Affiliations: Institute of Physics, Charles University, Ke Karlovu 5, CZ‐12116 Prague 2, Czech Republic | Department of Biochemistry, Faculty of Science, Charles University, Albertov 2030, CZ‐12840 Prague 2, Czech Republic | 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
Note: [] Corresponding author: V. Kopecký Jr., Institute of Physics, Charles University, Ke Karlovu 5, CZ‐12116 Prague 2, Czech Republic. Fax: +420 224 922 797; E‐mail: kopecky@karlov.mff.cuni.cz.
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 published 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.
