A Cluster Analysis on the Structural Diversity of Protein Crystals, Exemplified by Human Immunodeficiency Virus Type 1 Protease

Abstract

Information on many protein crystal structures has recently become available due to developments in crystallographic techniques. Even for a single kind of protein, several and sometimes many crystal structures are available. Human immunodeficiency virus type 1 (HIV-1) protease is one of the most extensively studied viral proteins, and about six hundred crystal structures have been determined. In this work, we examined the structural diversity of HIV-1 protease, classifying crystal structures into several groups from the viewpoint of similarity in atom geometry. Using 499 crystal structures downloaded from the Protein Data Bank (PDB), cluster analysis was applied to the whole body of HIV-1 protease and also to a limited number of residues at the binding pocket. As a consequence of clustering with regard to the whole body, 499 crystal structures were separated into 6 groups. It was found that a major factor for this separation is the space group of the crystals and that the space group strongly depends on the agents used in the protein crystallization. Amino acid mutation is a minor factor for separation in clustering. In cluster analysis for a limited number of residues at the binding pocket, crystal structures were not distinctly separated, and no clear factor linked to the separation was clarified. The results suggest that amino acid mutations have little effect on the coordinates of the main-chain atoms of HIV-1 protease. Hence, the changes in drug efficacy or substrate fitness caused by mutations are mainly due to the physicochemical features of amino acid side chains.Key words clustering analysis; crystal structure; amino acid mutation; drug resistance; space group Due to the progress in techniques for protein crystallization and in software for model building, crystal structures of many proteins have been elucidated. The reliability of solved protein structures has also increased.1) The development of a high-energy X-ray source has also been important for advancing crystallographic studies.2) Due to the progress in crystallographic technology, the availability of crystal structures in good quality has enabled us to examine structural differences in proteins in detail. Even for a single kind of protein, an amino acid mutation will cause the difference in its activity. Mutagenesis is one of the best approaches for clarifying the relationship between the protein activity and the mutated amino acid residue. Since protein activity has a close relation with its structure, 3,4) it is of great interest in molecular biology that the influence of amino acid mutation induces the change in protein structure.Apart from artificial mutagenesis, amino acid mutation ceaselessly occurs in the process of evolution. There is a common consensus that the accumulation of amino acid mutations generates a genetic diversity and that the diversity is observed as a difference in protein function in phenotype. 5,6) In general, the mutation rate of viral proteins is much higher than that of protein in eukaryotes. Variants of a virus som...

A Dominant Factor for Structural Classification of Protein Crystals

“…It was found that the primary factor to distinguish the crystal structures of Hb was the space group of the crystal as shown in Table 1. This is in agreement with the results of our previous study for HIV-1 PR 16 . The major space group in the crystals of Hb is P 21 21 2, and the second one is P 1 21 1.…”

“…In our previous study for HIV-1 PR 16 , in addition to the space group and chemical agents for crystallization, the pH condition, the resolution of X-ray diffraction, the temperature factor and the inhibitor molecules were surveyed for every cluster groups to find the influence on the separation of crystal structures. No obvious factor was identified except for the space group and the chemical agent.…”

“…HIV-1 PR is composed of functional regions named flap, cantilever, elbow, catalytic triad, and fulcrum ( Fig. 1(f)) 16 .…”

Identification of the Inhibitory Compounds for Metallo-β-lactamases and Structural Analysis of the Binding Modes

“…The force field parameters were ff14SB for proteins 24) and gaff2 for the compound. 25) Atom charges of the compound were determined by the quantum chemical calculation in a similar manner to the previous works. [26][27][28] Compound 1 stayed at the catalytic site all through the simulations both for poses A and B.…”

Simulation Time Required for Diminishing the Initial Conformational Deviations among Protein Crystal Structures

“…Furthermore, our study suggested that the precipitating agent had a strong influence on this separation. 22,23 Fudo et al crystallized a single kind of protein with three different precipitating agents and further performed MD simulations with setting the three protein crystal structures as the initial models. 24 They suggested that the precipitating agent interacted with the protein so that the agent molecule restricted the contact sites of proteins to enhance a specific molecular packing for crystal growth.…”