Chiral symmetry breaking via crystallization of the glycine and \alpha-amino acid system: a mathematical model

We introduce and numerically solve a mathematical model of the experimentally established mechanisms responsible for the symmetry breaking transition observed in the chiral crystallization experiments reported by I. Weissbuch, L. Addadi, L. Leiserowitz and M. Lahav, J. Am. Chem. Soc. 110 (1988), 561-567. The mathematical model is based on five basic processes: (1) The formation of achiral glycine clusters in solution, (2) The nucleation of oriented glycine crystals at the air/water interface in the presence of hydrophobic amino acids, (3) A kinetic orienting effect which inhibits crystal growth, (4) The enantioselective occlusion of the amino acids from solution, and (5) The growth of oriented host glycine crystals at the interface. We translate these processes into differential rate equations. We first study the model with the orienting process (2) without (3) and then combine both allowing us to make detailed comparisons of both orienting effects which actually act in unison in the experiment. Numerical results indicate that the model can yield a high percentage orientation of the mixed crystals at the interface and the consequent resolution of the initially racemic mixture of amino acids in solution. The model thus leads to separation of enantiomeric territories, the generation and amplification of optical activity by enantioselective occlusion of chiral additives through chiral surfaces of glycine crystals

Класифікація злочинів проти радіаційної безпеки

Торбєєв М. О. / М. О. Торбєєв // Правове життя сучасної України : матеріали Міжнар. наук. конф. проф.-викл. та аспірант. складу (м. Одеса, 16-17 травня 2013 р.) / відп. за вип. В. М. Дрьомін ; НУ "ОЮА". Півд. регіон. центр НАПрН України. - Одеса : Фенікс, 2013. - Т. 2. - С. 304-306

Chemical synthesis of transactivation domain (TAD) of tumor suppressor protein p53 by native chemical ligation of three peptide segments

Chemical composition of tumor suppressor protein p53 is altered via multiple post-translational modifications which modulate its cellular lifetime and interactions with other biomolecules. Here we report total chemical synthesis of a 61-residue form of transactivation domain (TAD) of p53 based on native chemical ligation of three peptide segments. The experiments to characterize its binding to nuclear co-activator binding domain (NCBD) of CREB-binding protein confirmed native-like induced folding upon binding to NCBD. Thus, the synthetic approach described herein can be useful for the preparation of various post-translationally modified analogues of TAD-p53 for further functional biochemical and biophysical studies.The research was supported by the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme (ERC-2016-StG, grant number 715062-HiChemSynPro)

Catalytic Water Co-Existing with a Product Peptide in the Active Site of HIV-1 Protease Revealed by X-Ray Structure Analysis

BACKGROUND: It is known that HIV-1 protease is an important target for design of antiviral compounds in the treatment of Acquired Immuno Deficiency Syndrome (AIDS). In this context, understanding the catalytic mechanism of the enzyme is of crucial importance as transition state structure directs inhibitor design. Most mechanistic proposals invoke nucleophilic attack on the scissile peptide bond by a water molecule. But such a water molecule coexisting with any ligand in the active site has not been found so far in the crystal structures. PRINCIPAL FINDINGS: We report here the first observation of the coexistence in the active site, of a water molecule WAT1, along with the carboxyl terminal product (Q product) peptide. The product peptide has been generated in situ through cleavage of the full-length substrate. The N-terminal product (P product) has diffused out and is replaced by a set of water molecules while the Q product is still held in the active site through hydrogen bonds. The position of WAT1, which hydrogen bonds to both the catalytic aspartates, is different from when there is no substrate bound in the active site. We propose WAT1 to be the position from where catalytic water attacks the scissile peptide bond. Comparison of structures of HIV-1 protease complexed with the same oligopeptide substrate, but at pH 2.0 and at pH 7.0 shows interesting changes in the conformation and hydrogen bonding interactions from the catalytic aspartates. CONCLUSIONS/SIGNIFICANCE: The structure is suggestive of the repositioning, during substrate binding, of the catalytic water for activation and subsequent nucleophilic attack. The structure could be a snap shot of the enzyme active site primed for the next round of catalysis. This structure further suggests that to achieve the goal of designing inhibitors mimicking the transition-state, the hydrogen-bonding pattern between WAT1 and the enzyme should be replicated

The role of the IT-state in D76N β2-microglobulin amyloid assembly: a crucial intermediate or an innocuous bystander?

The D76N variant of human β2-microglobulin (β2m) is the causative agent of a hereditary amyloid disease. Interestingly, D76N-associated amyloidosis has a distinctive pathology compared with aggregation of wild-type (WT) β2m which occurs in dialysis-related amyloidosis. A folding intermediate of WT-β2m, known as the IT-state, which contains a non-native trans Pro32, has been shown to be a key precursor of WT-β2m aggregation in vitro. However, how a single amino acid substitution enhances the rate of aggregation of D76N-β2m and gives rise to a different amyloid disease remained unclear. Using real-time refolding experiments monitored by CD and NMR, we show that the folding mechanisms of WT- and D76N-β2m are conserved in that both proteins fold slowly via an IT-state that has similar structural properties. Surprisingly, however, direct measurement of the equilibrium population of IT using NMR showed no evidence for an increased population of the IT-state for D76N-β2m, ruling out previous models suggesting that this could explain its enhanced aggregation propensity. Producing a kinetically trapped analogue of IT by deleting the N-terminal six amino acids increases the aggregation rate of WT-β2m, but slows aggregation of D76N-β2m, supporting the view that while the folding mechanisms of the two proteins are conserved, their aggregation mechanisms differ. The results exclude the IT-state as the cause of the rapid aggregation of D76N-β2m, suggesting that other non-native states must cause its high aggregation rate. The results highlight how a single substitution at a solvent-exposed site can affect the mechanism of aggregation and the resulting disease

Total chemical synthesis and biophysical properties of a designed soluble 24 kDa amyloid analogue

Discovering molecular probes that specifically recognize distinct amyloid structures is highly important for physiological studies of protein-misfolding diseases as well as for the development of diagnostic reagents and inhibitors of amyloid self-assembly. Here, we demonstrate an approach that allows for identification of N-methylated peptides that are specific binders for a particular amyloid fiber subtype (or polymorph). Protein design and chemical synthesis were used to produce covalently tethered amyloid analogues with molecular masses approaching 24 kDa and containing nine copies of an amyloidogenic peptide. Such engineered constructs served as a molecular testing platform to evaluate the aggregation properties and solubility as a function of N-methylation pattern. An advantage of the method is the possibility of biophysical characterization of amyloid constructs in solution