Alpha-helical regions of the protein molecule as organic nanotubes

From normal to competo-allosteric regulation: insights into the binding pattern dynamics of DSPI protein of Pseudomonas aeruginosa

DSPI, a putative enoyl-coenzyme A (CoA) hydratase/isomerase, is anticipated to be involved in the synthesis of cis-2-decenoic acid (CDA), a quorum sensing (QS) signal molecule present in the superbug Pseudomonas aeruginosa. The current study not only adapts a broad-spectrum strategy for the lucid design of small molecule modulators but also provides novel allosteric inhibitors for DSPI, to investigate its function and potential as a therapeutic target. Docking analysis revealed that the compound 10252273, bound to the specific allosteric site, interacted with Glu118, unique amino acid residue of the active binding pocket, hence indicates the presence of a competitive allosteric site. The current study thus identifies and characterizes inhibitors by targeting the normal binding site and also reports the presence of the competo-allosteric site in the same binding tunnel as the normal site. Molecular docking studies proposed two chemical compounds that share a benzamide-benzimidazole (BB) backbone as potent inhibitors that can obstruct the mechanism of DSPI by targeting both the normal and proposed allosteric binding sites. MD simulations further revealed the disruption of the normal binding site due to the displacement of critical residues Cys146 and Glu118. The rearrangement of H-bond pattern, pi-pi interactions, and strong hydrophobic interactions were observed at both the binding sites. The allosteric pocket inhibitor exhibited improved binding energy than the normal site inhibitor based on MMGBSA and MMPBSA analysis. With subsequent characterization, the current study reveals the allosteric binding site and provides insights into the drug binding mechanism of DSPI.Communicated by Ramaswamy H. Sarma.

Features of the Generalized Dynamics of Quasiparticles in Graphene

The general dynamic properties of the electron, as quasiparticle in conduction band of graphene, were analyzed. It is shown that in graphene, these properties essentially differ from similar base properties for crystals with a simple lattice, despite insignificant, on the first sight, difference of dispersion law ε(p). Primarily, crystals with an elementary cell of arbitrary complexity of structure were considered. The obtained general relations were applied further to graphene. Herewith two-dimensional lattice of graphene has been considered as consisting of elementary cells with two atoms. Typically, graphene is considered as crystals consisting of two simple nested sublattices. It has been shown that both considerations lead to the analogous basic results. On the basis of obtained wave Hamiltonian, all the dynamic characteristics of the injected electron, considered as a quasiparticle, were found: speed, tensor of effective dynamic mass, and wave Lagrangian. Also, for some physically actual situations, the dynamic characteristics of an alternative description have been found: a mechanical momentum p _m , mechanical Hamiltonian, and mechanical Lagrangian. For these situations, a generalized Louis de Broglie relationship between mechanical p _m and wave p momenta was found also.

Current in the Protein Nanowires: Quantum Calculations of the Base States

It is known that synthesis of adenosine triphosphoric acid in mitochondrions may be only completed on the condition of transport of the electron pairs, which were created due to oxidation processes, to mitochondrions. As of today, many efforts were already taken in order to understand those processes that occur in the course of donor-acceptor electron transport between cellular organelles (that is, between various proteins and protein structures). However, the problem concerning the mechanisms of electron transport over these organelles still remains understudied. This paper is dedicated to the investigation of these same issues.It has been shown that regardless of the amino acid inhomogeneity of the primary structure, it is possible to apply a representation of the second quantization in respect of the protein molecule (hereinafter "numbers of filling representation"). Based on this representation, it has been established that the primary structure of the protein molecule is actually a semiconductor nanowire. In addition, at the same time, its conduction band, into which an electron is injected as the result of donor-acceptor processes, consists of five sub-bands. Three of these sub-bands have normal dispersion laws, while the rest two sub-bands have abnormal dispersion laws (reverse laws). Test calculation of the current density was made under the conditions of the complete absence of the factors, which may be interpreted as external fields. It has been shown that under such conditions, current density is exactly equal to zero. This is the evidence of correctness of the predictive model of the conductivity band of the primary structure of the protein molecule (protein nanowire). At the same time, it makes it possible to apply the obtained results in respect of the actual situation, where factors, which may be interpreted as external fields, exist.

Primary structure of proteins as a nanowire for metabolic electronic transport

It is considered that the major process in an organism is the synthesis of the adenosine triphosphate (ATP) molecules (its resumption from the adenosine diphosphate (ADP) molecules). These molecules are the basic (if not unique) energy resource of an organism. For the completion of process of the ATP synthesis in mitochondria, it is necessary to transfer to it a pair of electrons from places where electrons rise up as a result of oxidizing processes. Research of mechanisms of such transfer is important therefore, in particular, from the point of regulative influence on them in medical aims. Various proteins, the primary structure of which can provide the transport of electrons between donors and acceptors, saturate a volume and membranes of cages. A question about a possibility to examine this primary structure of proteins as a nanowire of a semiconductor nature is analyzed. The possibility of active transport of electrons through its conductivity band is analyzed also. In this paper, it was shown that a heterogeneous protein system is possible to be considered as a semiconductor with an average-nitrogen nuclear subsystem and with an average-oxygen electronic subsystem. Also, it was shown that in the potential energy of interaction between the electron and the nuclear subsystem indeed exists non-compensated contributions. These contributions are related to the radicals and provide the active transport of electrons along the primary structure of protein molecules. It was demonstrated also that external fields can have local regulative influence on the transport of electron in proteins by compensating the remaining field or strengthening it. Fulfilled analysis gives a possibility in zero approximation of the application of representation of numbers of filling to the protein molecule, considering it as the nanowire.