A Search for Energy Minimized Sequences of Proteins

In this paper, we present numerical evidence that supports the notion of minimization in the sequence space of proteins for a target conformation. We use the conformations of the real proteins in the Protein Data Bank (PDB) and present computationally efficient methods to identify the sequences with minimum energy. We use edge-weighted connectivity graph for ranking the residue sites with reduced amino acid alphabet and then use continuous optimization to obtain the energy-minimizing sequences. Our methods enable the computation of a lower bound as well as a tight upper bound for the energy of a given conformation. We validate our results by using three different inter-residue energy matrices for five proteins from protein data bank (PDB), and by comparing our energy-minimizing sequences with 80 million diverse sequences that are generated based on different considerations in each case. When we submitted some of our chosen energy-minimizing sequences to Basic Local Alignment Search Tool (BLAST), we obtained some sequences from non-redundant protein sequence database that are similar to ours with an E-value of the order of 10^-7. In summary, we conclude that proteins show a trend towards minimizing energy in the sequence space but do not seem to adopt the global energy-minimizing sequence. The reason for this could be either that the existing energy matrices are not able to accurately represent the inter-residue interactions in the context of the protein environment or that Nature does not push the optimization in the sequence space, once it is able to perform the function.     

蛋白质能带结构的晶体轨道法研究——Ⅱ蛋白质构象的变化对其能带结构的影响

本文用CNDO/2晶体轨道方法研究了蛋白质的构象变化对其能带结构的影响,结果表明这一因素是不可忽略的.本文还讨论了构象变化与蛋白质的半导体性质间的关系.     

Minimized virus binding for tests of barrier materials.

Viruses are used to test the barrier properties of materials. Binding of virus particles during passage through holes in the material may yield misleading test results. The choices of challenge virus and suspending medium may be important for minimizing confounding effects that might arise from such binding. In this study, different surrogate viruses, as well as different support media, were evaluated to determine optimal test parameters. Two membranes with high-binding properties (nitrocellulose and cationic polysulfone) were used as filters to compare binding activities of different surrogate challenge viruses (MS2, phi X174, T7, PRD1, and phi 6) in different media. The media consisted of buffered saline with surfactants, serum, or culture broth as additives. In addition, elution rates of viruses that bound to the membranes were determined. The results suggest that viruses can bind by hydrophobic and electrostatic interactions, with phi X174 displaying the lowest level of binding by either process. The nonionic detergents Triton X-100 and Tween 80 (0.1%) equally minimized hydrophobic interactions. Neither anionic nor cationic surfactants were as effective at nontoxic levels. Serum was effective at reducing both hydrophobic and electrostatic binding, with 2% being sufficient for eliminating binding under our test conditions. Thus, phi X174 remains the best choice as a surrogate virus to test barrier materials, and Triton X-100 (0.1%) remains a good choice for reducing hydrophobic binding. In addition, binding of viruses by barrier materials is unlikely to prevent passage of blood-borne pathogens.     

Linear Dichroism Studies of Conformations of Carcinogen-DNA Adducts Application to Covalent Complexes Derived from the Reactions of the Two Enantiomers of 9,10-epoxy-9,10,11,12-Tetrahydrobenzo(e)pyrene with DNA

Abstract

The conformations of the adducts derived from the covalent binding of the two enantiomeric forms of 9,10-epoxy-9,10,11,12-tetrahydrobenzo(e)pyrene (BePE) with native DNA were investigated by the electric linear dichroism technique. Both enantiomers give rise to two major adducts, one of which appears to be a quasi-intercalative site (I) while the other one is an external binding site (II). While the overall linear dichroism spectra are similar, in the case of the (—) enantiomer there is a greater contribution of site II adducts. These results are markedly different from the ones obtained with the two enantiomers of anti-benzo(a)pyrene-7,8-diol-9,10-epoxide (BaPDE), where the (+) enantiomer gives rise almost exclusively to site II binding, while the (—) enantiomer gives rise to both site I and site II covalent binding. The differences in the heterogeneity of binding between BePE and anti-BaPDE enantiomers may be due to the absence of hydroxyl groups in BePE which, in the case of BaPDE, are an important factor in determining the stereoselective properties of the covalent binding to double-stranded DNA.     

AM1 Study of N-2-Acetylaminofluorene bonded to Deoxyguanosine at the Minor Adduct Site

We have computed the total energy as a function of six important torsion angles of the carcinogen N-2-acetylaminofluorene (AAF) bonded to thenitrogen N2 of deoxyguanosine using the semiempirical quantum mechanical method AM1. One global minimum and one local minimum are found separated by a modest barrier. We have computed the normal-mode frequencies of the relevant torsional motions and have determined the rate of conversion betweenthe two minima.     

