Functionally relevant protein motions: extracting basin-specific collective coordinates from molecular dynamics trajectories

Functionally relevant motion of proteins has been associated with a number of atoms moving in a concerted fashion along so-called "collective coordinates." We present an approach to extract collective coordinates from conformations obtained from molecular dynamics simulations. The power of this technique for differentiating local structural fluctuations between classes of conformers obtained by clustering is illustrated by analyzing nanosecond-long trajectories for the response regulator protein Spo0F of Bacillus subtilis, generated both in vacuo and using an implicit-solvent representation. Conformational clustering is performed using automated histogram filtering of the inter-C(alpha) distances. Orthogonal (varimax) rotation of the vectors obtained by principal component analysis of these interresidue distances for the members of individual clusters is key to the interpretation of collective coordinates dominating each conformational class. The rotated loadings plots isolate significant variation in interresidue distances, and these are associated with entire mobile secondary structure elements. From this we infer concerted motions of these structural elements. For the Spo0F simulations employing an implicit-solvent representation, collective coordinates obtained in this fashion are consistent with the location of the protein's known active sites and experimentally determined mobile regions.     

Synthesis of cationic dialkylgold(III) complexes: nature of the facile reductive elimination of alkane

A series of gold(III) cations of the type cis-[CH₃)₂AuL₂]⁺ X^? where L  Ph₃, PMePh₂, PMe₂Ph, PMe₃, AsPh₃, AsPh₃, SbPh₃, $\text{1}\text{2}$H₂NCH₂CH₂NH₂, $\text{1}\text{2}$ Ph₂PCH₂CH₂-PPh₂, $\text{1}\text{2}$ Ph₂AsCH₂CH₂AsPh₂, and $\text{1}\text{2}$o-C₆H₄(AsMe₂)₂ and X  BF₄^?, PF₆^?, ClO₄^?, and F₃CSO₃^? has been prepared. In addition, the cis complexes [(CH₃)(CD₃)-Au(PPh₃)₂]F₃CSO₃, [(C₂H₅)₂Au(PPh₃)₂]F₃CSO and [(n-C₄H₉)₂Au(PPh₃)₂]F₃-CSO₃ have been synthesized. All have been characterized by PMR, Raman and infrared spectroscopy. These [R₂AuL₂]X compounds yield only ethane, butane, or octane via reductive elimination, and no disproportionation is observed. The alkane eliminations have been studied in CHCl₃, CH₃Cl₂, and CH₃COCH₃ solution as a function of temperature, concentration of the complex, and concentration of added ligand L. Elimination is fastest when L is bulky (PPh₃ > PMePh₂ > PMe₂Ph > PMe₃), decreases in the sequence SbPh₃ > AsPh₃ > PPh₃, is slow with chelating ligands, is inhibited by excess ligand, and there is small anion effect as X is varied. As R is varied, the rate of elimination decreases Bu ? Et > Me. An intramolecular dissociative mechanism is proposed which involves rapid elimination of alkane from an electron deficient dialkylgold(III) complex with nonequivalent gold—carbon bonds and produces the corresponding [AuL₂]X complex.     

Hyperfine structure in Ga NQR of Gas and GaSe

Fine structure is reported in the ^69,71Ga NQR spectra of GaS and GaSe. The ⁶⁹Ga (I = ³₂) and ⁷¹Ga (I = ³₂) spectra are $\text{qualitatively}$ different for each compound. This is attributed to an indirect spin-spin interaction between nearest-neighbour Ga atom pairs. A model giving reasonable quantitative agreement with experiment is presented.     

The effect of ion energy upon plasma polymerization deposition rate for acrylic acid

A novel technique, which allows the importance of ion energy in plasma polymer film growth to be investigated, without perturbation of any other plasma parameter (particle densities or temperatures) or, in principle, perturbation of particle (neutral or ion) fluxes is applied in the plasma polymerisation of acrylic acid and new insight into polymer formation is gleaned.     

Benzannelated analogs of phenanthro[1,2-b]- and [2,1-b]thiophene: Synthesis and structural characterization by two-dimensional NMR and X-ray techniques

Syntheses of benzo[3,4]phenanthro[1,2-b]thiophene, benzo[3,4]phenanthro[2,1-b]thiophene and their 1-methyl analogs are reported as potential constituents of solvent refined coal liquids and for mutagenicity testing. The attempted synthesis of the 13-methyl analogs which gave the 11-methyl isomers is also described. Total assignments of the ¹H- and ¹³C-nmr spectra based on long range optimized heteronuclear protoncarbon two-dimensional chemical shift correlation are reported. Carbon assignments obtained for benzo[3,4]-phenanthro[1,2-b]thiophene using this approach were confirmed with a 125 MHz ¹³C–¹³C INADEQUATE spectrum. X-Ray crystal structures were determined for benzo[3,4]phenanthro[1,2-b]thiophene and 1-methyl-benzo[3,4]phenanthro[2,1-b]thiophene. Both molecules were helically distorted from planarity. Close intramolecular contacts between the bay region H1–H13 and ClMe-H13 of 2.03 and 2.28 Å, respectively, were responsible for the distortions. There were no close intermolecular contacts of <3.5Å. both molecules refined to an R value of <0.05.     

