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PDBsum entry 1e0m

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De novo protein PDB id
1e0m
Jmol
Contents
Protein chain
37 a.a. *
* Residue conservation analysis
PDB id:
1e0m
Name: De novo protein
Title: Prototype ww domain
Structure: Wwprototype. Chain: a. Fragment: domain. Engineered: yes
Source: Expressed in: escherichia coli. Expression_system_taxid: 562. Other_details: synthetic gene
NMR struc: 10 models
Authors: M.J.Macias,V.Gervais,C.Civera,H.Oschkinat
Key ref:
M.J.Macias et al. (2000). Structural analysis of WW domains and design of a WW prototype. Nat Struct Biol, 7, 375-379. PubMed id: 10802733 DOI: 10.1038/75144
Date:
01-Apr-00     Release date:   20-Apr-00    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
No UniProt id for this chain
Struc: 37 a.a.
Key:    Secondary structure

 

 
DOI no: 10.1038/75144 Nat Struct Biol 7:375-379 (2000)
PubMed id: 10802733  
 
 
Structural analysis of WW domains and design of a WW prototype.
M.J.Macias, V.Gervais, C.Civera, H.Oschkinat.
 
  ABSTRACT  
 
Two new NMR structures of WW domains, the mouse formin binding protein and a putative 84.5 kDa protein from Saccharomyces cerevisiae, show that this domain, only 35 amino acids in length, defines the smallest monomeric triple-stranded antiparallel beta-sheet protein domain that is stable in the absence of disulfide bonds, tightly bound ions or ligands. The structural roles of conserved residues have been studied using site-directed mutagenesis of both wild type domains. Crucial interactions responsible for the stability of the WW structure have been identified. Based on a network of highly conserved long range interactions across the beta-sheet structure that supports the WW fold and on a systematic analysis of conserved residues in the WW family, we have designed a folded prototype WW sequence.
 
  Selected figure(s)  
 
Figure 2.
Figure 2. Pattern of secondary structure NOEs observed for Yap65WW (black), FBP28WW (green), YJQ8WW (red) and the WW prototype (blue). Arrows with asterisks denote undetected NOEs in the spectra of YJQ8WW. Hydrogen bonds (orange dotted lines) correspond to slow 2H[2]O/H[2]O exchanging amides of Yap65WW and FBP28WW. Residue numbers correspond to the constructs used for the structural studies. For the Yap65WW sequence, residue numbers are as in the published structure^7.
Figure 3.
Figure 3. Structures of the a, FBP28WW, b, YJQ8WW, and c, WW prototype domains. Stereo views showing the backbone superposition of 10 NMR structures selected on the basis of minimal total energy for FBP28WW (green), YJQ8WW (red) and the WW prototype (blue) are shown on the left. Selected conserved residues are shown in blue. Cartoon representations of the minimal energy structures are shown on the right.
 
