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PDBsum entry 4hb1
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Designed helical bundle PDB id
4hb1

 

 

 

 

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Contents
Protein chain
44 a.a.
Ligands
UNX ×2
Waters ×2
PDB id:
4hb1
Name: Designed helical bundle
Title: A designed four helix bundle protein.
Structure: Dhp1. Chain: a. Engineered: yes. Other_details: de novo design a 108 amino acid protein was designed and constructed from a reduced alphabet of seven amino acids. The 2.9 angstrom crystal structure confirms that the protein is a four helix bundle, as it was designed to be. The complete 108 residue sequence is presented on seqres records below. The helices were connected by loops of 3, 4, 3 glycines, respectively. The molecule contains a
Source: Synthetic construct. Organism_taxid: 32630. Gene: synthetic gene dhp1. Expressed in: escherichia coli. Expression_system_taxid: 562. Other_details: de novo designed four helix bundle protein
Biol. unit: Dimer (from PDB file)
Resolution:
2.90Å     R-factor:   0.234     R-free:   0.284
Authors: C.E.Schafmeister,S.L.Laporte,L.J.W.Miercke,R.M.Stroud
Key ref: C.E.Schafmeister et al. (1997). A designed four helix bundle protein with native-like structure. Nat Struct Biol, 4, 1039-1046. PubMed id: 9406555
Date:
10-Nov-97     Release date:   04-Mar-98    
PROCHECK
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 Headers
 References

Protein chain
No UniProt id for this chain
Struc: 44 a.a.
Key:    Secondary structure  CATH domain

 

 
Nat Struct Biol 4:1039-1046 (1997)
PubMed id: 9406555  
 
 
A designed four helix bundle protein with native-like structure.
C.E.Schafmeister, S.L.LaPorte, L.J.Miercke, R.M.Stroud.
 
