The folding and evolution of multidomain proteins.

CFTR: folding, misfolding and correcting the ΔF508 conformational defect. Trends Mol Med (2011) 1.99

Folding versus aggregation: polypeptide conformations on competing pathways. Arch Biochem Biophys (2007) 1.97

Evolution of protein domain promiscuity in eukaryotes. Genome Res (2008) 1.82

Correction of both NBD1 energetics and domain interface is required to restore ΔF508 CFTR folding and function. Cell (2012) 1.73

The ribosome as a hub for protein quality control. Mol Cell (2013) 1.53

Cooperative assembly and misfolding of CFTR domains in vivo. Mol Biol Cell (2009) 1.31

Single-molecule fluorescence spectroscopy maps the folding landscape of a large protein. Nat Commun (2011) 1.30

Edgotype: a fundamental link between genotype and phenotype. Curr Opin Genet Dev (2013) 1.12

1,3-Propanediol dehydrogenase from Klebsiella pneumoniae: decameric quaternary structure and possible subunit cooperativity. J Bacteriol (2008) 1.11

Frustration in the energy landscapes of multidomain protein misfolding. Proc Natl Acad Sci U S A (2013) 1.06

Frustration in biomolecules. Q Rev Biophys (2014) 1.05

Ubiquitin not only serves as a tag but also assists degradation by inducing protein unfolding. Proc Natl Acad Sci U S A (2010) 1.04

Folding the proteome. Trends Biochem Sci (2013) 1.03

Stability of domain structures in multi-domain proteins. Sci Rep (2011) 1.03

Folding of a large protein at high structural resolution. Proc Natl Acad Sci U S A (2013) 1.02

The single polypeptide restriction-modification enzyme LlaGI is a self-contained molecular motor that translocates DNA loops. Nucleic Acids Res (2009) 1.02

Reshaping of the conformational search of a protein by the chaperone trigger factor. Nature (2013) 1.01

Specific interaction between tomato HsfA1 and HsfA2 creates hetero-oligomeric superactivator complexes for synergistic activation of heat stress gene expression. J Biol Chem (2009) 1.00

Domain architecture evolution of pattern-recognition receptors. Immunogenetics (2010) 0.99

What lessons can be learned from studying the folding of homologous proteins? Methods (2010) 0.97

Domain stabilities in protein kinase R (PKR): evidence for weak interdomain interactions. Biochemistry (2008) 0.97

Studying the folding of multidomain proteins. HFSP J (2008) 0.96

Superhelical architecture of the myosin filament-linking protein myomesin with unusual elastic properties. PLoS Biol (2012) 0.96

Global and local structural changes of cytochrome c and lysozyme characterized by a multigroup unfolding process. Biophys J (2008) 0.95

Cohesion group approach for evolutionary analysis of aspartokinase, an enzyme that feeds a branched network of many biochemical pathways. Microbiol Mol Biol Rev (2009) 0.94

The interrelationship of helicase and nuclease domains during DNA translocation by the molecular motor EcoR124I. J Mol Biol (2008) 0.93

Comparative analysis of evolutionary dynamics of genes encoding leucine-rich repeat receptor-like kinase between rice and Arabidopsis. Genetica (2011) 0.93

The evolution of protein structures and structural ensembles under functional constraint. Genes (Basel) (2011) 0.91

Cooperativity, connectivity, and folding pathways of multidomain proteins. Proc Natl Acad Sci U S A (2008) 0.91

Fixing cystic fibrosis by correcting CFTR domain assembly. J Cell Biol (2012) 0.90

Understanding and identifying amino acid repeats. Brief Bioinform (2014) 0.90

Combining structural modeling with ensemble machine learning to accurately predict protein fold stability and binding affinity effects upon mutation. PLoS One (2014) 0.90

The structure of a folding intermediate provides insight into differences in immunoglobulin amyloidogenicity. Proc Natl Acad Sci U S A (2008) 0.88

Take home lessons from studies of related proteins. Curr Opin Struct Biol (2012) 0.87

FIEFDom: a transparent domain boundary recognition system using a fuzzy mean operator. Nucleic Acids Res (2008) 0.87

Short linear motifs - ex nihilo evolution of protein regulation. Cell Commun Signal (2015) 0.87

Evolutionary optimization of protein folding. PLoS Comput Biol (2013) 0.86

Mechanical stability and differentially conserved physical-chemical properties of titin Ig-domains. Proteins (2009) 0.86

Distinguishing specific and nonspecific interdomain interactions in multidomain proteins. Biophys J (2007) 0.86