A planning strategy for diversity-oriented synthesis

In contrast to target-oriented synthesis (TOS) and medicinal or combinatorial chemistry, which aim to access precise or dense regions of chemistry space, diversity-oriented synthesis (DOS) populates chemical space broadly with small-molecules having diverse structures. The goals of DOS include the development of pathways leading to the efficient (three- to five-step) synthesis of collections of small molecules having skeletal and stereochemical diversity with defined coordinates in chemical space. Ideally, these pathways also yield compounds having the potential to attach appendages site- and stereoselectively to a variety of attachment sites during a post-screening, maturation stage. The diverse skeletons and stereochemistries ensure that the appendages can be positioned in multiple orientations about the surface of the molecules. TOS as well as medicinal and combinatorial chemistries have been advanced by the development of retrosynthetic analysis. Although the distinct goals of DOS do not permit the application of retrosynthetic concepts and thinking, these foundations are being built on, by using parallel logic, to develop a complementary procedure known as forward-synthetic analysis. This analysis facilitates synthetic planning, communication, and teaching in this evolving discipline.     

Synthesis of the alkaloids julandine and ipalbidine-use of silicon (IV) chloride

Titanium (IV) chloride and silicon (IV) chloride with high oxygen affinity are the best Lewis acid catalysts, of a number tested, for cyclisation of an enamine-ketone (1) leading to the alkaloid, julandine (2); cyclisation of (6) in methanol solution without catalyst yields $\text{O}$-methylipalbidine (7) .     

Electrostatic free energy of weakly charged macromolecules in solution and intermacromolecular complexes consisting of oppositely charged polymers

When oppositely charged polyelectrolytes are mixed in water, attraction between oppositely charged groups may lead to the formation of polyelectrolyte complexes (associative phase separation, complex coacervation, interpolymer complexes). Theory is presented to describe the electrostatic free energy change when ionizable (annealed) (macro-)molecules form a macroscopic polyelectrolyte complex. The electrostatic free energy includes an electric term as well as a chemical term that is related to the dissociation of the ionic groups in the polymer. An example calculation for complexation of polyacid with polybase uses a cylindrical diffuse double layer model for free polymer in solution and electroneutrality within the complex and calculates the free energy of the system when the polymer is in solution or in a polyelectrolyte complex. Combined with a term for the nonelectrostatic free energy change upon complexation, a theoretical stability diagram is constructed that relates pH, salt concentration, and mixing ratio, which is in qualitative agreement with an experimental diagram obtained by Bungenberg de Jong (1949) for complex coacervation of arabic gum and gelatin. The theory furthermore explains the increased tendency toward phase separation when the polymer becomes more strongly charged and suggests that complexation of polyacid or polybase with zwitterionic polymer (e.g., protein) of the same charge sign (at the "wrong side" of the iso-electric point) may be due (in part) to an induced charge reversal of the protein.     

Synthesis and Characterization of Sterically Encumbered Derivatives of Aluminum Hydrides and Halides: Assessment of Steric Properties of Bulky Terphenyl Ligands

The synthesis and characterization of several sterically encumbered monoterphenyl derivatives of aluminum halides and aluminum hydrides are described. These compounds are [2,6-Mes(2)C(6)H(3)AlH(3)LiOEt(2)](n)() (1), (Mes = 2,4,6-Me(3)C(6)H(2)-), 2,6-Mes(2)C(6)H(3)AlH(2)OEt(2) (2), [2,6-Mes(2)C(6)H(3)AlH(2)](2) (3), 2,6-Mes(2)C(6)H(3)AlCl(2)OEt(2) (4), [2,6-Mes(2)C(6)H(3)AlCl(3)LiOEt(2)](n)() (5), [2,6-Mes(2)C(6)H(3)AlCl(2)](2) (6), TriphAlBr(2)OEt(2) (7), (Triph = 2,4,6-Ph(3)C(6)H(2)-), [2,6-Trip(2)C(6)H(3)AlH(3)LiOEt(2)](2) (8) (Trip = 2,4,6-i-Pr(3)C(6)H(2)-), 2,6-Trip(2)C(6)H(3)AlH(2)OEt(2) (9), [2,6-Trip(2)C(6)H(3)AlH(2)](2) (10), 2,6-Trip(2)C(6)H(3)AlCl(2)OEt(2) (11), and the partially hydrolyzed derivative [2,6-Trip(2)C(6)H(3)Al(Cl)(0.68)(H)(0.32)(&mgr;-OH)](2).2C(6)H(6) (12). The structures of 2, 3a, 4, 6, 7, 9a, 10a, 10b, 11, and 12 were determined by X-ray crystallography. The structures of 3a, 9a, 10a, and 10b, are related to 3, 9, and 10, respectively, by partial occupation of chloride or hydride by hydroxide. The compounds were also characterized by (1)H, (13)C, (7)Li, and (27)Al NMR and IR spectroscopy. The major conclusions from the experimental data are that a single ortho terphenyl substituent of the kind reported here are not as effective as the ligand Mes (Mes = 2,4,6-t-Bu(3)C(6)H(2)-) in preventing further coordination and/or aggregation involving the aluminum centers. In effect, one terphenyl ligand is not as successful as a Mes substituent in masking the metal through agostic and/or steric effects.     

Synthesis and anticholinesterase activity of some new fluorogenic analogues of organophosphorus nerve agents

Eighteen new fluorogenic analogues of organophosphorus nerve agents were synthesised and characterised. They included analogues of tabun, sarin, cyclosarin, soman, VX, and Russian VX, with the 7-oxy-4-methylcoumarin or 7-oxy-4-(trifluoromethyl)coumarin leaving group. These analogues inhibited acetylcholinesterase (AChE) effectively in vitro and therefore have potential as tools for the identification of novel organophosphatases in biological systems. Analogues of VX and Russian VX with the 7-amino-4-methylcoumarin group, although poor AChE inhibitors, may have utility for screening enzyme libraries for phosphoramidases capable of cleaving P-N bonds.