The effect of the Glu342Lys mutation in a 1 -antitrypsin on its struc- ture, studied by molecular modelling methods *+. Grzegorz Jezierski ½ and Marta Pasenkiewicz-Gierula Biophysics Department, Institute of Molecular Biology, Jagiellonian University, Kraków, Poland Received: 8 January, 2001; revised: 26 January, 2001; accepted: 6 February, 2001 Key words: molecular dynamics simulation, energy minimisation, serpins, protein structure The structure of native a 1 -antitrypsin, the most abundant protease inhibitor in human plasma, is characterised primarily by a reactive loop containing the centre of proteinase inhibition, and a b-sheet composed of five strands. Mobility of the reactive loop is confined as a result of electrostatic interactions between side chains of Glu342 and Lys290, both lo- cated at the junction of the reactive loop and the b structure. The most common mutation in the protein, resulting in its inactivation, is Glu342®Lys, named the Z mutation. The main goal of this work was to investigate the influence of the Z mutation on the structure of a 1 -antitrypsin. Commonly used molecular modelling methods have been ap- plied in a comparative study of two protein models: the wild type and the Z mutant. The results indicate that the Z mutation introduces local instabilities in the region of the reactive loop. Moreover, even parts of the protein located far apart from the mutation re- gion are affected. The Z mutation causes a relative change in the total energy of about 3%. Relatively small root mean square differences between the optimised structures of the wild type and the Z mutant, together with detailed analysis of ‘conformational searching’ process, lead to the hypothesis that the Z mutation principally induces a change in the dy- namics of a 1 -antitrypsin. Human a 1 -antitrypsin is a serine proteinase in- hibitor belonging to the group of serpins [1, 2]. It is the most abundant protease inhibitor in human plasma, and is widely investigated at present [3–6]. Structural features characteristic of serpins and crucial for biological function of a 1 -antitrypsin include: u a reactive loop, exposed to solvent and con- taining the centre of proteinase inhibition (see Fig. 1), Vol. 48 No. 1/2001 65–75 QUARTERLY * Presented at the International Conference on “Conformation of Peptides, Proteins and Nucleic Acids”, Debrzyno, Po- land, 2000. + The calculations were performed at the Interdisciplinary Centre for Mathematical Modelling, Warsaw, Poland, on Cray T3E ‘Tsunami’. . This work has been supported by the State Committee for Scientific Research (KBN); grant no. 4 P05A 081 14. ½ Corresponding author: Grzegorz Jezierski, Institute of Molecular Biology, al. A. Mickiewicza 3, 31-120 Kraków, Poland; phone: (12) 6341305, ext. 291, fax: 6336907, e-mail: gj@mol.uj.edu.pl Abbreviations: AMBER, assisted model building for energy refinement; MD, molecular dynamics; FFT, fast Fourier transform; NMR, nuclear magnetic resonance; OPLS, optimized potentials for liquid simulations; r.m.s., root mean square; r.m.s.d., root mean square displacement.