X-ray diffraction data have been collected at both low (120 K) and room temperature from triclinic crystals of hen egg-white lysozyme to 0.925 and 0.950 A resolution, respectively, using synchrotron radiation. Data from one crystal were sufficient for the low-temperature study, whereas three crystals were required at room temperature. Refinement was carried… (More)
The interaction between ubiquitinated proteins and intracellular proteins harboring ubiquitin binding domains (UBDs) is critical to a multitude of cellular processes. Here, we report that Rabex-5, a guanine nucleotide exchange factor for Rab5, binds to Ub through two independent UBDs. These UBDs determine a number of properties of Rabex-5, including its… (More)
SNARE proteins are crucial for intracellular membrane fusion in all eukaryotes. These proteins assemble into tight complexes that connect membranes and may induce fusion. The crystal structure of the neuronal core complex is represented by an unusually long bundle of four alpha-helices connected by 16 layers of mostly hydrophobic amino acids. Here we report… (More)
Rapid alignment of proteins in terms of domains (RAPIDO) is a web server for the 3D alignment of crystal structures of different protein molecules in the presence of conformational change. The structural alignment algorithm identifies groups of equivalent atoms whose interatomic distances are constant (within a defined tolerance) in the two structures being… (More)
Sinc-shaped Nyquist pulses possess a rectangular spectrum, enabling data to be encoded in a minimum spectral bandwidth and satisfying by essence the Nyquist criterion of zero inter-symbol interference (ISI). This property makes them very attractive for communication systems since data transmission rates can be maximized while the bandwidth usage is… (More)
BACKGROUND Structural alignment is an important step in protein comparison. Well-established methods exist for solving this problem under the assumption that the structures under comparison are considered as rigid bodies. However, proteins are flexible entities often undergoing movements that alter the positions of domains or subdomains with respect to each… (More)
Iterative interpretation of error-scaled difference distance matrices is suggested as a means of dividing a protein into structural domains on the basis of conformational differences between different models. Two conformers of Src kinase [PDB codes 1fmk [Xu et al. (1997). Nature (London), 385, 595-602] and 2src [Xu et al. (1999). Mol. Cell, 3, 629-638]] in… (More)
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