As an easy technique for phase determination in X-ray analysis of macromolecular crystals, the molecular replacement method is widely used. Available computer programs are highly sophisticated to user friendly so that users can use them without knowledge on the theoretical backgrounds. To develop the technique to more powerful tool, as well as to resolve individual problems in special cases, it is essential to understand the details of the backgrounds. Here the theories of the method with the historical backgrounds, its availability and capability, practical usage and trouble shooting will be described.
Protein model building is a process in which the electron density map is interpreted and protein model is constructed. Resolution limit of protein crystal, inherent thermal vibration of atoms, and experimental errors in data collection and in phasing, make interpreting electron density more difficult. Nevertheless, it is possible to build protein model with the help of sequence information and the stereo-chemical knowledge of amino acids and peptide bond. Recently, automatic methods for model binding have been developed based on the pattern recognition techniques. In this manuscript, we learn how the electron density map is interpreted and how the building process is automated.
Aminoacyl-tRNA synthetases (aaRSs) catalyze ligation of their cognate transfer RNAs (tRNAs) with a specific amino acid, which guarantees the correct protein biosynthesis. The 20 aaRSs are divided into two classes based on the catalytic folds and reaction properties. Up to date, crystal structures of all the 20 members have been reported, and it's time to discuss the structure-function relationships of this enzyme family. Recent genome analyses provide a novel insight, which may unveil the molecular evolution of the 20 members.
X-ray diffraction patterns were recorded from the frozen-hydrated myofibrils of insect flight muscle. X-ray microbeams, generated at the high-flux BL40XU beamline of SPring-8, were irradiated along the myofibrillar axis so that the diffraction patterns were recorded from single myofibrils (diameter, 2-3 μm) . A total of 50 insect species, covering all the major winged insect orders, were examined. The results show that insects with an asynchronous flight muscle operation have giant single-crystal type myofibrils, in which the orientations of the myofilament lattice planes are preserved along their entire length. The functional significance of having such a highly regular structure is discussed.
The crystal structure of the T110078 protein from Thermosynechococcus elongatus BP-1, which contains a BLUF (a sensor of blue-light using FAD) domain bound to FAD was determined at 2 Å resolution. The overall structure of BLUF domain consists of a five-stranded mixed-β-sheet with two α-helices running parallel with it. The isoalloxazine ring of FAD is accommodated in a pocket formed by several highly conserved amino acid residues in the BLUF domain.
The photoprotein aequorin emits light by an intramolecular reaction in the presence of a trace of Ca2+. Semi-synthetic aequorins, produced by replacing the coelenterazine moiety in aequorin with the analogues of coelenterazine, show widely different sensitivities to Ca2+. To understand the structural basis of the Ca2+-sensitivity, we determined the crystal structures of four semi-synthetic aequorins (cp-, i-, br- and n-aequorins) . In general, the protein structures of these semi-synthetic aequorins are almost identical with that of native aequorin. Of the four EF-hand domains in the molecule, EF-hand II does not bind Ca2+, and the loop of EF-hand IV is clearly deformed. It is most likely that the binding of Ca2+ with EF-hands I and III triggers luminescence. Although little difference was found in the overall structures of aequorins investigated, some significant differences were found in the interactions between the substituents of coelenterazine moiety and the amino-acid residues in the binding pocket. The coelenterazine moieties in i-, br- and n-aequorins have bulky 2-substitutions, which can interfere with the conformational changes of protein structure that follow the binding of Ca2+ to aequorin. In cp-aequorin, the cyclopentylmethyl group that substitutes for the original 8-benzyl group does not interact hydrophobically with the protein part, giving the coelenterazine moiety more conformational freedom to promote the light-emitting reaction. The differences of various semisynthetic aequorins in the Ca2+-sensitivity and reaction rate are explained by the capability of the involved groups and structures to undergo conformational changes in response to the Ca2+-binding.
Biotin protein ligase (BPL) catalyses the synthesis of an activated form of biotin, biotinyl-5'-AMP, from substrates biotin and ATP followed by biotinylation of the biotin carboxyl carrier protein subunit of acetyl-CoA carboxylase. In order to visualize the structural feature of the BPL reaction, crystal structures of BPL from Pyrococcus horikoshii OT3 have been determined in an unliganded form and three liganded forms with biotin, ADP and the reaction intermediate biotinyl-5'-AMP. The exact locations of the ligands and the active site residues allow us to propose a general scheme for the first step of the reaction carried out by BPL.
Bacteriorhodopsin (bR), a membrane protein found in Halobacterium salinarum, contains retinal as chromophore and functions as a light-driven proton pump. We have carried out four-dimensional X-ray crystallographic studies of bR and its homologous proteins, to elucidate the proton pumping mechanism. A novel crystallization method, called the membrane fusion method, has been developed to prepare a 3D crystal that is stable over a wide pH range. This enabled us to investigate pH-induced as well as light-induced structural changes. Structural analyses of reaction intermediates revealed that water relocation, which affects the pKa values of ionizable residues in the proton channel, takes place in the early stage of the proton pumping cycle. On the basis of this observation, we hypothesized that bR is a water/proton anti-porter. Since some of internal cavities are highly conserved during the evolution, it is suggested that their morphological changes initiated by the retinal photo-isomerization play an important role for water relocation and proton tranlocation across the membrane.
Flap endonuclease-1 (FEN1) removes the RNA primer during Okazaki fragment maturation in lagging strand DNA synthesis. FEN1 also plays a crucial role in the long-patch base excision repair. FEN1 endonuclease activity is markedly stimulated by binding to proliferating cell nuclear antigen (PCNA), which is well known as the‘DNA sliding clamp’. We determined the crystal structure of human FEN 1 complexed to PCNA. A hinge region found in FEN1 endows the enzyme with a degree of freedom to swing and direct its core domain toward the flap-DNA substrate.