Mechanism of proteolysis in matrix metalloproteinase-2 revealed by QM/MM modeling

The mechanism of enzymatic peptide hydrolysis in matrix metalloproteinase-2 (MMP-2) was studied at atomic resolution through quantum mechanics/molecular mechanics (QM/MM) simulations. An all-atom three-dimensional molecular model was constructed on the basis of a crystal structure from the Protein Data Bank (ID: 1QIB), and the oligopeptide Ace-Gln-Gly∼Ile-Ala-Gly-Nme was considered as the substrate. Two QM/MM software packages and several computational protocols were employed to calculate QM/MM energy profiles for a four-step mechanism involving an initial nucleophilic attack followed by hydrogen bond rearrangement, proton transfer, and C—N bond cleavage. These QM/MM calculations consistently yield rather low overall barriers for the chemical steps, in the range of 5–10 kcal/mol, for diverse QM treatments (PBE0, B3LYP, and BB1K density functionals as well as local coupled cluster treatments) and two MM force fields (CHARMM and AMBER). It, thus, seems likely that product release is the rate-limiting step in MMP-2 catalysis. This is supported by an exploration of various release channels through QM/MM reaction path calculations and steered molecular dynamics simulations

Ситуаційні тестові завдання як засіб діагностики предметних компетенцій майбутніх учителів технологій профільної школи (на прикладі дисципліни «Основи швейного виробництва»)

The article deals with the creation of situational tests as a means of diagnosing the level of formation of subject competencies students-future teachers technology that will teach high school students the basics of sewing business. It analyses the essence of the concepts of «test», «testing». Based on the analysis of scientific publications in the studied subjects found type tests that can be used as a tool for diagnosing competencies of future teachers technology specialized schools. Competence-oriented situational test tasks (by the example of the subject «Fundamentals of Sewing Production») are developed and presented.Стаття присвячена проблемі створення ситуаційних тестових завдань як засобу діагностики рівня сформованості предметних компетенцій студентів-майбутніх учителів технології, що навчатимуть учнів старшої школи основам швейної справи. Здійснено аналіз та визначено сутність понять «тест», «тестування». Подано класифікацію тестів за характерними ознаками. На підставі аналізу наукових публікацій з досліджуваної тематики з’ясовано вид тестів, які доцільно використовувати як засіб діагностики компетенцій майбутніх учителів технологій профільної школи. Розроблено та представлено компетентнісно-орієнтовані ситуаційні тестові завдання (на прикладі дисципліни «Основи швейного виробництва»)

Role of the flat-designed surface in improving the cyclic fatigue resistance of endodontic NiTi rotary instruments

The aim of this study was to investigate the role of the flat-designed surface in improving the resistance to cyclic fatigue by comparing heat-treated F-One (Fanta Dental, Shanghai, China) nickel-titanium (NiTi) rotary instruments and similar prototypes, differing only by the absence of the flat side. The null hypothesis was that there were no differences between the two tested instruments in terms of cyclic fatigue lifespan. A total of 40 new NiTi instruments (20 F-One and 20 prototypes) were tested in the present study. The instruments were rotated with the same speed (500 rpm) and torque (2 N) using an endodontic motor (Elements Motor, Kerr, Orange, CA, USA) in the same stainless steel, artificial canal (90° angle of curvature and 5 mm radius). A Wilcoxon-Mann-Whitney test was performed to assess the differences in terms of time to fracture and the length of the fractured segment between the flat- and non-flat-sided instruments. Significance was set at p = 0.05. The differences in terms of time to fracture between non-flat and flat were statistically significant (p < 0.001). In addition, the differences in terms of fractured segment length were statistically significant (p = 0.034). The results of this study highlight the importance of flat-sided design in increasing the cyclic fatigue lifespan of NiTi rotary instruments

Особливості використання інноваційних технологій, форм та методів у професійній підготовці майбутнього вчителя трудового навчання до викладання художньо-технічних дисциплін

