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When I was investigating the differences between protein structures obtained by X-ray crystallography and NMR spectroscopy, I found the paper [1] compairing structures of several proteins resolved both with X-ray and NMR. The average root-mean-square deviation (RMSD) between NMR and Xray structures is 1.4Å (max. 3.6Å), and the average RMSD between different NMR structures for same protein is 0.4Å (max. 1.3Å). I've checked some proteins studied in this paper, and they are mostly within 100–200 residues long.

However, there are plenty of papers (e.g. [2], [3], dealing with similarly sized proteins) that base their statements about conformational transitions on structures with RMSD difference 1–2Å.

I wonder what is considered reliable RMSD between two structures to draw any solid conlusions about conformational transitions (e.g. upon ligand binding) as opposed to simple thermal fluctuations or perturbance caused by the method to obtain structure?

Of course, the best way (at least in my opinion) to distinguish actual conformational transition from thermal fluctuations is to measure its lifetime, but it is often not an option.

  1. Andrec M, Snyder DA, Zhou Z, Young J, Montelione GT, Levy RM. 2007. A large data set comparison of protein structures determined by crystallography and NMR: statistical test for structural differences and the effect of crystal packing. Proteins 69: 449–65.

  2. Grant BJ, Gorfe AA, McCammon JA. 2009. Ras conformational switching: simulating nucleotide-dependent conformational transitions with accelerated molecular dynamics. PLoS Computational Biology 5(3): e1000325.

  3. Kumaraswami M, Newberry KJ, Brennan RG. 2010. Conformational plasticity of the coiled-coil domain of BmrR is required for bmr operator binding: the structure of unliganded BmrR. Journal of Molecular Biology 398: 264–75.

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The best way to distinguish "actual conformational transition from thermal fluctuations" in a protein is to (determine and) compare atomic-resolution structures of the ligand-free and ligand-bound protein.

http://www.rcsb.org/pdb/home/home.do

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