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (2000, 7, 375-379) copyright 2000.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
  21365688 J.Xu, L.Huang, and E.I.Shakhnovich (2011).
The ensemble folding kinetics of the FBP28 WW domain revealed by an all-atom Monte Carlo simulation in a knowledge-based potential.
  Proteins, 79, 1704-1714.  
21051320 R.D.Schaeffer, and V.Daggett (2011).
Protein folds and protein folding.
  Protein Eng Des Sel, 24, 11-19.  
20166738 G.G.Maisuradze, P.Senet, C.Czaplewski, A.Liwo, and H.A.Scheraga (2010).
Investigation of protein folding by coarse-grained molecular dynamics with the UNRES force field.
  J Phys Chem A, 114, 4471-4485.  
20401924 I.Coin (2010).
The depsipeptide method for solid-phase synthesis of difficult peptides.
  J Pept Sci, 16, 223-230.  
20159161 J.Juraszek, and P.G.Bolhuis (2010).
(Un)Folding mechanisms of the FBP28 WW domain in explicit solvent revealed by multiple rare event simulation methods.
  Biophys J, 98, 646-656.  
20949088 Q.S.Du, C.H.Wang, S.M.Liao, and R.B.Huang (2010).
Correlation analysis for protein evolutionary family based on amino acid position mutations and application in PDZ domain.
  PLoS One, 5, e13207.  
  20017135 U.Kozłowska, G.G.Maisuradze, A.Liwo, and H.A.Scheraga (2010).
Determination of side-chain-rotamer and side-chain and backbone virtual-bond-stretching potentials of mean force from AM1 energy surfaces of terminally-blocked amino-acid residues, for coarse-grained simulations of protein structure and folding. II. Results, comparison with statistical potentials, and implementation in the UNRES force field.
  J Comput Chem, 31, 1154-1167.  
20007785 C.T.Wong Po Foo, J.S.Lee, W.Mulyasasmita, A.Parisi-Amon, and S.C.Heilshorn (2009).
Two-component protein-engineered physical hydrogels for cell encapsulation.
  Proc Natl Acad Sci U S A, 106, 22067-22072.  
19658975 G.G.Maisuradze, A.Liwo, and H.A.Scheraga (2009).
How adequate are one- and two-dimensional free energy landscapes for protein folding dynamics?
  Phys Rev Lett, 102, 238102.  
18952103 G.G.Maisuradze, A.Liwo, and H.A.Scheraga (2009).
Principal component analysis for protein folding dynamics.
  J Mol Biol, 385, 312-329.  
19565466 M.Jäger, M.Dendle, and J.W.Kelly (2009).
Sequence determinants of thermodynamic stability in a WW domain--an all-beta-sheet protein.
  Protein Sci, 18, 1806-1813.  
19399235 V.A.Voelz, E.Luttmann, G.R.Bowman, and V.S.Pande (2009).
Probing the nanosecond dynamics of a designed three-stranded Beta-sheet with a massively parallel molecular dynamics simulation.
  Int J Mol Sci, 10, 1013-1030.  
19592703 X.Huang, M.Beullens, J.Zhang, Y.Zhou, E.Nicolaescu, B.Lesage, Q.Hu, J.Wu, M.Bollen, and Y.Shi (2009).
Structure and function of the two tandem WW domains of the pre-mRNA splicing factor FBP21 (formin-binding protein 21).
  J Biol Chem, 284, 25375-25387.
PDB code: 2jxw
18942730 X.Periole, L.R.Allen, K.Tamiola, A.E.Mark, and E.Paci (2009).
Probing the free energy landscape of the FBP28WW domain using multiple techniques.
  J Comput Chem, 30, 1059-1068.  
19242966 Y.He, Y.Xiao, A.Liwo, and H.A.Scheraga (2009).
Exploring the parameter space of the coarse-grained UNRES force field by random search: selecting a transferable medium-resolution force field.
  J Comput Chem, 30, 2127-2135.  
17847091 A.F.Pereira de Araújo, A.L.Gomes, A.A.Bursztyn, and E.I.Shakhnovich (2008).
Native atomic burials, supplemented by physically motivated hydrogen bond constraints, contain sufficient information to determine the tertiary structure of small globular proteins.
