Showing papers by "Paul Langan published in 2013"
TL;DR: A room-temperature joint X-ray/neutron structure of the protease in complex with clinical drug amprenavir has been determined and suggests that some hydrogen bonds may be weaker than deduced from the non-hydrogen interatomic distances.
Abstract: HIV-1 protease is an important target for the development of antiviral inhibitors to treat AIDS. A room-temperature joint X-ray/neutron structure of the protease in complex with clinical drug amprenavir has been determined at 2.0 A resolution. The structure provides direct determination of hydrogen atom positions in the enzyme active site. Analysis of the enzyme–drug interactions suggests that some hydrogen bonds may be weaker than deduced from the non-hydrogen interatomic distances. This information may be valuable for the design of improved protease inhibitors.
55 citations
TL;DR: Comparison of X-ray structures of several ternary substrate and product complexes of the catalytic subunit of cAMP-dependent protein kinase (PKAc) with different bound metal ions reveals conformational, coordination, and hydrogen bonding changes that might occur during the reaction and shed new light on its mechanism, roles of metals, and active site residues.
Abstract: X-ray structures of several ternary substrate and product complexes of the catalytic subunit of cAMP-dependent protein kinase (PKAc) have been determined with different bound metal ions. In the PKAc complexes, Mg2+, Ca2+, Sr2+, and Ba2+ metal ions could bind to the active site and facilitate the phosphoryl transfer reaction. ATP and a substrate peptide (SP20) were modified, and the reaction products ADP and the phosphorylated peptide were found trapped in the enzyme active site. Finally, we determined the structure of a pseudo-Michaelis complex containing Mg2+, nonhydrolyzable AMP-PCP (β,γ-methyleneadenosine 5′-triphosphate) and SP20. The product structures together with the pseudo-Michaelis complex provide snapshots of different stages of the phosphorylation reaction. Comparison of these structures reveals conformational, coordination, and hydrogen bonding changes that might occur during the reaction and shed new light on its mechanism, roles of metals, and active site residues.
26 citations
TL;DR: Examples of chemistry seen with neutrons for the first time in biological macromolecules over the past few years are described.
Abstract: New developments in macromolecular neutron crystallography have led to an increasing number of structures published over the last decade. Hydrogen atoms, normally invisible in most X-ray crystal structures, become visible with neutrons. Using X-rays allows one to see structure, while neutrons allow one to reveal the chemistry inherent in these macromolecular structures. A number of surprising and sometimes controversial results have emerged; because it is difficult to see or predict hydrogen atoms in X-ray structures, when they are seen by neutrons they can be in unexpected locations with important chemical and biological consequences. Here we describe examples of chemistry seen with neutrons for the first time in biological macromolecules over the past few years.
20 citations
TL;DR: The crystal structure of a complex of β-chitin with ethylenediamine (EDA) was determined by synchrotron X-ray fiber diffraction by finding one amino group tightly bound to the primary alcohol hydroxyl group O6 atom of the N-acetylglucosamine residue in an arrangement similar to that found in the EDA-cellulose I complex.
18 citations
TL;DR: The neutron structure of a complex of EDA with cellulose has been determined to reveal the location of hydrogen atoms involved in hydrogen-bonding, and quantum chemistry and molecular dynamics calculations show that O3 prefers to donate to EDA as discussed by the authors.
Abstract: The neutron structure of a complex of EDA with cellulose has been determined to reveal the location of hydrogen atoms involved in hydrogen-bonding. EDA disrupts the hydrogen-bonding pattern of naturally occurring cellulose by accepting a strong hydrogen-bond from the O6 hydroxymethyl group as the conformation of this group is rotated from tg to gt. The O3-H·O5 intrachain hydrogen-bond commonly found in cellulose allomorphs is observed to be disordered in the neutron structure, and quantum chemistry and molecular dynamics calculations show that O3 prefers to donate to EDA. The hydrogen-bonding arrangement is highly dynamic with bonds continually being formed and broken thus explaining the difficulty in locating all of the hydrogen atoms in the neutron scattering density maps. Comparison with other polysaccharide-amino complexes supports a common underlying mechanism for amine disruption of cellulose.
16 citations
TL;DR: Crystallographic studies of Xylanase II from Trichoderma reesei have been initiated to investigate its reaction mechanism, substrate binding and dependence on basic pH conditions.
Abstract: Xylanase II from Trichoderma reesei catalyzes the hydrolysis of glycosidic bonds in xylan. Crystallographic studies of this commercially important enzyme have been initiated to investigate its reaction mechanism, substrate binding and dependence on basic pH conditions. The wild-type protein was heterologously expressed in an Escherichia coli host using the defined medium and four active-site amino acids were replaced to abolish its activity (E177Q and E86Q) or to change its pH optimum (N44D and N44H). Cation-exchange and size-exclusion chromatography were used to obtain >90% protein purity. The ligand-free proteins and variant complexes containing substrate (xylohexaose) or product (xylotriose) were crystallized in several different space groups and diffracted to high resolutions (from 1.07 to 1.55 A).
2 citations