmembrane conductance regulator from the ER uses a di-acidic exit code , 2004, The Journal of cell biology.

[5]  J. Riordan,et al.  The role of cystic fibrosis transmembrane conductance regulator phenylalanine 508 side chain in ion channel gating , 2006, The Journal of physiology.

[6]  W. Balch,et al.  A di-acidic signal required for selective export from the endoplasmic reticulum. , 1997, Science.

[7]  Adrian W. R. Serohijos,et al.  Phenylalanine-508 mediates a cytoplasmic–membrane domain contact in the CFTR 3D structure crucial to assembly and channel function , 2008, Proceedings of the National Academy of Sciences.

[8]  H. Stanley,et al.  Scaling of the Distribution of Shortest Paths in Percolation , 1998, cond-mat/9908435.

[9]  W. Marsden I and J , 2012 .

[10]  J. Marshall,et al.  Defective intracellular transport and processing of CFTR is the molecular basis of most cystic fibrosis , 1990, Cell.

[11]  Amitava Roy,et al.  Long-distance correlations of rhinovirus capsid dynamics contribute to uncoating and antiviral activity , 2012, Proceedings of the National Academy of Sciences.

[12]  G. G. Stokes "J." , 1890, The New Yale Book of Quotations.

[13]  L. Tsui,et al.  Erratum: Identification of the Cystic Fibrosis Gene: Cloning and Characterization of Complementary DNA , 1989, Science.

[14]  Andrew L. Lee,et al.  Evaluation of energetic and dynamic coupling networks in a PDZ domain protein. , 2006, Journal of molecular biology.

[15]  Zhengrong Yang,et al.  Thermal unfolding studies show the disease causing F508del mutation in CFTR thermodynamically destabilizes nucleotide‐binding domain 1 , 2010, Protein science : a publication of the Protein Society.

[16]  L. Gansheroff,et al.  Mutations in the Nucleotide Binding Domain 1 Signature Motif Region Rescue Processing and Functional Defects of Cystic Fibrosis Transmembrane Conductance Regulator ΔF508* , 2002, The Journal of Biological Chemistry.

[17]  D. Thirumalai,et al.  Low-frequency normal modes that describe allosteric transitions in biological nanomachines are robust to sequence variations , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[18]  Feng Ding,et al.  Emergence of Protein Fold Families through Rational Design , 2006, PLoS Comput. Biol..

[19]  H. Stanley,et al.  Discrete molecular dynamics studies of the folding of a protein-like model. , 1998, Folding & design.

[20]  E. Schwiebert,et al.  Differential expression of ORCC and CFTR induced by low temperature in CF airway epithelial cells. , 1995, The American journal of physiology.

[21]  N. Goodey,et al.  Allosteric regulation and catalysis emerge via a common route. , 2008, Nature chemical biology.

[22]  M. Welsh,et al.  Mutation of R555 in CFTR-delta F508 enhances function and partially corrects defective processing. , 1996, Receptors & channels.

[23]  宁北芳,et al.  疟原虫var基因转换速率变化导致抗原变异[英]/Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A , 2005 .

[24]  F. Ding,et al.  Ab initio folding of proteins with all-atom discrete molecular dynamics. , 2008, Structure.

[25]  Pradeep Kota,et al.  Automated minimization of steric clashes in protein structures , 2011, Proteins.

[26]  Feng Ding,et al.  Modeling backbone flexibility improves protein stability estimation. , 2007, Structure.

[27]  Matthew P. Anderson,et al.  Processing of mutant cystic fibrosis transmembrane conductance regulator is temperature-sensitive , 1992, Nature.

[28]  J. M. Sauder,et al.  Structure and dynamics of NBD1 from CFTR characterized using crystallography and hydrogen/deuterium exchange mass spectrometry. , 2010, Journal of molecular biology.

[29]  Eugene I Shakhnovich,et al.  Expanding protein universe and its origin from the biological Big Bang , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[30]  R. Nussinov,et al.  Is allostery an intrinsic property of all dynamic proteins? , 2004, Proteins.