  ABSTRACT  
 
A 108 amino acid protein was designed and constructed from a reduced alphabet of seven amino acids. The 2.9 A resolution X-ray crystal structure confirms that the protein is a four helix bundle, as it was designed to be. Hydrogen/deuterium exchange experiments reveal buried amide protons with protection factors in excess of 1 x 10(6) in the range characteristic of well protected protons in functional folded proteins (10(3)-10(8)) rather than protons in rapid exchange (0-10(2)). The protein is monomeric at 1 mM, the concentration at which the exchange experiments were undertaken, indicating that the exchange factors are due to a unique stable tertiary structure fold, and not due to any higher order quaternary structure. Thermodynamic analysis provides an estimate of the free energy of folding of -9.3 kcal mole-1 at 25 degrees C, consistent with the free energy of folding derived from the protection factors of the most protected protons, indicating that global unfolding is required for exchange of the most protected protons.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
19937649 G.Bellesia, A.I.Jewett, and J.E.Shea (2010).
Sequence periodicity and secondary structure propensity in model proteins.
  Protein Sci, 19, 141-154.  
19351620 E.L.Peterson, J.Kondev, J.A.Theriot, and R.Phillips (2009).
Reduced amino acid alphabets exhibit an improved sensitivity and selectivity in fold assignment.
  Bioinformatics, 25, 1356-1362.  
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.  
19367367 T.S.Kang, and R.M.Kini (2009).
Structural determinants of protein folding.
  Cell Mol Life Sci, 66, 2341-2361.  
18829434 M.M.Islam, S.Sohya, K.Noguchi, M.Yohda, and Y.Kuroda (2008).
Crystal structure of an extensively simplified variant of bovine pancreatic trypsin inhibitor in which over one-third of the residues are alanines.
  Proc Natl Acad Sci U S A, 105, 15334-15339.
PDB codes: 2zjx 3ci7
18676973 M.N.Davies, A.Secker, A.A.Freitas, E.Clark, J.Timmis, and D.R.Flower (2008).
Optimizing amino acid groupings for GPCR classification.
  Bioinformatics, 24, 1980-1986.  
18830805 R.Razeghifard (2008).
Artificial photoactive proteins.
  Photosynth Res, 98, 677-685.  
17572080 K.A.Dill, S.B.Ozkan, T.R.Weikl, J.D.Chodera, and V.A.Voelz (2007).
The protein folding problem: when will it be solved?
  Curr Opin Struct Biol, 17, 342-346.  
17609939 S.J.Shepherd, C.B.Beggs, and S.Jones (2007).
Amino acid partitioning using a Fiedler vector model.
  Eur Biophys J, 37, 105-109.  
16506243 F.Melo, and M.A.Marti-Renom (2006).
Accuracy of sequence alignment and fold assessment using reduced amino acid alphabets.
  Proteins, 63, 986-995.  
16584182 M.K.Yadav, L.J.Leman, D.J.Price, C.L.Brooks, C.D.Stout, and M.R.Ghadiri (2006).
Coiled coils at the edge of configurational heterogeneity. Structural analyses of parallel and antiparallel homotetrameric coiled coils reveal configurational sensitivity to a single solvent-exposed amino acid substitution.
  Biochemistry, 45, 4463-4473.
PDB codes: 1w5h 1w5j 1w5k 1w5l 2cce 2ccf 2ccn
16144843 K.U.Walter, K.Vamvaca, and D.Hilvert (2005).
An active enzyme constructed from a 9-amino acid alphabet.
  J Biol Chem, 280, 37742-37746.  
16193455 Rudresh, M.Gupta, S.Ramakumar, and V.S.Chauhan (2005).
Helix packing motif common to the crystal structures of two undecapeptides containing dehydrophenylalanine residues: implications for the de novo design of helical bundle super secondary structural modules.
  Biopolymers, 80, 617-627.  
15684085 S.L.Laporte, C.M.Forsyth, B.C.Cunningham, L.J.Miercke, D.Akhavan, and R.M.Stroud (2005).
De novo design of an IL-4 antagonist and its structure at 1.9 A.
  Proc Natl Acad Sci U S A, 102, 1889-1894.
PDB code: 1y4c
15300830 C.J.Weston, C.H.Cureton, M.J.Calvert, O.S.Smart, and R.K.Allemann (2004).
A stable miniature protein with oxaloacetate decarboxylase activity.
  Chembiochem, 5, 1075-1080.  
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.  
15096199 Y.Bai, and H.Feng (2004).
Selection of stably folded proteins by phage-display with proteolysis.
  Eur J Biochem, 271, 1609-1614.  
12649436 Q.Yi, P.Rajagopal, R.E.Klevit, and D.Baker (2003).
Structural and kinetic characterization of the simplified SH3 domain FP1.
  Protein Sci, 12, 776-783.  
12361984 S.Akanuma, T.Kigawa, and S.Yokoyama (2002).
Combinatorial mutagenesis to restrict amino acid usage in an enzyme to a reduced set.
  Proc Natl Acad Sci U S A, 99, 13549-13553.  
12241213 X.Liu, D.Liu, J.Qi, and W.M.Zheng (2002).
Simplified amino acid alphabets based on deviation of conditional probability from random background.
  Phys Rev E Stat Nonlin Soft Matter Phys, 66, 021906.  
11288876 C.Das, S.C.Shankaramma, and P.Balaram (2001).
Molecular carpentry: piecing together helices and hairpins in designed peptides.
  Chemistry, 7, 840-847.  
11551463 L.Baltzer, and J.Nilsson (2001).
Emerging principles of de novo catalyst design.
  Curr Opin Biotechnol, 12, 355-360.  
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
  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
11087311 R.B.Hill, D.P.Raleigh, A.Lombardi, and W.F.DeGrado (2000).
De novo design of helical bundles as models for understanding protein folding and function.
  Acc Chem Res, 33, 745-754.  
10801318 Y.Isogai, A.Ishii, T.Fujisawa, M.Ota, and K.Nishikawa (2000).
Redesign of artificial globins: effects of residue replacements at hydrophobic sites on the structural properties.
  Biochemistry, 39, 5683-5690.  
  10493590 B.R.Gibney, and P.L.Dutton (1999).
Histidine placement in de novo-designed heme proteins.
  Protein Sci, 8, 1888-1898.  
10449377 C.M.Summa, A.Lombardi, M.Lewis, and W.F.DeGrado (1999).
Tertiary templates for the design of diiron proteins.
  Curr Opin Struct Biol, 9, 500-508.  
10393541 F.Arnesano, L.Banci, I.Bertini, J.Faraone-Mennella, A.Rosato, P.D.Barker, and A.R.Fersht (1999).
The solution structure of oxidized Escherichia coli cytochrome b562.
  Biochemistry, 38, 8657-8670.
PDB code: 1qpu
  10386867 K.A.Dill (1999).
Polymer principles and protein folding.
  Protein Sci, 8, 1166-1180.  
10567389 R.G.Maroun, D.Krebs, S.El Antri, A.Deroussent, E.Lescot, F.Troalen, H.Porumb, M.E.Goldberg, and S.Fermandjian (1999).
Self-association and domains of interactions of an amphipathic helix peptide inhibitor of HIV-1 integrase assessed by analytical ultracentrifugation and NMR experiments in trifluoroethanol/H(2)O mixtures.
  J Biol Chem, 274, 34174-34185.  
  10210186 S.Nautiyal, and T.Alber (1999).
Crystal structure of a designed, thermostable, heterotrimeric coiled coil.
  Protein Sci, 8, 84-90.
PDB code: 1bb1
10318910 S.T.Walsh, H.Cheng, J.W.Bryson, H.Roder, and W.F.DeGrado (1999).
Solution structure and dynamics of a de novo designed three-helix bundle protein.
  Proc Natl Acad Sci U S A, 96, 5486-5491.
PDB code: 2a3d
10872466 W.F.DeGrado, C.M.Summa, V.Pavone, F.Nastri, and A.Lombardi (1999).
De novo design and structural characterization of proteins and metalloproteins.
  Annu Rev Biochem, 68, 779-819.  
10360940 Y.Isogai, M.Ota, T.Fujisawa, H.Izuno, M.Mukai, H.Nakamura, T.Iizuka, and K.Nishikawa (1999).
Design and synthesis of a globin fold.
  Biochemistry, 38, 7431-7443.  
9720261 C.E.Schafmeister, and R.M.Stroud (1998).
Helical protein design.
  Curr Opin Biotechnol, 9, 350-353.  
  9655345 J.W.Bryson, J.R.Desjarlais, T.M.Handel, and W.F.DeGrado (1998).
From coiled coils to small globular proteins: design of a native-like three-helix bundle.
  Protein Sci, 7, 1404-1414.  
9519299 K.W.Plaxco, D.S.Riddle, V.Grantcharova, and D.Baker (1998).
Simplified proteins: minimalist solutions to the 'protein folding problem'.
  Curr Opin Struct Biol, 8, 80-85.  
9729738 L.Baltzer (1998).
Functionalization of designed folded polypeptides.
  Curr Opin Struct Biol, 8, 466-470.  
9822371 P.B.Harbury, J.J.Plecs, B.Tidor, T.Alber, and P.S.Kim (1998).
High-resolution protein design with backbone freedom.
  Science, 282, 1462-1467.
PDB code: 1rh4
9657719 T.Kortemme, M.Ramírez-Alvarado, and L.Serrano (1998).
Design of a 20-amino acid, three-stranded beta-sheet protein.
  Science, 281, 253-256.  
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 codes are shown on the right.

 

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