Symmetry versus Asymmetry in the Molecules of Life: Homomeric Protein Assemblies

The essay is dedicated to the relation of symmetry and asymmetry-chirality in Nature. The Introduction defines symmetry and its impact on basic definitions in science and human activities. The following section Chirality of molecules reveals breifly development of notion of chirality and its significance in living organisms and science. Homochirality is a characteristic hallmark of life and its significance is presented in the section Homochirality of Life. Proteins, important constituents of living cells performing versatile functions are chiral macromolecules composed of L-amino acids. In particular, the protein assemblies are of a great importance in functions of a cell. Therefore, they have attracted researches to examine them from different points of view. Among proteins of known three-dimensional structures about 50–80% of them exist as homomeric protein complexes. Protein monomers lack any intrinsic, underlying symmetry, i.e. enantiomorphic protein molecules involve left-handed amino acids but their asymmetry does not appear to extend to the level of quaternary structures (homomeric complexes) as observed by Chothia in 1991. In the section Homomeric assemblies we performed our analysis of very special cases of homomers revealing non-crystallographic symmetry in crystals. Homochiral proteins can crystallize only in enantiomorphic space groups. Among 230 existing space groups 65 are enantiomorphic containing limited symmetry elements that are rotation and screw-rotation axes. Any axis of rotation symmetry of a crystal lattice must be two-fold, three-fold, four-fold, or six-fold. Five-fold, seven-fold, and higher-fold rotation symmetry axes are incompatible with the symmetry under spatial displacement of the three-dimensional crystal lattice

The Role of Phosphate Binding in Purine Nucleoside Phosphorylase of Helicobacter pylori

Purine nucleoside phosphorylase (PNP) is an essential enzyme in the purine salvage pathway of Helicobacter pylori. Since H. pylori lacks the ability to synthesize purine nucleosides de novo, inhibition of this enzyme could stop the growth of this bacterium. However, for the design of successful inhibitors the details of the mechanism of this enzyme should be fully understood. PNPs catalyze cleavage of the glycosidic bond of purine nucleosides, and phosphate is one of the substrates. It is thought that binding of phosphate induces the conformational change as a necessary initial step in the catalysis. This conformational change is manifested in closing of either one of the six active sites in the homohexameric PNPs. It is unclear whether the binding of phosphate is sufficient or just a necessary condition for the closing of the active site. In this paper we conducted an experiment to check this by soaking the crystals of the apo form of the enzyme in increasing concentrations of phosphate. This work is licensed under a Creative Commons Attribution 4.0 International License

Hydrogen Bonding and Molecular Assemblies

The old concept of complementarity, connected with the process of molecular recognition represents a simple approach to understanding molecular assembling. The noncovalent interactions governing (self)assemblies are fundamental to supramolecular chemistry and crystal engineering. Among noncovalent interactions governing molecular assembling, hydrogen bonding plays the leading role. A few examples of molecular assembling relevant to life processes and (bio)nano materials reveal the importance of this phenomenon. Systematic analysis of hydrogen bonding patterns, as a function of proton donor and acceptor properties, and stereochemical parameters, including chirality, is presented for a large number of di(amino acid) and di(amino alcohol) derivatives with oxalyl, phthaloyl, and fumaroyl bridges. Particular attention will be given to the molecular topology of such hydrogen bonded assemblies in terms of crystal engineering

Still a Long Way to Fully Understanding the Molecular Mechanism of Escherichia coli Purine Nucleoside Phosphorylase

The results of several decades of studying the catalytic mechanism of Escherichia colt purine nucleoside phosphorylases (PNP) by solution studies and crystal structure determinations are presented. Potentially PNPs can be used for enzyme-activating prodrug gene therapy against solid tumours because of the differences in specificity between human and E. coli PNPs. Biologically active form of PNP from E. coli is a homohexamer that catalyses the phosphorolytic cleavage of the glycosidic bond of purine nucleosides. Two conformations of the active site are possible after substrate(s) binding: open and closed. A series of determined 3D-structures of PNP binary and ternary complexes facilitated the prediction of the main steps in the catalytic mechanism. For their validation the active site mutants: Arg24Ala, Asp204Ala, Arg217Ala, Asp204Asn and double mutant Asp204Ala/Arg217Ala were prepared, The activity tests confirm that catalysis involves protonation of the purine base at position N7 and give better insight into the cooperativity between subunits in this oligomeric enzyme

