Biomedical subjects

G David Smith

Publications and source records attributed to G David Smith.

7 recordsLinked to original sources

PubMed2007

Substructure determination in multiwavelength anomalous diffraction, single anomalous diffraction, and single isomorphous replacement with anomalous scattering data using Shake-and-Bake.

A general method for selenium and sulfur substructure determination using the Shake-and-Bake (SnB) algorithm as implemented in SnB in conjunction with anomalous difference E magnitudes is presented. The protocol can be used for Se-Met multiwavelength anomalous diffraction, seleneomethionine single anomalous diffraction (SAD), S-SAD and S/Se-single isomorphous replacement with anomalous scattering data and with minor modifications for other heavy atom derivatives, such as the location of halides.

Algorithms↗

PubMed2005

The structure of T6 bovine insulin.

Porcine insulin differs in sequence from bovine insulin at residues A8 (Thr in porcine-->Ala in bovine) and A10 (Ile in porcine-->Val in bovine). The structure of T6 hexameric bovine insulin has been determined to 2.25 A resolution at room temperature and refined to a residual of 0.162. The structure of the independent dimer is nearly identical to the T6 porcine insulin dimer: the mean displacement of all backbone atoms is 0.16 A, with the largest displacements occurring at AlaB30. Each of two independent zinc ions is octahedrally coordinated by three HisB10 side chains and three water molecules. As has been observed in both human and porcine insulin, the GluB13 side chains are directed towards the center of the hexamer, where a short contact of 2.57 A occurs between two independent carboxyl O atoms, again suggesting the presence of a centered hydrogen bond. No significant displacements of backbone atoms or changes in conformation are observed at A8 or A10. Since there are no interhexamer hydrogen-bonded contacts involving A8 in either porcine or bovine insulin, the change in the identity of this residue appears to have little or no effect upon the packing of the hexamers in the unit cell. In contrast, the side chains of the three A10 residues in one trimer make van der Waals contacts with the A10 side chains in a translationally related hexamer. As a consequence of the loss of the C(delta1) atom from the isoleucine residue in porcine insulin to produce valine in bovine insulin, there is a 0.36 A decrease in the distance between independent pairs of C(beta) atoms and a 0.24 A decrease in the c dimension of the unit cell. Thus, the net effect of the change in sequence at A10 is to strengthen the stabilizing hydrophobic interactions between hexamers.

Animals↗

PubMed2005

Structural snapshots of MTA/AdoHcy nucleosidase along the reaction coordinate provide insights into enzyme and nucleoside flexibility during catalysis.

MTA/AdoHcy nucleosidase (MTAN) irreversibly hydrolyzes the N9-C1' bond in the nucleosides, 5'-methylthioadenosine (MTA) and S-adenosylhomocysteine (AdoHcy) to form adenine and the corresponding thioribose. MTAN plays a vital role in metabolic pathways involving methionine recycling, biological methylation, polyamine biosynthesis, and quorum sensing. Crystal structures of a wild-type (WT) MTAN complexed with glycerol, and mutant-enzyme and mutant-product complexes have been determined at 2.0A, 2.0A, and 2.1A resolution, respectively. The WT MTAN-glycerol structure provides a purine-free model and in combination with the previously solved thioribose-free MTAN-ADE structure, we now have separate apo structures for both MTAN binding subsites. The purine and thioribose-free states reveal an extensive enzyme-immobilized water network in their respective binding subsites. The Asp197Asn MTAN-MTA and Glu12Gln MTAN-MTR.ADE structures are the first enzyme-substrate and enzyme-product complexes reported for MTAN, respectively. These structures provide representative snapshots along the reaction coordinate and allow insight into the conformational changes of the enzyme and the nucleoside substrate. A "catalytic movie" detailing substrate binding, catalysis, and product release is presented.

Amino Acid Substitution↗

PubMed2004

Structural studies of duck delta2 crystallin mutants provide insight into the role of Thr161 and the 280s loop in catalysis.

Delta crystallin, a taxon-specific crystallin present in avian eye lenses, is homologous to the urea cycle enzyme ASL (argininosuccinate lyase). Although there are two delta crystallin isoforms in duck lenses, ddeltac1 (duck delta1 crystallin) and ddeltac2 (duck delta2 crystallin), only ddeltac2 is catalytically active. Previous structural studies have suggested that residues Ser283 and His162 in the multi-subunit active site of ddeltac2/ASL are the putative catalytic acid/base, while the highly conserved, positively charged Lys289 is thought to help stabilize the carbanion intermediate. The strict conservation of a small hydroxy-containing residue (Thr or Ser) at position 161 adjacent to the putative catalytic base, as well as its proximity to the substrate in the S283A ddeltac2 enzyme-substrate complex, prompted us to investigate further the role this residue. Structures of the active T161S and inactive T161D ddeltac2 mutants, as well as T161D complexed with argininosuccinate, have been determined to 2.0 A resolution. The structures suggest that a hydroxy group is required at position 161 to help correctly position the side chain of Lys289 and the fumarate moiety of the substrate. Threonine is probably favoured over serine, because the interaction of its methyl group with Leu206 would restrict its conformational flexibility. Residues larger than Thr or Ser interfere with substrate binding, supporting previous suggestions that correct positioning of the substrate's fumarate moiety is essential for catalysis to occur. The presence of the 280s loop (i.e. a loop formed by residues 270-290) in the 'open' conformation suggests that loop closure, thought to be essential for sequestration of the substrate, may be triggered by the formation of the carbanion or aci-carboxylate intermediates, whose charge distribution more closely mimics that of the sulphate ion found in the active-site region of the inactive ddeltac1. The 280s loop in ddeltac1 is in the closed conformation.

