3N4Z

Crystal structure of quintuple Arg-to-Lys variant of T. celer L30e

Summary for 3N4Z

• Entry DOI: 10.2210/pdb3n4z/pdb
• Related: 1H7M 3N4Y
• Descriptor: 50S ribosomal protein L30e (2 entities in total)
• Functional Keywords: ribosomal protein, l30e, quintuple, arg-to-lys
• Biological source: Thermococcus celer
• Total number of polymer chains: 2
• Total formula weight: 21683.28

Authors

Chan, C.H.,Wong, K.B. (deposition date: 2010-05-24, release date: 2010-06-09, Last modification date: 2023-11-01)

Primary citation

Chan, C.H.,Wilbanks, C.C.,Makhatadze, G.I.,Wong, K.B.
Electrostatic contribution of surface charge residues to the stability of a thermophilic protein: benchmarking experimental and predicted pKa values
Plos One, 7:e30296-e30296, 2012

PubMed Abstract: Optimization of the surface charges is a promising strategy for increasing thermostability of proteins. Electrostatic contribution of ionizable groups to the protein stability can be estimated from the differences between the pKa values in the folded and unfolded states of a protein. Using this pKa-shift approach, we experimentally measured the electrostatic contribution of all aspartate and glutamate residues to the stability of a thermophilic ribosomal protein L30e from Thermococcus celer. The pKa values in the unfolded state were found to be similar to model compound pKas. The pKa values in both the folded and unfolded states obtained at 298 and 333 K were similar, suggesting that electrostatic contribution of ionizable groups to the protein stability were insensitive to temperature changes. The experimental pKa values for the L30e protein in the folded state were used as a benchmark to test the robustness of pKa prediction by various computational methods such as H++, MCCE, MEAD, pKD, PropKa, and UHBD. Although the predicted pKa values were affected by crystal contacts that may alter the side-chain conformation of surface charged residues, most computational methods performed well, with correlation coefficients between experimental and calculated pKa values ranging from 0.49 to 0.91 (p<0.01). The changes in protein stability derived from the experimental pKa-shift approach correlate well (r = 0.81) with those obtained from stability measurements of charge-to-alanine substituted variants of the L30e protein. Our results demonstrate that the knowledge of the pKa values in the folded state provides sufficient rationale for the redesign of protein surface charges leading to improved protein stability.

PubMed: 22279578
DOI: 10.1371/journal.pone.0030296

Experimental method

X-RAY DIFFRACTION (2.3973 Å)