  Proteins, 70, 971-983.  
18161737 H.Heise (2008).
Solid-state NMR spectroscopy of amyloid proteins.
  Chembiochem, 9, 179-189.  
20011673 H.Shen, C.Czaplewski, A.Liwo, and H.A.Scheraga (2008).
Implementation of a Serial Replica Exchange Method in a Physics-Based United-Residue (UNRES) Force Field.
  J Chem Theory Comput, 4, 1386-1400.  
18642254 J.Becker, N.Ferguson, J.Flinders, B.J.van Rossum, A.R.Fersht, and H.Oschkinat (2008).
A sequential assignment procedure for proteins that have intermediate line widths in MAS NMR spectra: amyloid fibrils of human CA150.WW2.
  Chembiochem, 9, 1946-1952.  
18242977 R.D.Schaeffer, A.Fersht, and V.Daggett (2008).
Combining experiment and simulation in protein folding: closing the gap for small model systems.
  Curr Opin Struct Biol, 18, 4-9.  
17905840 T.R.Weikl (2008).
Transition states in protein folding kinetics: modeling phi-values of small beta-sheet proteins.
  Biophys J, 94, 929-937.  
17099082 A.Fleissner, and N.L.Glass (2007).
SO, a protein involved in hyphal fusion in Neurospora crassa, localizes to septal plugs.
  Eukaryot Cell, 6, 84-94.  
17211889 F.Dulin, I.Callebaut, N.Colloc'h, and J.P.Mornon (2007).
Sequence-based modeling of Abeta42 soluble oligomers.
  Biopolymers, 85, 422-437.  
18079725 I.Coin, M.Beyermann, and M.Bienert (2007).
Solid-phase peptide synthesis: from standard procedures to the synthesis of difficult sequences.
  Nat Protoc, 2, 3247-3256.  
17600832 J.Maupetit, P.Tuffery, and P.Derreumaux (2007).
A coarse-grained protein force field for folding and structure prediction.
  Proteins, 69, 394-408.  
17355961 M.Brucet, J.Querol-Audí, M.Serra, X.Ramirez-Espain, K.Bertlik, L.Ruiz, J.Lloberas, M.J.Macias, I.Fita, and A.Celada (2007).
Structure of the dimeric exonuclease TREX1 in complex with DNA displays a proline-rich binding site for WW Domains.
  J Biol Chem, 282, 14547-14557.
PDB codes: 2o4g 2o4i
17586778 M.Jäger, H.Nguyen, M.Dendle, M.Gruebele, and J.W.Kelly (2007).
Influence of hPin1 WW N-terminal domain boundaries on function, protein stability, and folding.
  Protein Sci, 16, 1495-1501.  
17766370 T.Sharpe, A.L.Jonsson, T.J.Rutherford, V.Daggett, and A.R.Fersht (2007).
The role of the turn in beta-hairpin formation during WW domain folding.
  Protein Sci, 16, 2233-2239.  
17513360 Z.Luo, J.Ding, and Y.Zhou (2007).
Temperature-dependent folding pathways of Pin1 WW domain: an all-atom molecular dynamics simulation of a Gō model.
  Biophys J, 93, 2152-2161.  
16963647 A.M.Fernández-Escamilla, S.Ventura, L.Serrano, and M.A.Jiménez (2006).
Design and NMR conformational study of a beta-sheet peptide based on Betanova and WW domains.
  Protein Sci, 15, 2278-2289.  
16575938 J.Przezdziak, S.Tremmel, I.Kretzschmar, M.Beyermann, M.Bienert, and R.Volkmer-Engert (2006).
Probing the ligand-binding specificity and analyzing the folding state of SPOT-synthesized FBP28 WW domain variants.
  Chembiochem, 7, 780-788.  
16807295 M.Jäger, Y.Zhang, J.Bieschke, H.Nguyen, M.Dendle, M.E.Bowman, J.P.Noel, M.Gruebele, and J.W.Kelly (2006).
Structure-function-folding relationship in a WW domain.
  Proc Natl Acad Sci U S A, 103, 10648-10653.
PDB codes: 1zcn 2f21
18797518 M.Nanias, C.Czaplewski, and H.A.Scheraga (2006).
Replica Exchange and Multicanonical Algorithms with the coarse-grained UNRES force field.
  J Chem Theory Comput, 2, 513-528.  
17060612 N.Ferguson, J.Becker, H.Tidow, S.Tremmel, T.D.Sharpe, G.Krause, J.Flinders, M.Petrovich, J.Berriman, H.Oschkinat, and A.R.Fersht (2006).
General structural motifs of amyloid protofilaments.
