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PDBsum entry 2a3d
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protein links
Three-helix bundle PDB id
2a3d

 

 

 

 

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Contents
Protein chain
73 a.a.
PDB id:
2a3d
Name: Three-helix bundle
Title: Solution structure of a de novo designed single chain three-helix bundle (a3d)
Structure: Protein (de novo three-helix bundle). Chain: a. Engineered: yes
Source: Synthetic construct. Organism_taxid: 32630. Strain: bl21(de3). Cellular_location: cytoplasm. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Other_details: synthetic gene
NMR struc: 1 models
Authors: S.T.R.Walsh,H.Cheng,J.W.Bryson,H.Roder,W.F.Degrado
Key ref:
S.T.Walsh et al. (1999). Solution structure and dynamics of a de novo designed three-helix bundle protein. Proc Natl Acad Sci U S A, 96, 5486-5491. PubMed id: 10318910 DOI: 10.1073/pnas.96.10.5486
Date:
01-Apr-99     Release date:   05-May-99    
PROCHECK
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 Headers
 References

Protein chain
No UniProt id for this chain
Struc: 73 a.a.
Key:    Secondary structure  CATH domain

 

 
DOI no: 10.1073/pnas.96.10.5486 Proc Natl Acad Sci U S A 96:5486-5491 (1999)
PubMed id: 10318910  
 
 
Solution structure and dynamics of a de novo designed three-helix bundle protein.
S.T.Walsh, H.Cheng, J.W.Bryson, H.Roder, W.F.DeGrado.
 
  ABSTRACT  
 
Although de novo protein design is an important endeavor with implications for understanding protein folding, until now, structures have been determined for only a few 25- to 30-residue designed miniproteins. Here, the NMR solution structure of a complex 73-residue three-helix bundle protein, alpha3D, is reported. The structure of alpha3D was not based on any natural protein, and yet it shows thermodynamic and spectroscopic properties typical of native proteins. A variety of features contribute to its unique structure, including electrostatics, the packing of a diverse set of hydrophobic side chains, and a loop that incorporates common capping motifs. Thus, it is now possible to design a complex protein with a well defined and predictable three-dimensional structure.
 
  Selected figure(s)  
 
Figure 1.
Fig. 1. Sequences of the [3] family and of Coil-Ser. The residues are aligned with their corresponding heptad position in a coiled coil (26). [3]A through [3]C and Coil-Ser were chemically synthesized whereas [3]D was cloned and expressed in E. coli. The residues that are different between [3]D and [3]C are labeled in bold. 		Figure 3.
Fig. 3. (a) Stereo diagrams of the 13 superimposed [3]D structures are shown with the hydrophobic core residues depicted in red and W4 and Y45 in yellow. The structures were aligned by using only the backbone atoms (residues 4-21, 24-45, and 51-70). The figure was generated by using the program MOLMOL (58). (b) Stereo display of a ribbon diagram with the hydrophobic residues in red and W4 and Y45 in yellow of the lowest energy structure of [3]D. The figure was created by using the programs MOLSCRIPT (59) and RASTER3D (60).
 
