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Bacterial microcompartments (BMCs) encapsulate enzymes within a selectively permeable, proteinaceous shell. Carboxysomes are BMCs containing ribulose-1,5-bisphosphate carboxylase oxygenase and carbonic anhydrase that enhance carbon dioxide fixation. The carboxysome shell consists of three structurally characterized protein types, each named after the oligomer they form: BMC-H (hexamer), BMC-P (pentamer), and BMC-T (trimer). These three protein types form cyclic homooligomers with pores at the center of symmetry that enable metabolite transport across the shell. Carboxysome shells contain multiple BMC-H paralogs, each with distinctly conserved residues surrounding the pore, which are assumed to be associated with specific metabolites. We studied the regulation of β-carboxysome shell composition by investigating the BMC-H genes ccmK3 and ccmK4 situated in a locus remote from other carboxysome genes. We made single and double deletion mutants of ccmK3 and ccmK4 in Synechococcus elongatus PCC7942 and show that, unlike CcmK3, CcmK4 is necessary for optimal growth. In contrast to other CcmK proteins, CcmK3 does not form homohexamers; instead CcmK3 forms heterohexamers with CcmK4 with a 1:2 stoichiometry. The CcmK3-CcmK4 heterohexamers form stacked dodecamers in a pH-dependent manner. Our results indicate that CcmK3-CcmK4 heterohexamers potentially expand the range of permeability properties of metabolite channels in carboxysome shells. Moreover, the observed facultative formation of dodecamers in solution suggests that carboxysome shell permeability may be dynamically attenuated by "capping" facet-embedded hexamers with a second hexamer. Because β-carboxysomes are obligately expressed, heterohexamer formation and capping could provide a rapid and reversible means to alter metabolite flux across the shell in response to environmental/growth conditions.

Using density functional theory with an accurate treatment of van der Waals interactions, we investigate the enantioselective recognition and separation of chiral molecules on stepped metal surfaces. Our calculations demonstrate that the separation ability of metal substrates can be significantly enhanced by surface decoration and external strain. For example, applying 2% tensile strain to the Ag-alloyed Au(532) surface leads to a dramatic increase (by 89%) in cysteine enantioselectivity as compared to that of pristine Au(532). Analysis on the computed binding energies shows that the interaction energy is the predominant factor that affects the separation efficiency in strongly bound systems. Our study presents a new strategy to modify the enantioselectivity of stepped metal surfaces and paves the way for exploring high efficiency chiral separation technology in pharmaceutical industry. [ABSTRACT FROM AUTHOR]

The structure, tautomeric preferences, base-pairing ability, stacking interactions and HOMO-LUMO gaps of the naphtho-homologated DNA bases are studied using theoretical techniques. The bases have structures similar to the benzo-fused predecessors and show a tautomeric preference to naphtho-thymine and naphtho-adenine resulting in formation of hydrogen-bonded dimers.

The effect of the insertion/addition of a benzene ring to the natural nucleic acid bases on the local aromaticity of the so-called size-expanded (xN, with N being adenine, guanine, cytosine, and thymine) bases is studied. The results reveal notable differences in the aromatic character of the natural and size-expanded bases, which generally are hardly affected upon hydrogen bonding.

We investigate the possibility of tailoring the electronic properties of isoreticular metal-organic materials by replacing the metal atom in the metal-organic cluster and by doping. The electronic structure of M-IRMOF1, where IRMOF1 stands for isoreticular metal-organic framework 1 and M=Be, Mg, Ca, Zn, and Cd, was examined using density-functional theory. The results show that these materials have similar band gaps (ca. 3.5 eV) and a conduction band that is split into two bands, the lower of which has a width that varies with metal substitution. This variation prompted us to investigate whether doping with Al or Li could be used to tailor the electronic properties of the Zn-IRMOF1 and Be-IRMOF1 materials. It is shown that replacing one metal atom with Al can effectively be used to create IRMOFs with different metallic properties. On the other hand, adding Li produces structural changes that render this approach less suitable. [ABSTRACT FROM AUTHOR]

Molecular dynamics simulations of the DNA duplex d(CCAACGTTGG)2 were used to study the relationship between DNA sequence and structure in a crystal environment. Three different force fields were used: a traditional description based on atomic point charges, a polarizable force field, and an “extra-point” force field (with additional charges on extranuclear sites). It is found that all the force fields reproduce fairly well the sequence-dependent features of the experimental structure. The polarizable force field, however, provides the most accurate representation of the crystal structure and the sequence-dependent effects observed in the experiment. These results point out to the need of the inclusion of polarization for accurate descriptions of DNA. © 2004 American Institute of Physics. [ABSTRACT FROM AUTHOR]

The results from investigation of the electronic properties of an xDNA duplex made of natural and benzo-homologated bases and a natural one with an analogous sequence suggest that xDNA has a smaller [pi]-[pi]* gap than B-DNA suggests and could be used as plausible candidate for molecular-wire applications.

A comprehensive ab initio study is used to observe and analyze the structure, stability and electronic properties of guanine-zinc-cytosine (G-Zn-C) base pair, which when combined with metals like Zn and Co lead to the formation of M-DNA at high values of pH. The analysis suggest that a lot of things should be taken care of while studying the electronic properties of such base-pairs, as M-DNAs with functionals do not account for strong electronic correlations.

Second-order Moller-Plesset perturbation theory and density functional theory (DFT) are used to investigate the structural and electronic properties of size-expanded DNA bases, xA, xC, xG, and xT, and their natural counterparts. The results show that natural and size-expanded bases have both nonplanar amino groups, but the latter also has nonplanar aromatic rings, and xG is easier to oxidize than G.