Efficient long-distance NMR-PRE and EPR-DEER restraints for two-domain protein structure determination. Protein Cell (2013) 0.84

Modulation of folding kinetics of repeat proteins: interplay between intra- and interdomain interactions. Biophys J (2012) 0.84

Revisiting Vitis vinifera Subtilase Gene Family: A Possible Role in Grapevine Resistance against Plasmopara viticola. Front Plant Sci (2016) 0.84

General mechanism of two-state protein folding kinetics. J Am Chem Soc (2014) 0.83

The organization of domains in proteins obeys Menzerath-Altmann's law of language. BMC Syst Biol (2015) 0.83

Concerted release of substrate domains from GroEL by ATP is demonstrated with FRET. J Mol Biol (2008) 0.82

ProRepeat: an integrated repository for studying amino acid tandem repeats in proteins. Nucleic Acids Res (2011) 0.82

Computing the origin and evolution of the ribosome from its structure - Uncovering processes of macromolecular accretion benefiting synthetic biology. Comput Struct Biotechnol J (2015) 0.82

In vitro folding and assembly of the Escherichia coli ATP-binding cassette transporter, BtuCD. J Biol Chem (2011) 0.81

A novel function prediction approach using protein overlap networks. BMC Syst Biol (2013) 0.81

The folding pathway of a single domain in a multidomain protein is not affected by its neighbouring domain. J Mol Biol (2008) 0.81

Folding pathway of a multidomain protein depends on its topology of domain connectivity. Proc Natl Acad Sci U S A (2014) 0.81

Cold denaturation of monoclonal antibodies. MAbs (2010) 0.80

Identification of inhibitors of biological interactions involving intrinsically disordered proteins. Int J Mol Sci (2015) 0.80

Prediction of protein domain boundaries from inverse covariances. Proteins (2012) 0.80

Single-molecule Force Spectroscopy Predicts a Misfolded, Domain-swapped Conformation in human γD-Crystallin Protein. J Biol Chem (2015) 0.80

Autonomous and in trans functions for the two halves of Srv2/CAP in promoting actin turnover. Cytoskeleton (Hoboken) (2014) 0.80

Circular permutation directs orthogonal assembly in complex collagen peptide mixtures. J Biol Chem (2013) 0.80

Nonspecific yet decisive: Ubiquitination can affect the native-state dynamics of the modified protein. Protein Sci (2015) 0.79

AIDA: ab initio domain assembly for automated multi-domain protein structure prediction and domain-domain interaction prediction. Bioinformatics (2015) 0.79

Functional Amyloid Signaling via the Inflammasome, Necrosome, and Signalosome: New Therapeutic Targets in Heart Failure. Front Cardiovasc Med (2015) 0.79

Probing conformational stability and dynamics of erythroid and nonerythroid spectrin: effects of urea and guanidine hydrochloride. PLoS One (2015) 0.78

How Co-translational Folding of Multi-domain Protein Is Affected by Elongation Schedule: Molecular Simulations. PLoS Comput Biol (2015) 0.78

Evolutionary history of exon shuffling. Genetica (2012) 0.78

bMERB domains are bivalent Rab8 family effectors evolved by gene duplication. Elife (2016) 0.78

Linking fold, function and phylogeny: a comparative genomics view on protein (domain) evolution. Curr Genomics (2008) 0.78

Computational approaches for predicting mutant protein stability. J Comput Aided Mol Des (2016) 0.78

Chaperones rescue luciferase folding by separating its domains. J Biol Chem (2014) 0.77

Importance of hydrophobic cavities in allosteric regulation of formylglycinamide synthetase: insight from xenon trapping and statistical coupling analysis. PLoS One (2013) 0.77

In the multi-domain protein adenylate kinase, domain insertion facilitates cooperative folding while accommodating function at domain interfaces. PLoS Comput Biol (2014) 0.77

Diversity in protein domain superfamilies. Curr Opin Genet Dev (2015) 0.77

Inferences from structural comparison: flexibility, secondary structure wobble and sequence alignment optimization. BMC Bioinformatics (2012) 0.77

Search by proteins for their DNA target site: 2. The effect of DNA conformation on the dynamics of multidomain proteins. Nucleic Acids Res (2014) 0.77

Selective forces acting during multi-domain protein evolution: the case of multi-domain globins. Springerplus (2015) 0.77

The nature of protein domain evolution: shaping the interaction network. Curr Genomics (2010) 0.77