Effects of Ellagic Acid by Oral Administration on N-Acetylation and Metabolism of 2-Aminofluorene in Rat Brain Tissues

Numerous studies have demonstrated that the Acetyl Coenzyme A-dependent arylamine NAT enzyme exist in many tissues of experimental animals including humans, and that NAT has been shown to be exist in mouse brain tissue. Increased NAT activity levels are associated with increased sensitivity to the mutagenic effects of arylamine carcinogens. Attenuation of liver NAT activity is related to breast and bladder cancer processes. Therefore, the effects of ellagic acid (EA) on the in vitro and in vivo N-acetylation of 2-aminofluorene (AF) were investigated in cerebrum, cerebellum and pineal gland tissues from male Sprague-Dawley rats. For in vitro examination, cytosols with or without EA (0.5–500 M) co-treatment decreased 7–72%, 15–63% and 10–78% of AF acetylation for cerebrum, cerebellum and pineal gland tissues, respectively. For in vivo examination, EA and AF at the same time treated groups with all 3 examined tissues did show significant differences (the changes of total amounts of AF and AF metabolites based on the Anova analysis) when compared to the ones without EA cotreatment rats. The pretreatment of male rats with EA (10 mg/kg) 24 hr prior to the administration of AF (50 mg/kg) (one day of EA administration suffice to induce large changes in phase II enzyme activity) resulted in a 76% decrease in total AF and metabolites in pineal gland but did not show significant differences in cerebrum and cerebellum tissues. This is the first demonstration to show that EA decreases the N-acetylation of carcinogens in rat brain tissues.     

Kinetics of Deoxy-CTP Incorporation Opposite a dG-C8-N-2-Aminofluorene Adduct by a High-Fidelity DNA Polymerase

The model carcinogen N-2-acetylaminofluorene covalently binds to the C8 position of guanine to form two adducts, the N-(2′-deoxyguanosine-8-yl)-aminofluorene (G-AF) and the N-2-(2′-deoxyguanosine-8-yl)-acetylaminofluorene (G-AAF). Although they are chemically closely related, their biological effects are strongly different and they are processed by different damage tolerance pathways. G-AF is bypassed by replicative and high-fidelity polymerases, while specialized polymerases ensure synthesis past of G-AAF. We used the DNA polymerase I fragment of a Bacillus stearothermophilus strain as a model for a high-fidelity polymerase to study the kinetics of incorporation of deoxy-CTP (dCTP) opposite a single G-AF. Pre-steady-state kinetic experiments revealed a drastic reduction in dCTP incorporation performed by the G-AF-modified ternary complex. Two populations of these ternary complexes were identified: (i) a minor productive fraction (20%) that readily incorporates dCTP opposite the G-AF adduct with a rate similar to that measured for the adduct-free ternary complexes and (ii) a major fraction of unproductive complexes (80%) that slowly evolve into productive ones. In the light of structural data, we suggest that this slow rate reflects the translocation of the modified base within the active site, from the pre-insertion site into the insertion site. By making this translocation rate limiting, the G-AF lesion reveals a novel kinetic step occurring after dNTP binding and before chemistry.     

Effect of Curvature-Induced Superlattice Structures on Energy Band Structures of Helically Coiled Carbon Nanotubes

We studied electronic properties of a two-dimensional electron gas confined on the surface of helical curved tube, specifically, curvature induced by the geometry of helically coiled carbon nanotubes. The curvature generates two types of effective couplings that are (i) Penney-Kronig potential and (ii) a periodic spin-orbit potential. The energy-momentum dispersion relations are theoretically calculated using new variables to explain the electron spiraling around the circular helix line in counterclockwise and clockwise directions. Then we have to set up the formalism for dealing with a periodic potential as Bloch’s theorem. For calculation, we rewrite the Dirac equation in curved space-time in the form of a block matrix equation. Our numerical results demonstrate that there are pseudo-Landau quantization levels and the motion of an electron in circumference direction coupling with the arc length motion coupling. In addition, the one-dimensional dispersion relation lines present characteristics of time reversal symmetry and inversion symmetry. Finally, we also investigated the differential energy of band structures for the case where the periodic spin-orbit potential increased with respect to the increase of curvature. We found that the non-linearly increase of the differential energy was due to the periodic spin-orbit potential, corresponding to Zeeman effect.