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Atom, Atom-Type, and Total Linear Indices of the “Molecular Pseudograph’s Atom Adjacency Matrix”: Application to QSPR/QSAR Studies of Organic Compounds
Molecules 2004, 9(12), 1124-1147; doi:10.3390/91201124
Article

Protein Quadratic Indices of the “Macromolecular Pseudograph’s α-Carbon Atom Adjacency Matrix”. 1. Prediction of Arc Repressor Alanine-mutant’s Stability

1,* , 3, 4, 2, 2, 5 and 6
1 Department of Pharmacy, Faculty of Chemical-Pharmacy, Central University of Las Villas, Santa Clara, 54830, Villa Clara, Cuba 2 Department of Drug Design, Chemical Bioactive Center, Central University of Las Villas, Santa Clara, 54830, Villa Clara, Cuba 3 Department of Microbiology, Chemical Bioactive Center, Central University of Las Villas, Santa Clara, 54830, Villa Clara, Cuba 4 INIFTA, División Química Teórica, Suc.4, C.C. 16, La Plata 1900, Buenos Aires, Argentina 5 Faculty of Informatics, University of Cienfuegos, Cienfuegos, Cuba 6 Institut Universitari de Ciència Molecular, Universitat de València, Dr. Moliner 50, E-46100 Burjassot (València), Spain
* Author to whom correspondence should be addressed.
Received: 2 June 2004 / Revised: 12 December 2004 / Accepted: 13 December 2004 / Published: 31 December 2004
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Abstract

This report describes a new set of macromolecular descriptors of relevance toprotein QSAR/QSPR studies, protein’s quadratic indices. These descriptors are calculatedfrom the macromolecular pseudograph’s α-carbon atom adjacency matrix. A study of theprotein stability effects for a complete set of alanine substitutions in Arc repressorillustrates this approach. Quantitative Structure-Stability Relationship (QSSR) modelsallow discriminating between near wild-type stability and reduced-stability A-mutants. Alinear discriminant function gives rise to excellent discrimination between 85.4% (35/41)and 91.67% (11/12) of near wild-type stability/reduced stability mutants in training andtest series, respectively. The model’s overall predictability oscillates from 80.49 until82.93, when n varies from 2 to 10 in leave-n-out cross validation procedures. This valuestabilizes around 80.49% when n was
Keywords: Protein Stability; Arc Repressor; Alanine-Substitution Mutant; TOMOCOMD Software; Protein Quadratic Indices; QSPR. Protein Stability; Arc Repressor; Alanine-Substitution Mutant; TOMOCOMD Software; Protein Quadratic Indices; QSPR.
This is an open access article distributed under the Creative Commons Attribution License (CC BY 3.0).
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Ponce, Y.M.; Marrero, R.M.; Castro, E.A.; Ramos de Armas, R.; Díaz, H.; Zaldivar, V.R.; Torrens, F. Protein Quadratic Indices of the “Macromolecular Pseudograph’s α-Carbon Atom Adjacency Matrix”. 1. Prediction of Arc Repressor Alanine-mutant’s Stability. Molecules 2004, 9, 1124-1147.

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