3OR0

Semi-synthetic ribonuclease S: cyanylated homocysteine at position 13

3OR0 の概要

• エントリーDOI: 10.2210/pdb3or0/pdb
• 関連するPDBエントリー: 3OQY 3OQZ
• 分子名称: Ribonuclease pancreatic (3 entities in total)
• 機能のキーワード: artificial, non-natural, vibrational, probe, nitrile, cyano, thiocyanate, hydrolase
• 由来する生物種: Bos taurus (bovine,cow,domestic cattle,domestic cow); 詳細
• 細胞内の位置: Secreted: P61823 P61823
• タンパク質・核酸の鎖数: 4
• 化学式量合計: 26639.82

構造登録者

Fafarman, A.T.,Boxer, S.G. (登録日: 2010-09-05, 公開日: 2010-10-20, 最終更新日: 2024-11-06)

主引用文献

Fafarman, A.T.,Boxer, S.G.
Nitrile bonds as infrared probes of electrostatics in ribonuclease S.
J.Phys.Chem.B, 114:13536-13544, 2010

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: 20883003
DOI: 10.1021/jp106406p

実験手法

X-RAY DIFFRACTION (2.3 Å)