[31]  J. Riordan,et al.  Relationship between nucleotide binding and ion channel gating in cystic fibrosis transmembrane conductance regulator , 2009, The Journal of physiology.

[32]  Edsger W. Dijkstra,et al.  A note on two problems in connexion with graphs , 1959, Numerische Mathematik.

[33]  Miss A.O. Penney (b) , 1974, The New Yale Book of Quotations.

[34]  J. Changeux,et al.  Allosteric Mechanisms of Signal Transduction , 2005, Science.

[35]  Johanna M. Rommens,et al.  The cystic fibrosis mutation (ΔF508) does not influence the chloride channel activity of CFTR , 1993, Nature Genetics.

[36]  R. Ranganathan,et al.  Evolutionarily conserved pathways of energetic connectivity in protein families. , 1999, Science.

[37]  R. Rosenfeld Nature , 2009, Otolaryngology--head and neck surgery : official journal of American Academy of Otolaryngology-Head and Neck Surgery.

[38]  Nikolay V. Dokholyan,et al.  Multiple Membrane-Cytoplasmic Domain Contacts in the Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) Mediate Regulation of Channel Gating* , 2008, Journal of Biological Chemistry.

[39]  A. Markham,et al.  A deletion mutation of the cystic fibrosis transmembrane conductance regulator (CFTR) locus: Delta I507. , 1991, Advances in experimental medicine and biology.

[40]  J. Riordan,et al.  Protein kinase A (PKA) still activates CFTR chloride channel after mutagenesis of all 10 PKA consensus phosphorylation sites. , 1993, The Journal of biological chemistry.

[41]  G Schreiber,et al.  Energetics of protein-protein interactions: analysis of the barnase-barstar interface by single mutations and double mutant cycles. , 1995, Journal of molecular biology.

[42]  N. Dokholyan,et al.  Highly Covarying Residues Have a Functional Role in Antibody Constant Domains , 2022 .

[43]  E. Shakhnovich,et al.  Understanding hierarchical protein evolution from first principles. , 2001, Journal of molecular biology.

[44]  Zhengrong Yang,et al.  Integrated biophysical studies implicate partial unfolding of NBD1 of CFTR in the molecular pathogenesis of F508del cystic fibrosis , 2010, Protein science : a publication of the Protein Society.

[45]  H. A. Berger,et al.  Identification of revertants for the cystic fibrosis ΔF508 mutation using STE6-CFTR chimeras in yeast , 1993, Cell.

[46]  R. Ebright,et al.  Dynamically driven protein allostery , 2006, Nature Structural &Molecular Biology.

[47]  Charalampos G. Kalodimos,et al.  Dynamic activation of an allosteric regulatory protein , 2009, Nature.

[48]  Shuangye Yin,et al.  Eris: an automated estimator of protein stability , 2007, Nature Methods.

[49]  Ruth Nussinov,et al.  A Unified View of “How Allostery Works” , 2014, PLoS Comput. Biol..

[50]  Feng Ding,et al.  Multiscale modeling of nucleosome dynamics. , 2007, Biophysical journal.

[51]  Philip J. Thomas,et al.  The Primary Folding Defect and Rescue of ΔF508 CFTR Emerge during Translation of the Mutant Domain , 2010, PloS one.

[52]  John F Hunt,et al.  Cooperative, ATP-dependent Association of the Nucleotide Binding Cassettes during the Catalytic Cycle of ATP-binding Cassette Transporters* , 2002, The Journal of Biological Chemistry.

[53]  Pradeep Kota,et al.  Allosteric modulation balances thermodynamic stability and restores function of ΔF508 CFTR. , 2012, Journal of molecular biology.

[54]  Gürol M. Süel,et al.  Evolutionarily conserved networks of residues mediate allosteric communication in proteins , 2003, Nature Structural Biology.

[55]  F. Collins,et al.  Chloride conductance expressed by delta F508 and other mutant CFTRs in Xenopus oocytes. , 1991, Science.

[56]  J. Wells,et al.  Searching for new allosteric sites in enzymes. , 2004, Current opinion in structural biology.