The electrostatic role of the Zn-Cys2His2 complex in binding of operator DNA with transcription factors: mouse EGR-1 from the Cys2His2 family.

The mouse factor Zif268, known also as early growth response protein EGR-1, is a classical representative for the Cys2His2 transcription factor family. It is required for binding the RNA polymerase with operator dsDNA to initialize the transcription process. We have shown that only in this family of total six Zn-finger protein families the Zn complex plays a significant role in the protein-DNA binding. Electrostatic feature of this complex in the binding of factor Zif268 from Mus musculus with operator DNA has been considered. The factor consists of three similar Zn-finger units which bind with triplets of coding DNA. Essential contacts of the factor with the DNA phosphates are formed by three conservative His residues, one in each finger. We describe here the results of calculations of the electrostatic potentials for the Zn-Cys2His2 complex, Zn-finger unit 1, and the whole transcription factor. The potential of Zif268 has a positive area on the factor surface, and it corresponds exactly to the binding sites of each of Zn-finger units. The main part of these areas is determined by conservative His residues, which form contacts with the DNA phosphate groups. Our result shows that the electrostatic positive potential of this histidine residue is enhanced due to the Zn complex. The other contacts of the Zn-finger with DNA are related to nucleotide bases, and they are responsible for the sequence-specific binding with DNA. This result may be extended to all other members of the Cys2His2 transcription factor family.

A third blind test of crystal structure prediction.

Following the interest generated by two previous blind tests of crystal structure prediction (CSP1999 and CSP2001), a third such collaborative project (CSP2004) was hosted by the Cambridge Crystallographic Data Centre. A range of methodologies used in searching for and ranking the likelihood of predicted crystal structures is represented amongst the 18 participating research groups, although most are based on the global minimization of the lattice energy. Initially the participants were given molecular diagrams of three molecules and asked to submit three predictions for the most likely crystal structure of each. Unlike earlier blind tests, no restriction was placed on the possible space group of the target crystal structures. Furthermore, Z' = 2 structures were allowed. Part-way through the test, a partial structure report was discovered for one of the molecules, which could no longer be considered a blind test. Hence, a second molecule from the same category (small, rigid with common atom types) was offered to the participants as a replacement. Success rates within the three submitted predictions were lower than in the previous tests - there was only one successful prediction for any of the three ;blind' molecules. For the ;simplest' rigid molecule, this lack of success is partly due to the observed structure crystallizing with two molecules in the asymmetric unit. As in the 2001 blind test, there was no success in predicting the structure of the flexible molecule. The results highlight the necessity for better energy models, capable of simultaneously describing conformational and packing energies with high accuracy. There is also a need for improvements in search procedures for crystals with more than one independent molecule, as well as for molecules with conformational flexibility. These are necessary requirements for the prediction of possible thermodynamically favoured polymorphs. Which of these are actually realised is also influenced by as yet insufficiently understood processes of nucleation and crystal growth.

X-ray powder diffraction structure determination of gamma-butyrolactone at 180 K: phase-problem solution from the lattice energy minimization with two independent molecules.

The crystal structure of the solid phase of the dipolar aprotic solvent gamma-butyrolactone (BL1), C(4)H(6)O(2), has been solved using the atom-atom potential method and Rietveld-refined against powder diffraction data collected at T = 180 K with a curved position-sensitive detector (INEL CPS120) using Debye-Scherrer diffraction geometry with monochromatic X-rays. It was first deduced from the X-ray experiment that the lattice parameters are a = 10.1282 (4), b = 10.2303 (5), c = 8.3133 (4) A, beta = 93.291 (2) degrees and that the space group is P2(1)/a, with Z = 8 and two independent molecules in the asymmetric unit. The structure was then solved by global energy minimization of the crystal-lattice atom-atom potentials. The subsequent GSAS-based Rietveld refinement converged to the final crystal-structure model indicator R(F(2)) = 0.0684, profile factors R(p) = 0.0517 and R(wp) = 0.0694, and a reduced chi(2) = 1.671. After further cycles of heating and cooling, a powder diffraction pattern markedly different from the first pattern was obtained, again at T = 180 K, which we tentatively assign to a second polymorph (BL2). All the observed diffraction peaks are well indexed by a triclinic unit cell essentially featuring a doubling of the a axis. An excellent Le Bail fit is obtained, for which R(p) = 0.0312 and R(wp) = 0.0511.

Topochemical polymerization of C70 controlled by monomer crystal packing.

Polymeric forms of C60 are now well known, but numerous attempts to obtain C70 in a polymeric state have yielded only dimers. Polymeric C70 has now been synthesized by treatment of hexagonally packed C70 single crystals under moderate hydrostatic pressure (2 gigapascals) at elevated temperature (300 degrees C), which confirms predictions from our modeling of polymeric structures of C70. Single-crystal x-ray diffraction shows that the molecules are bridged into polymeric zigzag chains that extend along the c axis of the parent structure. Solid-state nuclear magnetic resonance and Raman data provide evidence for covalent chemical bonding between the C70 cages.

Polymorphism of sulfanilamide: (II) Stability hierarchy of alpha-, beta-, and gamma-forms from energy calculations by the atom-atom potential method and from the construction of the p, T phase diagram.

PURPOSE: Sulfanilamide trimorphism was chosen as a model system for comparison between stability hierarchies obtained from lattice-energy calculations with those deduced from the relative locations of the sublimation curves of polymorphs in the sulfanilamide p, T diagram. METHODS: The atom-atom potential (AAP) method was used for lattice-energy calculations. The p, T diagram was constructed by using crystallographic and thermodynamic data for alpha-, beta-, and gamma-forms, and by assigning the temperatures of the experimentally observed phase transitions to triple points involving the vapour phase. RESULTS: The hierarchy obtained with the AAP method (E alpha > or = E gamma > > E beta) differs only slightly from that deduced from the positions of the sublimation curves (p gamma > p alpha > p beta) in the p, T diagram at room temperature. No stable phase region was found for form alpha. Thus it is really monotropic. CONCLUSIONS: Provided enthalpy and volume changes at the transitions are accurate enough, it is possible to draw a p, T diagram that accounts for the stability hierarchy of polymorphs.