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21156831 D.G.Metcalf, D.T.Moore, Y.Wu, J.M.Kielec, K.Molnar, K.G.Valentine, A.J.Wand, J.S.Bennett, and W.F.DeGrado (2010).
NMR analysis of the alphaIIb beta3 cytoplasmic interaction suggests a mechanism for integrin regulation.
  Proc Natl Acad Sci U S A, 107, 22481-22486.
PDB code: 2kv9
20544969 L.Dai, Y.Yang, H.R.Kim, and Y.Zhou (2010).
Improving computational protein design by using structure-derived sequence profile.
  Proteins, 78, 2338-2348.  
20822175 T.Bereau, M.Bachmann, and M.Deserno (2010).
Interplay between secondary and tertiary structure formation in protein folding cooperativity.
  J Am Chem Soc, 132, 13129-13131.  
19290357 A.F.Peacock, O.Iranzo, and V.L.Pecoraro (2009).
Harnessing natures ability to control metal ion coordination geometry using de novo designed peptides.
  Dalton Trans, (), 2271-2280.  
19548767 T.Bereau, and M.Deserno (2009).
Generic coarse-grained model for protein folding and aggregation.
  J Chem Phys, 130, 235106.  
18436954 A.Go, S.Kim, J.Baum, and M.H.Hecht (2008).
Structure and dynamics of de novo proteins from a designed superfamily of 4-helix bundles.
  Protein Sci, 17, 821-832.
PDB code: 2jua
19081056 X.Hu, H.Wang, H.Ke, and B.Kuhlman (2008).
Computer-based redesign of a beta sandwich protein suggests that extensive negative design is not required for de novo beta sheet design.
  Structure, 16, 1799-1805.
PDB code: 3b83
17510956 D.Seeliger, and B.L.de Groot (2007).
Atomic contacts in protein structures. A detailed analysis of atomic radii, packing, and overlaps.
  Proteins, 68, 595-601.  
17855563 J.López de la Osa, D.A.Bateman, S.Ho, C.González, A.Chakrabartty, and D.V.Laurents (2007).
Getting specificity from simplicity in putative proteins from the prebiotic earth.
  Proc Natl Acad Sci U S A, 104, 14941-14946.
PDB codes: 2jo4 2jo5
17097678 M.Sommerhalter, Y.Zhang, and A.C.Rosenzweig (2007).
Solution structure of the COMMD1 N-terminal domain.
  J Mol Biol, 365, 715-721.
PDB code: 2h2m
16488978 G.Chikenji, Y.Fujitsuka, and S.Takada (2006).
Shaping up the protein folding funnel by local interaction: lesson from a structure prediction study.
  Proc Natl Acad Sci U S A, 103, 3141-3146.  
16698546 N.Dobson, G.Dantas, D.Baker, and G.Varani (2006).
High-resolution structural validation of the computational redesign of human U1A protein.
  Structure, 14, 847-856.
PDB code: 2a3j
15189160 B.Gillespie, and K.W.Plaxco (2004).
Using protein folding rates to test protein folding theories.
  Annu Rev Biochem, 73, 837-859.  
15148684 C.L.Boon, D.Frost, and A.Chakrabartty (2004).
Identification of stable helical bundles from a combinatorial library of amphipathic peptides.
  Biopolymers, 76, 244-257.  
15372486 G.A.Manderson, and J.S.Johansson (2004).
Towards a three-alpha-helix bundle protein that binds volatile general anesthetics.
  Biopolymers, 75, 338-354.  
15313244 S.Park, X.Yang, and J.G.Saven (2004).
Advances in computational protein design.
  Curr Opin Struct Biol, 14, 487-494.  
15096199 Y.Bai, and H.Feng (2004).
Selection of stably folded proteins by phage-display with proteolysis.
  Eur J Biochem, 271, 1609-1614.  
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.  
14595023 M.M.Rosenblatt, J.Wang, and K.S.Suslick (2003).
De novo designed cyclic-peptide heme complexes.
  Proc Natl Acad Sci U S A, 100, 13140-13145.
PDB code: 1pbz
12592022 S.T.Walsh, R.P.Cheng, W.W.Wright, D.O.Alonso, V.Daggett, J.M.Vanderkooi, and W.F.DeGrado (2003).
The hydration of amides in helices; a comprehensive picture from molecular dynamics, IR, and NMR.
  Protein Sci, 12, 520-531.  
12737823 W.Jin, O.Kambara, H.Sasakawa, A.Tamura, and S.Takada (2003).