Two immunoglobulin tandem proteins with a linking β-strand reveal unexpected differences in cooperativity and folding pathways. J Mol Biol (2011) 0.76

Thermodynamic Protein Destabilization by GFP Tagging: A Case of Interdomain Allostery. Biophys J (2015) 0.76

The role of ACT-like subdomain in bacterial threonine dehydratases. PLoS One (2014) 0.76

Folding of a cyclin box: linking multitarget binding to marginal stability, oligomerization, and aggregation of the retinoblastoma tumor suppressor AB pocket domain. J Biol Chem (2013) 0.76

Understanding pathogenic single-nucleotide polymorphisms in multidomain proteins--studies of isolated domains are not enough. FEBS J (2013) 0.76

Characterizing Aciniform Silk Repetitive Domain Backbone Dynamics and Hydrodynamic Modularity. Int J Mol Sci (2016) 0.75

Conserved prosegment residues stabilize a late-stage folding transition state of pepsin independently of ground states. PLoS One (2014) 0.75

Parkinson's disease-associated receptor GPR37 is an ER chaperone for LRP6. EMBO Rep (2017) 0.75

Network analysis of circular permutations in multidomain proteins reveals functional linkages for uncharacterized proteins. Cancer Inform (2015) 0.75

ProViz-a web-based visualization tool to investigate the functional and evolutionary features of protein sequences. Nucleic Acids Res (2016) 0.75

Changes of protein stiffness during folding detect protein folding intermediates. J Biol Phys (2013) 0.75

Single-molecule Force Spectroscopy Reveals the Calcium Dependence of the Alternative Conformations in the Native State of a βγ-Crystallin Protein. J Biol Chem (2016) 0.75

Molecular evolution of threonine dehydratase in bacteria. PLoS One (2013) 0.75

Structural Determinants of Misfolding in Multidomain Proteins. PLoS Comput Biol (2016) 0.75

Event inference in multidomain families with phylogenetic reconciliation. BMC Bioinformatics (2015) 0.75

Competing Pathways and Multiple Folding Nuclei in a Large Multidomain Protein, Luciferase. Biophys J (2017) 0.75

Structural and functional diversity of EF-hand proteins: Evolutionary perspectives. Protein Sci (2017) 0.75

Fast H-DROP: A thirty times accelerated version of H-DROP for interactive SVM-based prediction of helical domain linkers. J Comput Aided Mol Des (2016) 0.75

The ribosome destabilizes native and non-native structures in a nascent multi-domain protein. Protein Sci (2017) 0.75

Synthetic biology of modular proteins. Bioengineered (2016) 0.75

Common variants near MC4R are associated with fat mass, weight and risk of obesity. Nat Genet (2008) 15.94

Genomic analysis of regulatory network dynamics reveals large topological changes. Nature (2004) 9.32

A census of human transcription factors: function, expression and evolution. Nat Rev Genet (2009) 9.19

An atlas of combinatorial transcriptional regulation in mouse and man. Cell (2010) 6.24

Structure and evolution of transcriptional regulatory networks. Curr Opin Struct Biol (2004) 4.48

Evolution of the protein repertoire. Science (2003) 4.24

Accounting for technical noise in single-cell RNA-seq experiments. Nat Methods (2013) 3.61

Tight regulation of unstructured proteins: from transcript synthesis to protein degradation. Science (2008) 3.48

DBD--taxonomically broad transcription factor predictions: new content and functionality. Nucleic Acids Res (2007) 3.18

Evolution of transcription factors and the gene regulatory network in Escherichia coli. Nucleic Acids Res (2003) 2.87

RNA sequencing reveals two major classes of gene expression levels in metazoan cells. Mol Syst Biol (2011) 2.77

The importance of sequence diversity in the aggregation and evolution of proteins. Nature (2005) 2.70

Structure, function and evolution of multidomain proteins. Curr Opin Struct Biol (2004) 2.58

Hidden complexity in the mechanical properties of titin. Nature (2003) 2.51

DBD: a transcription factor prediction database. Nucleic Acids Res (2006) 2.46

Evolutionary dynamics of prokaryotic transcriptional regulatory networks. J Mol Biol (2006) 2.44

Targeting CXCL12 from FAP-expressing carcinoma-associated fibroblasts synergizes with anti-PD-L1 immunotherapy in pancreatic cancer. Proc Natl Acad Sci U S A (2013) 2.41

Assembly reflects evolution of protein complexes. Nature (2008) 2.27

Single-molecule studies of protein folding. Annu Rev Biochem (2008) 2.22

3D complex: a structural classification of protein complexes. PLoS Comput Biol (2006) 2.21