  Proc Natl Acad Sci U S A, 103, 16248-16253.
PDB code: 2nnt
16463264 Y.Kato, Y.Hino, K.Nagata, and M.Tanokura (2006).
Solution structure and binding specificity of FBP11/HYPA WW domain as Group-II/III.
  Proteins, 63, 227-234.
PDB code: 1zr7
16533840 Y.Mu, L.Nordenskiöld, and J.P.Tam (2006).
Folding, misfolding, and amyloid protofibril formation of WW domain FBP28.
  Biophys J, 90, 3983-3992.  
15677316 A.Liwo, M.Khalili, and H.A.Scheraga (2005).
Ab initio simulations of protein-folding pathways by molecular dynamics with the united-residue model of polypeptide chains.
  Proc Natl Acad Sci U S A, 102, 2362-2367.  
16080152 J.A.Vila, D.R.Ripoll, Y.A.Arnautova, Y.N.Vorobjev, and H.A.Scheraga (2005).
Coupling between conformation and proton binding in proteins.
  Proteins, 61, 56-68.  
16088925 M.Nanias, M.Chinchio, S.Ołdziej, C.Czaplewski, and H.A.Scheraga (2005).
Protein structure prediction with the UNRES force-field using Replica-Exchange Monte Carlo-with-Minimization; Comparison with MCM, CSA, and CFMC.
  J Comput Chem, 26, 1472-1486.  
15977271 S.Tremmel, M.Beyermann, H.Oschkinat, M.Bienert, D.Naumann, and H.Fabian (2005).
13C-labeled tyrosine residues as local IR probes for monitoring conformational changes in peptides and proteins.
  Angew Chem Int Ed Engl, 44, 4631-4635.  
15044739 C.M.Santiveri, J.Santoro, M.Rico, and M.A.Jiménez (2004).
Factors involved in the stability of isolated beta-sheets: Turn sequence, beta-sheet twisting, and hydrophobic surface burial.
  Protein Sci, 13, 1134-1147.  
15180901 H.Mira, M.Vilar, V.Esteve, M.Martinell, M.J.Kogan, E.Giralt, D.Salom, I.Mingarro, L.Peñarrubia, and E.Pérez-Payá (2004).
Ionic self-complementarity induces amyloid-like fibril formation in an isolated domain of a plant copper metallochaperone protein.
  BMC Struct Biol, 4, 7.  
14981252 J.Karanicolas, and C.L.Brooks (2004).
Integrating folding kinetics and protein function: biphasic kinetics and dual binding specificity in a WW domain.
  Proc Natl Acad Sci U S A, 101, 3432-3437.  
15152081 L.K.Mosavi, T.J.Cammett, D.C.Desrosiers, and Z.Y.Peng (2004).
The ankyrin repeat as molecular architecture for protein recognition.
  Protein Sci, 13, 1435-1448.  
15139812 M.B.Yaffe, and S.J.Smerdon (2004).
The use of in vitro peptide-library screens in the analysis of phosphoserine/threonine-binding domain structure and function.
  Annu Rev Biophys Biomol Struct, 33, 225-244.  
15173166 O.Y.Fedoroff, S.A.Townson, A.P.Golovanov, M.Baron, and J.M.Avis (2004).
The structure and dynamics of tandem WW domains in a negative regulator of notch signaling, Suppressor of deltex.
  J Biol Chem, 279, 34991-35000.
PDB code: 1tk7
14760739 P.Forrer, H.K.Binz, M.T.Stumpp, and A.Plückthun (2004).
Consensus design of repeat proteins.
  Chembiochem, 5, 183-189.  
14500877 C.M.Kraemer-Pecore, J.T.Lecomte, and J.R.Desjarlais (2003).
A de novo redesign of the WW domain.
  Protein Sci, 12, 2194-2205.  
12737816 E.R.Main, Y.Xiong, M.J.Cocco, L.D'Andrea, and L.Regan (2003).
Design of stable alpha-helical arrays from an idealized TPR motif.
  Structure, 11, 497-508.
PDB codes: 1na0 1na3
12651955 H.Nguyen, M.Jager, A.Moretto, M.Gruebele, and J.W.Kelly (2003).
Tuning the free-energy landscape of a WW domain by temperature, mutation, and truncation.
  Proc Natl Acad Sci U S A, 100, 3948-3953.  
12737814 K.W.Tripp, and D.Barrick (2003).
Folding by consensus.
  Structure, 11, 486-487.  
12592019 L.Otte, U.Wiedemann, B.Schlegel, J.R.Pires, M.Beyermann, P.Schmieder, G.Krause, R.Volkmer-Engert, J.Schneider-Mergener, and H.Oschkinat (2003).
