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PDBsum entry 3b83
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protein Protein-protein interface(s) links
Unknown function PDB id
3b83

 

 

 

 

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Contents
Protein chains
(+ 2 more) 95 a.a. *
Waters ×47
* Residue conservation analysis
PDB id:
3b83
Name: Unknown function
Title: Computer-based redesign of a beta sandwich protein suggests that extensive negative design is not required for de novo beta sheet design.
Structure: Ten-d3. Chain: a, b, c, d, e, f, g, h. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.40Å     R-factor:   0.240     R-free:   0.290
Authors: X.Hu,H.Ke,B.Kuhlman
Key ref:
X.Hu et al. (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. PubMed id: 19081056 DOI: 10.1016/j.str.2008.09.013
Date:
31-Oct-07     Release date:   04-Nov-08    
PROCHECK
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 Headers
 References

Protein chains
No UniProt id for this chain
Struc: 95 a.a.
Key:    Secondary structure  CATH domain

 

 
DOI no: 10.1016/j.str.2008.09.013 Structure 16:1799-1805 (2008)
PubMed id: 19081056  
 
 
Computer-Based Redesign of a beta Sandwich Protein Suggests that Extensive Negative Design Is Not Required for De Novo beta Sheet Design.
X.Hu, H.Wang, H.Ke, B.Kuhlman.
 
  ABSTRACT  
 
The de novo design of globular beta sheet proteins remains largely an unsolved problem. It is unclear whether most designs are failing because the designed sequences do not have favorable energies in the target conformations or whether more emphasis should be placed on negative design, that is, explicitly identifying sequences that have poor energies when adopting undesired conformations. We tested whether we could redesign the sequence of a naturally occurring beta sheet protein, tenascin, with a design algorithm that does not include explicit negative design. Denaturation experiments indicate that the designs are significantly more stable than the wild-type protein and the crystal structure of one design closely matches the design model. These results suggest that extensive negative design is not required to create well-folded beta sandwich proteins. However, it is important to note that negative design elements may be encoded in the conformation of the protein backbone which was preserved from the wild-type protein.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. Sequences of the Wild-Type and Three Redesigned Proteins
TEN-WT, wild-type; TEN-D1, TEN-D2, and TEN-D3, redesigned sequences. The TEN-D1 sequence is from a previously published study (Dantas et al., 2003). 		Figure 5.
Figure 5. Structure Alignment between the Designed Model and the Crystal Structure of TEN-D3
Designed model, cyan; TEN-D3, green.
(A) Backbone only.
(B) Buried residues.
(C) Selected surface residues.
(D) A designed salt bridge between Asp48 and Arg74.
 
  The above figures are reprinted from an Open Access publication published by Cell Press: Structure (2008, 16, 1799-1805) copyright 2008.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
23135467 N.Koga, R.Tatsumi-Koga, G.Liu, R.Xiao, T.B.Acton, G.T.Montelione, and D.Baker (2012).
Principles for designing ideal protein structures.
  Nature, 491, 222-227.
PDB codes: 2kl8 2ln3 2lta 2lv8 2lvb
21128762 I.Samish, C.M.MacDermaid, J.M.Perez-Aguilar, and J.G.Saven (2011).
Theoretical and computational protein design.
  Annu Rev Phys Chem, 62, 129-149.  
21539773 M.T.Panteva, R.Salari, M.Bhattacharjee, and L.T.Chong (2011).
Direct Observations of Shifts in the β-Sheet Register of a Protein-Peptide Complex Using Explicit Solvent Simulations.
  Biophys J, 100, L50-L52.  
20623647 O.Sharabi, C.Yanover, A.Dekel, and J.M.Shifman (2011).
Optimizing energy functions for protein-protein interface design.
  J Comput Chem, 32, 23-32.  
  21544231 J.G.Saven (2010).
Computational protein design: Advances in the design and redesign of biomolecular nanostructures.
  Curr Opin Colloid Interface Sci, 15, 13-17.  
20017215 J.T.MacDonald, K.Maksimiak, M.I.Sadowski, and W.R.Taylor (2010).
De novo backbone scaffolds for protein design.
  Proteins, 78, 1311-1325.  
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.  
20920153 N.Bhattacharjee, and P.Biswas (2010).
Position-specific propensities of amino acids in the β-strand.
  BMC Struct Biol, 10, 29.  
20041208 M.Fromer, and J.M.Shifman (2009).
Tradeoff between stability and multispecificity in the design of promiscuous proteins.
  PLoS Comput Biol, 5, e1000627.  
19324680 M.Suárez, and A.Jaramillo (2009).
Challenges in the computational design of proteins.
  J R Soc Interface, 6, S477-S491.  
19081049 J.M.Shifman (2008).
Intricacies of Beta sheet protein design.
  Structure, 16, 1751-1752.  
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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