FlyTF: a systematic review of site-specific transcription factors in the fruit fly Drosophila melanogaster. Bioinformatics (2006) 2.13

The relationship between domain duplication and recombination. J Mol Biol (2004) 2.08

Mechanical unfolding of a titin Ig domain: structure of unfolding intermediate revealed by combining AFM, molecular dynamics simulations, NMR and protein engineering. J Mol Biol (2002) 2.00

The transcriptional program controlled by the stem cell leukemia gene Scl/Tal1 during early embryonic hematopoietic development. Blood (2009) 1.97

The immunoglobulin superfamily in Drosophila melanogaster and Caenorhabditis elegans and the evolution of complexity. Development (2003) 1.96

Evolution of protein complexes by duplication of homomeric interactions. Genome Biol (2007) 1.88

Supra-domains: evolutionary units larger than single protein domains. J Mol Biol (2004) 1.82

Polycomb associates genome-wide with a specific RNA polymerase II variant, and regulates metabolic genes in ESCs. Cell Stem Cell (2012) 1.80

Relative rates of gene fusion and fission in multi-domain proteins. Trends Genet (2005) 1.75

The origins and evolution of functional modules: lessons from protein complexes. Philos Trans R Soc Lond B Biol Sci (2006) 1.71

Parallel protein-unfolding pathways revealed and mapped. Nat Struct Biol (2003) 1.67

Versatile cloning system for construction of multimeric proteins for use in atomic force microscopy. Protein Sci (2002) 1.67

Statistical analysis of domains in interacting protein pairs. Bioinformatics (2004) 1.64

Experimental evidence for a frustrated energy landscape in a three-helix-bundle protein family. Nature (2010) 1.61

The interface of protein structure, protein biophysics, and molecular evolution. Protein Sci (2012) 1.54

Mechanical unfolding of a titin Ig domain: structure of transition state revealed by combining atomic force microscopy, protein engineering and molecular dynamics simulations. J Mol Biol (2003) 1.53

FlyTF: improved annotation and enhanced functionality of the Drosophila transcription factor database. Nucleic Acids Res (2009) 1.48

Novel specificities emerge by stepwise duplication of functional modules. Genome Res (2005) 1.47

Mechanical unfolding of proteins: insights into biology, structure and folding. Curr Opin Struct Biol (2007) 1.43

The folding of spectrin domains I: wild-type domains have the same stability but very different kinetic properties. J Mol Biol (2004) 1.40

Depletion of stromal cells expressing fibroblast activation protein-α from skeletal muscle and bone marrow results in cachexia and anemia. J Exp Med (2013) 1.40

What contributions to protein side-chain dynamics are probed by NMR experiments? A molecular dynamics simulation analysis. J Mol Biol (2005) 1.40

A simple method for probing the mechanical unfolding pathway of proteins in detail. Proc Natl Acad Sci U S A (2002) 1.39

Mechanical unfolding of TNfn3: the unfolding pathway of a fnIII domain probed by protein engineering, AFM and MD simulation. J Mol Biol (2005) 1.37

Single-molecule fluorescence reveals sequence-specific misfolding in multidomain proteins. Nature (2011) 1.37

The remarkable mechanical strength of polycystin-1 supports a direct role in mechanotransduction. J Mol Biol (2005) 1.34

Functional determinants of transcription factors in Escherichia coli: protein families and binding sites. Trends Genet (2003) 1.34

Functional protein divergence in the evolution of Homo sapiens. Genome Biol (2008) 1.32

Titin; a multidomain protein that behaves as the sum of its parts. J Mol Biol (2002) 1.30

The folding of spectrin domains II: phi-value analysis of R16. J Mol Biol (2004) 1.29

Integrated mapping, chromosomal sequencing and sequence analysis of Cryptosporidium parvum. Genome Res (2003) 1.29

Surgery or embolisation for varicoceles in subfertile men. Cochrane Database Syst Rev (2009) 1.28

Assessing computational methods of cis-regulatory module prediction. PLoS Comput Biol (2010) 1.27

The origin of protein sidechain order parameter distributions. J Am Chem Soc (2004) 1.25

BloodExpress: a database of gene expression in mouse haematopoiesis. Nucleic Acids Res (2008) 1.24

EpiChIP: gene-by-gene quantification of epigenetic modification levels. Nucleic Acids Res (2010) 1.23

Homology, pathway distance and chromosomal localization of the small molecule metabolism enzymes in Escherichia coli. J Mol Biol (2002) 1.22