WW domain sequence activity relationships identified using ligand recognition propensities of 42 WW domains.
  Protein Sci, 12, 491-500.  
12897238 N.Ferguson, J.Berriman, M.Petrovich, T.D.Sharpe, J.T.Finch, and A.R.Fersht (2003).
Rapid amyloid fiber formation from the fast-folding WW domain FBP28.
  Proc Natl Acad Sci U S A, 100, 9814-9819.  
12654927 P.C.Henry, V.Kanelis, M.C.O'Brien, B.Kim, I.Gautschi, J.Forman-Kay, L.Schild, and D.Rotin (2003).
Affinity and specificity of interactions between Nedd4 isoforms and the epithelial Na+ channel.
  J Biol Chem, 278, 20019-20028.  
12471608 T.Wang, and R.C.Wade (2003).
Implicit solvent models for flexible protein-protein docking by molecular dynamics simulation.
  Proteins, 50, 158-169.  
11786999 J.A.Kowalski, K.Liu, and J.W.Kelly (2002).
NMR solution structure of the isolated Apo Pin1 WW domain: comparison to the x-ray crystal structures of Pin1.
  Biopolymers, 63, 111-121.
PDB code: 2kcf
12461176 L.K.Mosavi, D.L.Minor, and Z.Y.Peng (2002).
Consensus-derived structural determinants of the ankyrin repeat motif.
  Proc Natl Acad Sci U S A, 99, 16029-16034.
PDB codes: 1n0q 1n0r
12181311 P.M.Irusta, Y.Luo, O.Bakht, C.C.Lai, S.O.Smith, and D.DiMaio (2002).
Definition of an inhibitory juxtamembrane WW-like domain in the platelet-derived growth factor beta receptor.
  J Biol Chem, 277, 38627-38634.  
12163066 W.P.Russ, and R.Ranganathan (2002).
Knowledge-based potential functions in protein design.
  Curr Opin Struct Biol, 12, 447-452.  
11604498 A.C.Goldstrohm, T.R.Albrecht, C.Suñé, M.T.Bedford, and M.A.Garcia-Blanco (2001).
The transcription elongation factor CA150 interacts with RNA polymerase II and the pre-mRNA splicing factor SF1.
  Mol Cell Biol, 21, 7617-7628.  
11562945 F.Forcellino, and P.Derreumaux (2001).
Computer simulations aimed at structure prediction of supersecondary motifs in proteins.
  Proteins, 45, 159-166.  
11241639 F.Toepert, J.R.Pires, C.Landgraf, H.Oschkinat, and J.Schneider-Mergener (2001).
Synthesis of an Array Comprising 837 Variants of the hYAP WW Protein Domain This work was supported by the DFG (INK 16/B1-1), by the Fonds der Chemischen Industrie, and by the Universitätsklinikum Charité Berlin.
  Angew Chem Int Ed Engl, 40, 897-900.  
11306348 J.Kasanov, G.Pirozzi, A.J.Uveges, and B.K.Kay (2001).
Characterizing Class I WW domains defines key specificity determinants and generates mutant domains with novel specificities.
  Chem Biol, 8, 231-241.  
11687613 N.Ferguson, C.M.Johnson, M.Macias, H.Oschkinat, and A.Fersht (2001).
Ultrafast folding of WW domains without structured aromatic clusters in the denatured state.
  Proc Natl Acad Sci U S A, 98, 13002-13007.  
11687614 N.Ferguson, J.R.Pires, F.Toepert, C.M.Johnson, Y.P.Pan, R.Volkmer-Engert, J.Schneider-Mergener, V.Daggett, H.Oschkinat, and A.Fersht (2001).
Using flexible loop mimetics to extend phi-value analysis to secondary structure interactions.
  Proc Natl Acad Sci U S A, 98, 13008-13013.
PDB code: 1k5r
  11179425 R.Dunn, and L.Hicke (2001).
Domains of the Rsp5 ubiquitin-protein ligase required for receptor-mediated and fluid-phase endocytosis.
  Mol Biol Cell, 12, 421-435.  
11420447 X.Jiang, J.Kowalski, and J.W.Kelly (2001).
Increasing protein stability using a rational approach combining sequence homology and structural alignment: Stabilizing the WW domain.
  Protein Sci, 10, 1454-1465.  
11206058 P.A.Dalby, R.H.Hoess, and W.F.DeGrado (2000).
Evolution of binding affinity in a WW domain probed by phage display.
  Protein Sci, 9, 2366-2376.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.