In this paper the authors have considered the necessity to implement the latest achievements of pedagogical science, modern forms, methods and innovative technologies in order to improve professional training of intending Handicraft teachers. Analysis of psychological and pedagogical literature has been carried out. The main approaches used by the leading scientists to differently define the notions of «forms of learning organization» and «organizational forms of learning» have been highlighted in this context. The notion of «learning technology» has been explained from the pedagogical and psychological perspectives as the way of interaction between the participants of learning process. Classification of forms of learning organization according to various criteria has been presented. The authors’ personal points of view as to the use of both traditional (classical) and non-standard (innovative) forms of learning organization to form professional readiness of an intending Handicraft teacher have been suggested. Classification of the main methods has been presented and the authors’ ideas of their appropriate selection to boost the formation of intending Handicraft teachers’ professional readiness to teach the Art and Technical subjects have been expressed. The most efficient innovative learning technologies facilitating the formation of the mentioned above intending teacher’s professional readiness have been identified. The conclusion has been made that using various education technologies, forms and methods in training intending Handicraft teachers one can encourage their creative approach to the performed tasks within the future professional activities. Key words: pedagogical sciences, Handicraft, forms of learning organization, learning methods, learning technologies, innovative technologies, professional readiness, achmeological technology.У статті авторами розглянуто необхідність упровадження новітніх досягнень педагогічної науки, сучасних форм, методів та інноваційних технологій з метою покращання професійної підготовки майбутніх учителів трудового навчання. Виконано аналіз психолого-педагогічної літератури, в контексті якого висвітлено основні підходи провідних науковців щодо різних тлумачень поняття «форми організації навчання» та «організаційні форми навчання». Розглянуто поняття «технології навчання» як спосіб взаємодії між суб’єктами навчального процесу з педагогічної та психологічної точки зору. Представлено класифікацію форм організації навчальної діяльності за різними критеріями. Запропоновано власне бачення використання як традиційних (класичних), так і нестандартних (інноваційних) форм організації навчання для формування професійної готовності майбутнього вчителя трудового навчання. Наведено класифікацію основних методів та запропоновано власне бачення їх підбору для поліпшення процесу формування професійної готовності майбутнього вчителя технологій до викладання художньо-технічних дисциплін. Виокремлено найбільш придатні інноваційні технології навчання, котрі сприятимуть формуванню зазначеної готовності майбутнього вчителя. Зроблено висновок, що використання різноманітних освітніх технологій, форм та методів у підготовці майбутнього вчителя трудового навчання сприятиме його творчому підходу до справи у майбутній професійній діяльності. Ключові слова: педагогічні науки, трудове навчання, форми організації навчання, методи навчання, технології навчання, інноваційні технології, професійна готовність, акмеологічна технологія

BLUF Domain Function Does Not Require a Metastable Radical Intermediate State

BLUF (blue light using flavin) domain proteins are an important family of blue light-sensing proteins which control a wide variety of functions in cells. The primary light-activated step in the BLUF domain is not yet established. A number of experimental and theoretical studies points to a role for photoinduced electron transfer (PET) between a highly conserved tyrosine and the flavin chromophore to form a radical intermediate state. Here we investigate the role of PET in three different BLUF proteins, using ultrafast broadband transient infrared spectroscopy. We characterize and identify infrared active marker modes for excited and ground state species and use them to record photochemical dynamics in the proteins. We also generate mutants which unambiguously show PET and, through isotope labeling of the protein and the chromophore, are able to assign modes characteristic of both flavin and protein radical states. We find that these radical intermediates are not observed in two of the three BLUF domains studied, casting doubt on the importance of the formation of a population of radical intermediates in the BLUF photocycle. Further, unnatural amino acid mutagenesis is used to replace the conserved tyrosine with fluorotyrosines, thus modifying the driving force for the proposed electron transfer reaction; the rate changes observed are also not consistent with a PET mechanism. Thus, while intermediates of PET reactions can be observed in BLUF proteins they are not correlated with photoactivity, suggesting that radical intermediates are not central to their operation. Alternative nonradical pathways including a keto–enol tautomerization induced by electronic excitation of the flavin ring are considered

Metal Fluorides as Analogs for Studies on Phosphoryl Transfer Enzymes

The 1994 structure of a transition state analog with AlF4- and GDP complexed to G1, a small G protein, heralded a new field of research into structure and mechanism of enzymes that manipulate transfer of the phosphoryl (PO3-) group. The list of enzyme structures that embrace metal fluorides, MFx, as ligands that imitate either the phosphoryl group or a phosphate, is now growing at over 80 per triennium. They fall into three distinct geometrical classes: (i) Tetrahedral complexes, based on BeF3-, mimic ground state phosphates; (ii) Octahedral complexes, primarily based on AlF4-, mimic "in-line" anionic transition state for phosphoryl transfer; and (iii) Trigonal bipyramidal complexes, represented by MgF3- and putative AlF30 moieties, additionally mimic the tbp geometry of the transition state. The interpretation of these structures provides a deeper mechanistic understanding of the behavior and manipulation of phosphate monoesters in molecular biology. This review provides a comprehensive overview of these structures, their uses, and their computational development. It questions the identification of AlF30 and MgF4= as tbp species in protein complexes and discusses the relevance of physical organic chemistry and water-based model studies for understanding phosphoryl group transfer in enzymes. It describes two roles for amino acid side-chains that mediate proton transfers during phosphoryl transfer, based on the analysis of protein/MFx structures. First, they deploy hydrogen bonding to neutral oxygen nucleophiles so as to orientate them for correct orbital overlap with the electrophilic phosphorus center. Secondly, they behave as classical general acid/base catalysts