3OQY
Semi-synthetic ribonuclease S: para-cyano-phenylalanine at position 8
Summary for 3OQY
| Entry DOI | 10.2210/pdb3oqy/pdb |
| Related | 3OQZ 3OR0 |
| Descriptor | Ribonuclease pancreatic (3 entities in total) |
| Functional Keywords | artificial, non-natural, vibrational, probe, nitrile, cyano, cyanophenylalanine, hydrolase |
| Biological source | Bos taurus (bovine,cow,domestic cattle,domestic cow) More |
| Total number of polymer chains | 4 |
| Total formula weight | 26667.87 |
| Authors | Fafarman, A.T.,Boxer, S.G. (deposition date: 2010-09-04, release date: 2010-10-20, Last modification date: 2024-10-30) |
| Primary citation | Fafarman, A.T.,Boxer, S.G. Nitrile bonds as infrared probes of electrostatics in ribonuclease S. J.Phys.Chem.B, 114:13536-13544, 2010 Cited by PubMed Abstract: Three different nitrile-containing amino acids, p-cyanophenylalanine, m-cyanophenylalanine, and S-cyanohomocysteine, have been introduced near the active site of the semisynthetic enzyme ribonuclease S (RNase S) to serve as probes of electrostatic fields. Vibrational Stark spectra, measured directly on the probe-modified proteins, confirm the predominance of the linear Stark tuning rate in describing the sensitivity of the nitrile stretch to external electric fields, a necessary property for interpreting observed frequency shifts as a quantitative measure of local electric fields that can be compared with simulations. The X-ray structures of these nitrile-modified RNase variants and enzymatic assays demonstrate minimal perturbation to the structure and function, respectively, by the probes and provide a context for understanding the influence of the environment on the nitrile stretching frequency. We examine the ability of simulation techniques to recapitulate the spectroscopic properties of these nitriles as a means to directly test a computational electrostatic model for proteins, specifically that in the ubiquitous Amber-99 force field. Although qualitative agreement between theory and experiment is observed for the largest shifts, substantial discrepancies are observed in some cases, highlighting the ongoing need for experimental metrics to inform the development of theoretical models of electrostatic fields in proteins. PubMed: 20883003DOI: 10.1021/jp106406p PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.494 Å) |
Structure validation
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