caa a22 4500 397494149 CHVBK 20180308164516.0 cr unu---uuuuu 161202e199507 xx s 000 0 eng 10.1093/oxfordjournals.jbchem.a124869 doi (NATIONALLICENCE)oxford-10.1093/oxfordjournals.jbchem.a124869 Detection of Protein 3D-1D Compatibility Characterized by the Evaluation of Side-Chain Packing and Electrostatic Interactions [Elektronische Daten] [Yo Matsuo, Haruki Nakamura, Ken Nishikawa] A new approach to evaluate protein structure (3D)-sequence (1D) compatibility has been developed. This approach uses four functions: side-chain packing, solvation, hydrogen-bonding, and local structure functions. The side-chain packing function takes into account not only inter-residue distance but also inter-residue contact and angle. Parameters defining the functions were statistically derived from 101 proteins with known 3D structures. The functions are combined to give a score quantifying the 3D-1D compatibility. The ability to identify the native structure of a protein among a large number of incorrect structures was tested. For 69 out of the 70 proteins examined, the native structures were successfully identified. Particularly, the side-chain packing function showed clear improvement over our previous function. The only unsuccessful case was observed for cytochrome C3 containing four haems; such prosthetic groups were ignored in the calculation. In addition to the above functions, two procedures for removing membrane-spanning regions and estimating electrostatic interactions were also adopted. A sequence for which membrane-spanning regions were predicted was considered incompatible with a structure irrespective of the compatibility score. A method to calculate the electrostatic interaction energy was developed and used for the detection of electrostatistically undesirable interactions between residues of a sequence threaded onto a structure. These procedures greatly help to remove false positives in the 3D-1D compatibility search. © by the Journal of Biochemistry Regular Papers nationallicence database search nationallicence electrostatic interaction nationallicence side-chain packing nationallicence structure prediction nationallicence 3D-1D compatibility nationallicence Matsuo Yo Protein Engineering Research Institute, 6-2-3 Furuedai, Suita, Osaka 565 aut Nakamura Haruki Protein Engineering Research Institute, 6-2-3 Furuedai, Suita, Osaka 565 aut Nishikawa Ken Protein Engineering Research Institute, 6-2-3 Furuedai, Suita, Osaka 565 aut The Journal of Biochemistry Oxford University Press 118/1(1995-07), 137-148 0021-924X 118:1<137 1995 118 jbchem https://doi.org/10.1093/oxfordjournals.jbchem.a124869 text/html Onlinezugriff via DOI 1 other jats NATIONALLICENCE 856 40 https://doi.org/10.1093/oxfordjournals.jbchem.a124869 text/html Onlinezugriff via DOI NATIONALLICENCE 700 1- Matsuo Yo Protein Engineering Research Institute, 6-2-3 Furuedai, Suita, Osaka 565 aut NATIONALLICENCE 700 1- Nakamura Haruki Protein Engineering Research Institute, 6-2-3 Furuedai, Suita, Osaka 565 aut NATIONALLICENCE 700 1- Nishikawa Ken Protein Engineering Research Institute, 6-2-3 Furuedai, Suita, Osaka 565 aut NATIONALLICENCE 773 0- The Journal of Biochemistry Oxford University Press 118/1(1995-07), 137-148 0021-924X 118:1<137 1995 118 jbchem Metadata rights reserved CC BY-NC-4.0 http://creativecommons.org/licenses/by-nc/4.0 nationallicence BK010053 XK010053 XK010000 NATIONALLICENCE NATIONALLICENCE NL-oxford