The folding pathway of spectrin R17 from experiment and simulation: using experimentally validated MD simulations to characterize States hinted at by experiment. J Mol Biol (2006) 1.21

Robotic surgery for benign gynaecological disease. Cochrane Database Syst Rev (2012) 1.21

Atomic force microscopy: mechanical unfolding of proteins. Methods (2004) 1.21

Cooperative folding in a multi-domain protein. J Mol Biol (2005) 1.20

Designing an extracellular matrix protein with enhanced mechanical stability. Proc Natl Acad Sci U S A (2007) 1.19

Genomic repertoires of DNA-binding transcription factors across the tree of life. Nucleic Acids Res (2010) 1.18

The (in)dependence of alternative splicing and gene duplication. PLoS Comput Biol (2007) 1.17

Spectrin R16: broad energy barrier or sequential transition states? Protein Sci (2005) 1.16

BPPred: a Web-based computational tool for predicting biophysical parameters of proteins. Protein Sci (2006) 1.14

Divergence of interdomain geometry in two-domain proteins. Structure (2006) 1.14

Probing the diverse landscape of protein flexibility and binding. Curr Opin Struct Biol (2012) 1.14

Cellular crowding imposes global constraints on the chemistry and evolution of proteomes. Proc Natl Acad Sci U S A (2012) 1.13

Localizing internal friction along the reaction coordinate of protein folding by combining ensemble and single-molecule fluorescence spectroscopy. Nat Commun (2012) 1.13

Sequence conservation in Ig-like domains: the role of highly conserved proline residues in the fibronectin type III superfamily. J Mol Biol (2002) 1.13

Protein complexes are under evolutionary selection to assemble via ordered pathways. Cell (2013) 1.12

Folding and binding of an intrinsically disordered protein: fast, but not 'diffusion-limited'. J Am Chem Soc (2013) 1.11

Multi-domain protein families and domain pairs: comparison with known structures and a random model of domain recombination. J Struct Funct Genomics (2003) 1.10

Spectrin domains lose cooperativity in forced unfolding. Biophys J (2006) 1.08

Hydrophobic core fluidity of homologous protein domains: relation of side-chain dynamics to core composition and packing. Biochemistry (2004) 1.08

Relative solvent accessible surface area predicts protein conformational changes upon binding. Structure (2011) 1.07

The impact of genomic neighborhood on the evolution of human and chimpanzee transcriptome. Genome Res (2009) 1.06

Comparison of the transition states for folding of two Ig-like proteins from different superfamilies. J Mol Biol (2004) 1.05

Biophysical investigations of engineered polyproteins: implications for force data. Biophys J (2004) 1.04

Staphylococcal biofilm-forming protein has a contiguous rod-like structure. Proc Natl Acad Sci U S A (2012) 1.04

Fusion of contrast-enhanced breast MR and mammographic imaging data. Med Image Anal (2003) 1.03

Complex folding kinetics of a multidomain protein. Biophys J (2005) 1.02

Different members of a simple three-helix bundle protein family have very different folding rate constants and fold by different mechanisms. J Mol Biol (2009) 1.00

What can atomic force microscopy tell us about protein folding? Chem Commun (Camb) (2002) 1.00

Folding of a LysM domain: entropy-enthalpy compensation in the transition state of an ideal two-state folder. J Mol Biol (2008) 1.00

Coupled folding and binding of the disordered protein PUMA does not require particular residual structure. J Am Chem Soc (2014) 1.00

Thermodynamic characterisation of two transition states along parallel protein folding pathways. J Mol Biol (2004) 0.99

Plasticity within the obligatory folding nucleus of an immunoglobulin-like domain. J Mol Biol (2007) 0.99

Patterns of evolutionary constraints on genes in humans. BMC Evol Biol (2008) 0.99

Quantifying heterogeneity and conformational dynamics from single molecule FRET of diffusing molecules: recurrence analysis of single particles (RASP). Phys Chem Chem Phys (2011) 0.98

What lessons can be learned from studying the folding of homologous proteins? Methods (2010) 0.97

Structure, dynamics, assembly, and evolution of protein complexes. Annu Rev Biochem (2014) 0.97

Remarkably fast coupled folding and binding of the intrinsically disordered transactivation domain of cMyb to CBP KIX. J Phys Chem B (2013) 0.97

Apparent cooperativity in the folding of multidomain proteins depends on the relative rates of folding of the constituent domains. Proc Natl Acad Sci U S A (2006) 0.97