Amino Acid Sequence↗

PubMed2003

Lessons from an aged, dried crystal of T(6) human insulin.

The structure of the T(6) hexameric form of human insulin has been determined at both room temperature and 100 K from a single air-dried crystal. At 100 K, the space group is R3 and the asymmetric unit consists of a dimer, as has been observed previously in hydrated structures. At room temperature, the space group is P1 and the unit cell contains a quasi-threefold-symmetric hexamer. In the absence of stabilizing water interactions, the N-termini of all six A chains in the room-temperature structure appear to have undergone partial unfolding, but the N-termini of these chains are well ordered in the 100 K structure. Other differences between the room-temperature and 100 K structures involve the coordination around the zinc ions. At 100 K, both zinc ions clearly exhibit dual coordination: zinc is octahedrally coordinated in one half of the zinc sites but tetrahedrally coordinated in the other half; at room temperature, the electron densities suggest tetrahedral coordination but the bond distances to the fourth ligands are longer than expected. Contrary to what has been observed to date in all other T(6) insulin structures, there are no contacts between pairs of GluB13 residues, either at room temperature or at 100 K, that would suggest the presence of a hydrogen bond. At room temperature, three of the six independent GluB13 side chains are disordered; at 100 K, both independent side chains are disordered. The disorder in the GluB13 side chains and the lack of contacts between carboxylate groups suggests that as a result of disruption of the hydration structure in the central core of the hexamer, all six B13 carboxylates bear a negative charge. This in turn suggests that in the hydrated structures the well ordered water structure in the central core is involved in stabilizing the B13 side-chain conformations and modulating charge repulsions among the six B13 glutamates if they are not protonated, or that, as is considered more likely, the water structure plays an important role in modulating the pK(a) values of the B13 glutamates, resulting in protonation and hydrogen-bond formation.

Crystallography, X-Ray↗

PubMed2003

The structure of T6 human insulin at 1.0 A resolution.

The structure of T(6) human insulin has been determined at 120 K at a resolution of 1.0 A and refined to a residual of 0.183. As a result of cryofreezing, the first four residues of the B chain in one of the two crystallographically independent AB monomers in the hexameric [Zn(1/3)(AB)(2)Zn(1/3)](3) complex undergo a conformational shift that displaces the C(alpha) atom of PheB1 by 7.86 A relative to the room-temperature structure. A least-squares superposition of all backbone atoms of the room-temperature and low-temperature structures yielded a mean displacement of 0.422 A. Omitting the first four residues of the B chain reduced the mean displacement to 0.272 A. At 120 K, nine residues were found to exhibit two discrete side-chain conformations, but only two of these residues are in common with the seven residues found to have disordered side chains in the room-temperature structure. As a result of freezing, the disorder observed at room temperature in both ArgB22 side chains is eliminated. The close contact between pairs of O( epsilon 2) atoms in GluB13 observed at room temperature is maintained at cryotemperature and suggests that a carboxylate-carboxylic acid centered hydrogen bond exists [-C(=O)-O.H.O-C(=O)-] such that the H atom is equally shared between the two partially charged O atoms.

Crystallization↗

PubMed2002

S-SAD, Se-SAD and S/Se-SIRAS using Cu Kalpha radiation: why wait for synchrotron time?

The structure of Escherichia coli argininosuccinate synthetase (EAS) has been determined using S-SAD, Se-SAD and S/Se-SIRAS data measured with Cu Kalpha radiation. EAS contains 16 methionines and three cysteines in 455 amino acids. At a wavelength of 1.54 A (Cu Kalpha), the native (S-Met) and derivative (Se-Met) proteins yield anomalous signals of approximately 0.86 and 1.6%, respectively. Highly redundant data were measured to 2.0 A from native and derivative EAS crystals. All three structure determinations were carried out in a highly automated manner using SnB and SOLVE/RESOLVE. Despite the minute Bijvoet differences at 1.54 A, the signal was sufficient to determine the heavy-atom substructure and produce high-quality electron-density maps in all three cases. These maps were readily interpretable by the RESOLVE automated building algorithm, which modeled greater than 75% of all three structures. The success of these methods has profound implications for crystallographers experiencing difficulty with heavy-atom incorporation or with limited access to a synchrotron source.

Argininosuccinate Synthase↗