Preliminary Crystallographic Study of Streptomyces coelicolor Single-stranded DNA-binding Protein

Single-stranded DNA-binding proteins (SSBs) play a crucial role in DNA processing such as replication, repair and recombination in all organisms, from bacteria to human. Streptomyces coelicolor ssb gene was overexpressed in a heterologous host, Escherichia coli NM522. 15 mg of purified protein from 1 dm3 of culture was obtained in one-step procedure applying Ni2+ chelating chromatography. Among bacterial SSBs with the solved crystal structure, the S. coelicolor SSB displayed significant sequence similarity with those from Mycobacterium tuberculosis and Mycobacterium smegmatis, slow growing bacteria with a high GC content. Moreover, conserved amino acid region that forms additional ß strand in mycobacterial SSBs was also found in S. coelicolor SSB. The full-length protein readily crystallises in space group I222 or I212121 with unit-cell parameters a = 100.8, b = 102.1, c = 164.2 Å. The asymmetric unit is expected to contain four monomers with solvent content of 52–55 %

Lean PLM - Information technology strategy for innovative and sustainable business environment

In today’s process manufacturing environment, innovation is viewed as critical to sustainable growth and business profitability. While innovation is regarded as the answer, the companies can effectively measure the return on R&D investment, have acceptable product success rates, achieve acceptable promotional effectiveness, or have visibility into their compliance risks or operational readiness for new product launches. Companies must have repeatable, compliant and responsive business processes, global ICT information infrastructure that provides a single source of the truth, alignment across departments and solutions that evolve without coding. With holistic strategy and supporting infrastructure, companies can consistently minimize the time to scale, improve product success rates and promotional effectiveness, and enjoy sustainable and profitable growth. The companies must first focus on the needs of their customer, continually minimize time to scale, eliminate waste, drive out costs and improve. These are core concepts of a Lean strategy. This paper will describe how Lean concept with PLM business strategy can leverage Lean with integrated compliance, continua

Gamma Radiation- and Ultraviolet-Induced Polymerization of Bis(amino acid)fumaramide Gel Assemblies

Controlling the polymerization of supramolecular self-assembly through external stimuli holds great potential for the development of responsive soft materials and manipulation at the nanoscale. Vinyl esters of bis(leu or val)fumaramide (1a and 2a) have been found to be gelators of various organic solvents and were applied in this investigation of the influence of organogelators’ self-assembly on solid-state polymerization induced by gamma and ultraviolet irradiation. Here, we report our investigation into the influences of self- assemblies of bis(amino acid vinyl ester) fumaramides on gamma-ray- and ultraviolet-induced polymerization. The gelator molecules self- assembled by non-covalent interactions, mainly through hydrogen bonds between the amide group (CONH) and the carboxyl group (COO), thus forming a gel network. NMR and FTIR spectroscopy were used to investigate and characterize supramolecular gels. TEM and SEM microscopy were used to investigate the morphology of gels and polymers. Morphology studies showed that the gels contained a filamentous structure of nanometer dimensions that was exhaustive in a threedimensional network. The prepared derivatives contained reactive alkyl groups suitable for carrying out the polymerization reaction initiated by gamma or ultraviolet radiation in the supramolecular aggregates of selected gels. It was found that the polymerization reaction occurred only in the network of the gel and was dependent on the structure of aggregates or the proximity and orientation of double bonds in the gel network. Polymers were formed by the gels exposure to gamma and ultraviolet radiation in toluene, and water/DMF gels with transcripts of their gel structure into polymers. The polymeric material was able to immobilize various solvents by swelling. Furthermore, methyl esters of bis(leu and val)fumaramide (1b and 2b) were synthesized ; these compounds showed no gelling properties, and the crystal structure of the valine derivative 2b was determined