Fast automated placement of polar hydrogen atoms in protein-ligand complexes

<p>Abstract</p> <p>Background</p> <p>Hydrogen bonds play a major role in the stabilization of protein-ligand complexes. The ability of a functional group to form them depends on the position of its hydrogen atoms. An accurate knowledge of the positions of hydrogen atoms in proteins is therefore important to correctly identify hydrogen bonds and their properties. The high mobility of hydrogen atoms introduces several degrees of freedom: Tautomeric states, where a hydrogen atom alters its binding partner, torsional changes where the position of the hydrogen atom is rotated around the last heavy-atom bond in a residue, and protonation states, where the number of hydrogen atoms at a functional group may change. Also, side-chain flips in glutamine and asparagine and histidine residues, which are common crystallographic ambiguities must be identified before structure-based calculations can be conducted.</p> <p>Results</p> <p>We have implemented a method to determine the most probable hydrogen atom positions in a given protein-ligand complex. Optimality of hydrogen bond geometries is determined by an empirical scoring function which is used in molecular docking. This allows to evaluate protein-ligand interactions with an established model. Also, our method allows to resolve common crystallographic ambiguities such as as flipped amide groups and histidine residues. To ensure high speed, we make use of a dynamic programming approach.</p> <p>Conclusion</p> <p>Our results were checked against selected high-resolution structures from an external dataset, for which the positions of the hydrogen atoms have been validated manually. The quality of our results is comparable to that of other programs, with the advantage of being fast enough to be applied on-the-fly for interactive usage or during score evaluation.</p

Proximity of Transmembrane Segments 5 and 8 of the Glutamate Transporter GLT-1 Inferred from Paired Cysteine Mutagenesis

BACKGROUND: GLT-1 is a glial glutamate transporter which maintains low synaptic concentrations of the excitatory neurotransmitter enabling efficient synaptic transmission. Based on the crystal structure of the bacterial homologue Glt(Ph), it has been proposed that the reentrant loop HP2, which connects transmembrane domains (TM) 7 and 8, moves to open and close access to the binding pocket from the extracellular medium. However the conformation change between TM5 and TM8 during the transport cycle is not clear yet. We used paired cysteine mutagenesis in conjunction with treatments with Copper(II)(1,10-Phenanthroline)(3) (CuPh), to verify the predicted proximity of residues located at these structural elements of GLT-1. METHODOLOGY/PRINCIPAL FINDINGS: To assess the proximity of transmembrane domain (TM) 5 relative to TM8 during transport by the glial glutamate transporter GLT-1/EAAT2, cysteine pairs were introduced at the extracellular ends of these structural elements. A complete inhibition of transport by Copper(II)(1,10-Phenanthroline)(3) is observed in the double mutants I295C/I463C and G297C/I463C, but not in the corresponding single mutants. Glutamate and potassium, both expected to increase the proportion of inward-facing transporters, significantly protected against the inhibition of transport activity of I295C/I463C and G297C/I463C by CuPh. Transport by the double mutants I295C/I463C and G297C/I463C also was inhibited by Cd(2+). CONCLUSIONS/SIGNIFICANCE: Our results suggest that TM5 (Ile-295, Gly-297) is in close proximity to TM8 (Ile-463) in the mammalian transporter, and that the spatial relationship between these domains is altered during the transport cycle

