2KL8

Solution NMR Structure of de novo designed ferredoxin-like fold protein, Northeast Structural Genomics Consortium Target OR15

Summary for 2KL8

• Entry DOI: 10.2210/pdb2kl8/pdb
• NMR Information: BMRB: 16387
• Descriptor: OR15 (1 entity in total)
• Functional Keywords: structural genomics, protein nmr, northeast structural genomics consortium (nesg), target or15, psi-2, protein structure initiative, de novo protein, ferrodoxin fold
• Biological source: artificial gene
• Total number of polymer chains: 1
• Total formula weight: 10066.48

Authors

Liu, G.,Koga, N.,Jiang, M.,Koga, R.,Xiao, R.,Ciccosanti, C.,Baker, D.,Montelione, G.T.,Northeast Structural Genomics Consortium (NESG) (deposition date: 2009-06-30, release date: 2009-07-28, Last modification date: 2024-05-01)

Primary citation

Koga, N.,Tatsumi-Koga, R.,Liu, G.,Xiao, R.,Acton, T.B.,Montelione, G.T.,Baker, D.
Principles for designing ideal protein structures.
Nature, 491:222-227, 2012

PubMed Abstract: Unlike random heteropolymers, natural proteins fold into unique ordered structures. Understanding how these are encoded in amino-acid sequences is complicated by energetically unfavourable non-ideal features--for example kinked α-helices, bulged β-strands, strained loops and buried polar groups--that arise in proteins from evolutionary selection for biological function or from neutral drift. Here we describe an approach to designing ideal protein structures stabilized by completely consistent local and non-local interactions. The approach is based on a set of rules relating secondary structure patterns to protein tertiary motifs, which make possible the design of funnel-shaped protein folding energy landscapes leading into the target folded state. Guided by these rules, we designed sequences predicted to fold into ideal protein structures consisting of α-helices, β-strands and minimal loops. Designs for five different topologies were found to be monomeric and very stable and to adopt structures in solution nearly identical to the computational models. These results illuminate how the folding funnels of natural proteins arise and provide the foundation for engineering a new generation of functional proteins free from natural evolution.

PubMed: 23135467
DOI: 10.1038/nature11600

Experimental method

SOLUTION NMR