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Ezra Peisach

Publications and source records attributed to Ezra Peisach.

5 recordsLinked to original sources
PubMed2006

Multiple solvent crystal structures: probing binding sites, plasticity and hydration.

Multiple solvent crystal structures (MSCS) of porcine pancreatic elastase were used to map the binding surface the enzyme. Crystal structures of elastase in neat acetonitrile, 95% acetone, 55% dimethylformamide, 80% 5-hexene-1,2-diol, 80% isopropanol, 80% ethanol and 40% trifluoroethanol showed that the organic solvent molecules clustered in the active site, were found mostly unclustered in crystal contacts and in general did not bind elsewhere on the surface of elastase. Mixtures of 40% benzene or 40% cyclohexane in 50% isopropanol and 10% water showed no bound benzene or cyclohexane molecules, but did reveal bound isopropanol. The clusters of organic solvent probe molecules coincide with pockets occupied by known inhibitors. MSCS also reveal the areas of plasticity within the elastase binding site and allow for the visualization of a nearly complete first hydration shell. The pattern of organic solvent clusters determined by MSCS for elastase is consistent with patterns for hot spots in protein-ligand interactions determined from database analysis in general. The MSCS method allows probing of hot spots, plasticity and hydration simultaneously, providing a powerful complementary strategy to guide computational methods currently in development for binding site determination, ligand docking and design.

Animals↗
PubMed2004

X-ray crystal structure of the hypothetical phosphotyrosine phosphatase MDP-1 of the haloacid dehalogenase superfamily.

The haloacid dehalogenase (HAD) superfamily is comprised of structurally homologous enzymes that share several conserved sequence motifs (loops I-IV) in their active site. The majority of HAD members are phosphohydrolases and may be divided into three subclasses depending on domain organization. In classes I and II, a mobile "cap" domain reorients upon substrate binding, closing the active site to bulk solvent. Members of the third class lack this additional domain. Herein, we report the 1.9 A X-ray crystal structures of a member of the third subclass, magnesium-dependent phosphatase-1 (MDP-1) both in its unliganded form and with the product analogue, tungstate, bound to the active site. The secondary structure of MDP-1 is similar to that of the "core" domain of other type I and type II HAD members with the addition of a small, 28-amino acid insert that does not close down to exclude bulk solvent in the presence of ligand. In addition, the monomeric oligomeric state of MDP-1 does not allow the participation of a second subunit in the formation and solvent protection of the active site. The binding sites for the phosphate portion of the substrate and Mg(II) cofactor are also similar to those of other HAD members, with all previously observed contacts conserved. Unlike other subclass III HAD members, MDP-1 appears to be equally able to dephosphorylate phosphotyrosine and closed-ring phosphosugars. Modeling of possible substrates in the active site of MDP-1 reveals very few potential interactions with the substrate leaving group. The mapping of conserved residues in sequences of MDP-1 from different eukaryotic organisms reveals that they colocalize to a large region on the surface of the protein outside the active site. This observation combined with the modeling studies suggests that the target of MDP-1 is most likely a phosphotyrosine in an unknown protein rather than a small sugar-based substrate.

Amino Acid Sequence↗
PubMed2004

X-ray structure analysis of a designed oligomeric miniprotein reveals a discrete quaternary architecture.

The x-ray crystal structure of an oligomeric miniprotein has been determined to a 1.2-A resolution by means of multiwavelength anomalous diffraction phasing with selenomethionine analogs that retain the biophysical characteristics of the native peptide. Peptide 1, comprising alpha and beta secondary structure elements with only 21 aa per monomer, associates as a discrete tetramer. The peptide adopts a previously uncharacterized quaternary structure in which alpha and beta components interact to form a tightly packed and well defined hydrophobic core. The structure provides insight into the origins of the unusual thermal stability of the oligomer. The miniprotein shares many characteristics of larger proteins, including cooperative folding, lack of 1-anilino-8-naphthalene sulfonate binding, and limited deuterium exchange, and possesses a buried surface area typical of native proteins.

Amino Acid Sequence↗
PubMed2003

Constraints for zinc finger linker design as inferred from X-ray crystal structure of tandem Zif268-DNA complexes.

Zinc-finger proteins offer a versatile and effective framework for the recognition of DNA binding sites. By connecting multiple fingers together with canonical TGEKP linkers, a protein may be designed to recognize almost any desired target DNA sequence. However, proteins containing more than three zinc-fingers do not bind as tightly as one might predict, and it appears that some type of strain is introduced when a six-finger protein is constructed with canonical linkers. In an attempt to understand the sources of this strain, we have solved the 2.2A resolution X-ray crystallographic structure of a complex that has two copies of the three-finger Zif268 protein bound to adjacent sites on one duplex DNA. Conceptually, this is equivalent to a six-finger protein in which the central linker has been removed and the complex has been allowed to "relax" to its most stable conformation. As in other Zif268-DNA complexes, the DNA is approximately linear and is slightly underwound. Surprisingly, the structure of the complex is similar (within 0.5A) to an arrangement that would allow a canonical linker at the center of the complex, and it seems possible that entropic effects (involving the librational degrees of freedom in the complex) could be important in determining optimal linker length.

Amino Acid Sequence↗