An Alternating GluN1-2-1-2 Subunit Arrangement in Mature NMDA Receptors

NMDA receptors (NMDARs) form glutamate-gated ion channels that play a critical role in CNS physiology and pathology. Together with AMPA and kainate receptors, NMDARs are known to operate as tetrameric complexes with four membrane-embedded subunits associating to form a single central ion-conducting pore. While AMPA and some kainate receptors can function as homomers, NMDARs are obligatory heteromers composed of homologous but distinct subunits, most usually of the GluN1 and GluN2 types. A fundamental structural feature of NMDARs, that of the subunit arrangement around the ion pore, is still controversial. Thus, in a typical NMDAR associating two GluN1 and two GluN2 subunits, there is evidence for both alternating 1/2/1/2 and non-alternating 1/1/2/2 arrangements. Here, using a combination of electrophysiological and cross-linking experiments, we provide evidence that functional GluN1/GluN2A receptors adopt the 1/2/1/2 arrangement in which like subunits are diagonal to one another. Moreover, based on the recent crystal structure of an AMPA receptor, we show that in the agonist-binding and pore regions, the GluN1 subunits occupy a “proximal” position, closer to the central axis of the channel pore than that of GluN2 subunits. Finally, results obtained with reducing agents that differ in their membrane permeability indicate that immature (intracellular) and functional (plasma-membrane inserted) pools of NMDARs can adopt different subunit arrangements, thus stressing the importance of discriminating between the two receptor pools in assembly studies. Elucidating the quaternary arrangement of NMDARs helps to define the interface between the subunits and to understand the mechanism and pharmacology of these key signaling receptors

Tumour vascularization: sprouting angiogenesis and beyond

Tumour angiogenesis is a fast growing domain in tumour biology. Many growth factors and mechanisms have been unravelled. For almost 30 years, the sprouting of new vessels out of existing ones was considered as an exclusive way of tumour vascularisation. However, over the last years several additional mechanisms have been identified. With the discovery of the contribution of intussusceptive angiogenesis, recruitment of endothelial progenitor cells, vessel co-option, vasculogenic mimicry and lymphangiogenesis to tumour growth, anti-tumour targeting strategies will be more complex than initially thought. This review highlights these processes and intervention as a potential application in cancer therapy. It is concluded that future anti-vascular therapies might be most beneficial when based on multimodal anti-angiogenic, anti-vasculogenic mimicry and anti-lymphangiogenic strategies

Hydrolysis of Diaryliodonium Salts

The products of hydrolysis of some unsymmetrically substituted diphenyliodonium salts to phenols and aryl iodides have been identified and their distributions determined. The direction of cleavage has been found to be insensitive to the nature of the substituents, the solvent, catalysts, and the nature of the associated anion, fluoride, fluoroborate, p-toluenesulfonate or trifluoroacetate. A rate study has shown that hydrolysis is a complex reaction which is retarded by acid and catalyzed by cuprous copper and also by oxygen when dioxane-water is used as the solvent. Possible mechanisms are discussed

Hydration energies of divalent beryllium and magnesium ions: An ab initio molecular orbital study

Ab initio molecular orbital calculations have been used to investigate contributions of water molecules in the first and second coordination shells to the overall hydration energy of divalent beryllium and magnesium cations. Enthalpy and free energy changes at 298 K have been calculated at a variety of computational levels for the reactions M2+ + [H2O]p → M2+·nH2O·mH2O, where M = Be or Mg, [H2O]p (p = 2, 4, 6, 8; p = n + m) are water clusters, and M2+·nH2O·mH2O are ion-water complexes with n and m water molecules in the first and second coordination shells, respectively. These reactions involve the disruption of the water cluster and naturally include the competitive effects of ion-water and water-water interactions inherent in the hydration process. At the MP2(FULL)/6-311++G**//RHF/6-31G* computational level, the values of ΔG298 for the reactions which complete the first hydration shells, Be2+ + [H2O]4 → Be2+·4H2O and Mg2+ + [H2O]6 → Mg2+·6H2O, are -352.0 and -266.7 kcal/mol, accounting for 61.2% and 60.7% of the experimental free energies of hydration of Be2+ and Mg2+. Reactions that incorporate two additional water molecules into a second hydration shell only change ΔG298 by -43.0 and -24.2 kcal/mol, whereas the values of ΔG298 for the corresponding reactions that incorporate the first two water molecules in the primary hydration shell are -244.6 and -135.2 kcal/mol, respectively. The calculated values of ΔG298 for the formation of the complexes Be2+·4H2O·4H2O and Mg2+·6H2O-2H2O from eight-water clusters account for approximately 73.2% and 66.2% of the overall free energies for Be2+ and Mg2+, respectively, but convergence toward the experimental hydration energies will be quite slow as additional water molecules are added to the outer hydration shells. This is consistent with the concept of the importance of long-range interactions to the hydration energy. © 1996 American Chemical Society