De novo design of foldable proteins with smooth folding funnel: automated negative design and experimental verification.
  Structure, 11, 581-590.  
12493832 Y.Wei, T.Liu, S.L.Sazinsky, D.A.Moffet, I.Pelczer, and M.H.Hecht (2003).
Stably folded de novo proteins from a designed combinatorial library.
  Protein Sci, 12, 92.  
14671331 Y.Zhu, D.O.Alonso, K.Maki, C.Y.Huang, S.J.Lahr, V.Daggett, H.Roder, W.F.DeGrado, and F.Gai (2003).
Ultrafast folding of alpha3D: a de novo designed three-helix bundle protein.
  Proc Natl Acad Sci U S A, 100, 15486-15491.  
11900551 G.A.Manderson, and J.S.Johansson (2002).
Role of aromatic side chains in the binding of volatile general anesthetics to a four-alpha-helix bundle.
  Biochemistry, 41, 4080-4087.  
12163067 J.G.Saven (2002).
Combinatorial protein design.
  Curr Opin Struct Biol, 12, 453-458.  
11979279 J.W.Neidigh, R.M.Fesinmeyer, and N.H.Andersen (2002).
Designing a 20-residue protein.
  Nat Struct Biol, 9, 425-430.
PDB code: 1l2y
11331012 A.M.Grosset, B.R.Gibney, F.Rabanal, C.C.Moser, and P.L.Dutton (2001).
Proof of principle in a de novo designed protein maquette: an allosterically regulated, charge-activated conformational switch in a tetra-alpha-helix bundle.
  Biochemistry, 40, 5474-5487.  
11288876 C.Das, S.C.Shankaramma, and P.Balaram (2001).
Molecular carpentry: piecing together helices and hairpins in designed peptides.
  Chemistry, 7, 840-847.  
11171963 N.L.Ogihara, G.Ghirlanda, J.W.Bryson, M.Gingery, W.F.DeGrado, and D.Eisenberg (2001).
Design of three-dimensional domain-swapped dimers and fibrous oligomers.
  Proc Natl Acad Sci U S A, 98, 1404-1409.
PDB code: 1g6u
11158562 U.A.Ramagopal, S.Ramakumar, D.Sahal, and V.S.Chauhan (2001).
De novo design and characterization of an apolar helical hairpin peptide at atomic resolution: Compaction mediated by weak interactions.
  Proc Natl Acad Sci U S A, 98, 870-874.  
10841536 A.Lombardi, C.M.Summa, S.Geremia, L.Randaccio, V.Pavone, and W.F.DeGrado (2000).
Inaugural article: retrostructural analysis of metalloproteins: application to the design of a minimal model for diiron proteins.
  Proc Natl Acad Sci U S A, 97, 6298-6305.
PDB code: 1ec5
11095184 C.Das, V.Nayak, S.Raghothama, and P.Balaram (2000).
Synthetic protein design: construction of a four-stranded beta-sheet structure and evaluation of its integrity in methanol-water systems.
  J Pept Res, 56, 307-317.  
  10850811 C.L.Boon, and A.Chakrabartty (2000).
Nonpolar contributions to conformational specificity in assemblies of designed short helical peptides.
  Protein Sci, 9, 1011-1023.  
  10850804 P.Barthe, S.Rochette, C.Vita, and C.Roumestand (2000).
Synthesis and NMR solution structure of an alpha-helical hairpin stapled with two disulfide bridges.
  Protein Sci, 9, 942-955.
PDB code: 1ei0
10984405 P.Forns, J.L.Lauer-Fields, S.Gao, and G.B.Fields (2000).
Induction of protein-like molecular architecture by monoalkyl hydrocarbon chains.
  Biopolymers, 54, 531-546.  
10600720 C.Micklatcher, and J.Chmielewski (1999).
Helical peptide and protein design.
  Curr Opin Chem Biol, 3, 724-729.  
  10631975 G.A.Lazar, E.C.Johnson, J.R.Desjarlais, and T.M.Handel (1999).
Rotamer strain as a determinant of protein structural specificity.
  Protein Sci, 8, 2598-2610.
PDB code: 1c3t
10580642 M.D.Smith, and G.W.Fleet (1999).
Designing secondary structures: 5-azidomethyl tetrahydrofuran-2-carboxylates as carbohydrate-derived dipeptide isosteres.
  J Pept Sci, 5, 425-441.  
  10452602 R.Li, and C.Woodward (1999).
The hydrogen exchange core and protein folding.
  Protein Sci, 8, 1571-1590.  
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.

 

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