原创力文档vibrational spectroscopy and computer modeling of proteins solving structure of α1-acid glycoprotein振动光谱和计算机模拟蛋白质的解决α1-acid糖蛋白的结构.pdf
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vibrational spectroscopy and computer modeling of proteins solving structure of α1-acid glycoprotein振动光谱和计算机模拟蛋白质的解决α1-acid糖蛋白的结构
Spectroscopy 18 (2004) 323–330 323
IOS Press
Vibrational spectroscopy and computer
modeling of proteins: solving structure of
α1-acid glycoprotein
a,b,∗ c ˇ b a
Vladimír Kopecký Jr. , Rüdiger Ettrich , Katerina Hofbauerová and Vladimír Baumruk
a Institute of Physics, Charles University, Ke Karlovu 5, CZ-12116 Prague 2, Czech Republic
b Department of Biochemistry, Faculty of Science, Charles University, Albertov 2030,
CZ-12840 Prague 2, Czech Republic
c Laboratory of High Performance Computing, Institute of Physical Biology USB and Institute of
Landscape Ecology AS CR, Zámek 136, CZ-37333 Nové Hrady, Czech Republic
Abstract. This work introduces a new approach connecting vibrational spectroscopy with homology and energetic molecular
modeling of proteins. Combination of both methods can compensate their disadvantages and result in realistic three-dimensional
protein models. The approach is most powerful for membrane proteins or glycoproteins with high carbohydrate content where
X-ray or NMR analysis is not always successful. Nevertheless, it can also serve as a tool of preliminary analysis of any protein
with unknown structure. Power of the approach is demonstrated on human α1-acid glycoprotein. Its predicted structure pub-
lished in [V. Kopecký Jr. et al., Biochem. Biophys. Res. Commun. 300 (2003), 41–46] is discussed in detail with respect to the
approach and its general employment.
Keywords: Raman spectroscopy, Fourier transform infrared spectroscopy, molecular modeling, orosomucoid, binding site,
thermal dynamics
1. Introduction
1.1. Determination of protein structures
Determination of the protein structure represents one of the key tasks of present molecular biology.
There is an urgent need for
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