Evaluation of protein-ligand binding free energy focused on its entropic components

The binding free energy for FK506-binding protein-ligand systems is evaluated as a sum of two entropic components, the water-entropy gain, and the configurational-entropy loss for the protein and ligand molecules upon the binding. The two entropic components are calculated using morphometric thermodynamics combined with a statistical-mechanical theory for molecular liquids and the normal mode analysis, respectively. We find that there is an excellent correlation between the calculated and experimental values of the binding free energy. This result is compared with those of several other binding-free energy calculation methods, including MM-PB/SA. The binding can well be elucidated by competition of the two entropic components. Upon the protein-ligand binding, the total volume available to the translational displacement of the coexisting water molecules increases, leading to an increase in the number of accessible configurations of the water. The water-entropy gain, by which the binding is driven, originates primarily from this effect. This study sheds new light on the theoretical prediction of the protein-ligand binding free energy.     

Imidazo[2,1‐b]thiazoles,imidazo[2,1‐b]imidazoles and Pyrrolo[1,2‐c]imidazoles. synthesis,structure and evaluation of benzodiazepine receptor binding

As a continuation of our studies on bicyclic heterocycles with benzodiazepine receptor affinity, derivatives with a 5:5 bicyclic skeleton, namely imidazo[2,1‐b]thiazoles, imidazo[2,1‐b]imidazoles and pyrrolo[1,2‐c]imidazoles were prepared. The compounds possessed an aromatic substituent with different spatial arrangement and distance to the bicyclic skeleton. X‐ray structure analysis was performed for Z‐2‐(4‐chlorobenzylidene)‐5,5‐diphenyl‐2,3,5,6‐tetrahydroimidazo[2,1‐b]imidazoline‐3,6‐dione ( 6a ) and 5‐amino‐6‐cyano‐7‐phenyl‐1‐oxo‐3‐thioxo‐2,3‐dihydro‐1H‐pyrrolo[1,2‐c]imidazole ( 20a ). In contrast to the previously described arylideneimidazo[2,1‐b]thiazepinones the smaller heterocyclic ring systems investigated in this study were devoid of meaningful benzodiazepine receptor affinity as well as anti‐convulsant activity.     

Correctionto Chin .J .Chem .2002,20,851— 857

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Comment on "Using quaternions to calculate RMSD" [J. Comp. Chem. 25, 1849 (2004)

Coutsias et al. have recently published a method to find the optimal rotational superposition of two molecular structures, which is based on a representation of rotations by quaternions (J. Comp. Chem. 25(15), 1849 (2004)). The method, which has been suggested by other authors before, is compared to the one by Kabsch, where the elements of the rotation matrix are directly used as variables of the optimization problem. The statement that the two methods are equivalent is misleading in the sense that the Kabsch method may yield an improper optimal rotation, which must be explicitly checked for, whereas the quaternion method does not mix proper and improper rotations. Nevertheless, both types of solutions can be considered by solving the same eigenvector problem. The relation between the two types of solutions is briefly discussed and bounds for the eigenvalues are given.     

Computational study of ligand binding in lipid transfer proteins: Structures,interfaces, and free energies of protein‐lipid complexes

Plant nonspecific lipid transfer proteins (nsLTPs) bind a wide variety of lipids, which allows them to perform disparate functions. Recent reports on their multifunctionality in plant growth processes have posed new questions on the versatile binding abilities of these proteins. The lack of binding specificity has been customarily explained in qualitative terms on the basis of a supposed structural flexibility and nonspecificity of hydrophobic protein‐ligand interactions. We present here a computational study of protein‐ligand complexes formed between five nsLTPs and seven lipids bound in two different ways in every receptor protein. After optimizing geometries in molecular dynamics calculations, we computed Poisson‐Boltzmann electrostatic potentials, solvation energies, properties of the protein‐ligand interfaces, and estimates of binding free energies of the resulting complexes. Our results provide the first quantitative information on the ligand abilities of nsLTPs, shed new light into protein‐lipid interactions, and reveal new features which supplement commonly held assumptions on their lack of binding specificity. © 2012 Wiley Periodicals, Inc.     

Darstellung,Kristallstrukturen und Schwingungsspektren von Verbindungen mit den linearen Dipnictidoborat(3–)‐Anionen [P–B–P]3–, [As–B–As]3– und [P–B–As]3–

Synthesis, Crystal Structure, and Vibrational Spectra of Compounds with the Linear Dipnictidoborate (3–) Anions [P–B–P]^3–, [As–B–As]^3–, and [P–B–As]^3– The alkali metal boron compounds M₃[BX₂] with X = P, As are synthesized from the alkali metals M and the binary components MX or M₄X₆ and BX in sealed steel ampoules (phosphides) or niobium ampoules (arsenides) at 1000 K. The compounds are obtained as bright yellow prisms (M₃[BP₂]) or plates (K₂Na[BP₂]) and yellow‐red prismatic crystals (M₃[BAs₂], Cs₃[BPAs]) which are very sensitive against oxidation and hydrolysis. Three different structure types are formed, namely K₂Na[BP₂] (C2/m (No. 12); Z = 4; a new mC24 structure type); Na₃[BP₂] (P2₁/c (No. 14); Z = 4, β‐Li₃[BN₂] type), M₃[BX₂] with M = K, Rb, Cs and X = P, As and Cs₃[P–B–As] (C2/c, (No. 15); Z = 4, K₃[BP₂] type). The bond lengths of the linear [BX₂]^3– anions are hardly changed and correspond to a Pauling bond order PBO = 1.9 (d(B–P) = 176.7–177.1 pm; d(B–As) = 186.5–188.0 pm). The vibrational spectra confirm the existence of unmixed and mixed units [P–B–P]^3–, [As–B–As]^3– and [P–B–As]^3– with D_∞h and C_∞v symmetry, respectively. The valence force constants f(B–X) and the corresponding Siebert bond orders, calculated from the frequencies, are discussed and compared with those of the isoelectronic anions and molecules.