Pendampingan Penggunaan Software Komputasi bagi Guru MGMP Kimia Kota Ternate

Pemanfaatan perangkat lunak kimia komputasi bagi siswa sekolah menengah atas merupakan hal yang sangat penting dalam peningkatan pemahaman mereka terkait dengan hal-hal mendasar dari sebuah mekanisme reaksi kimia. Selain itu, pemahaman yang baik juga penting dalam rangka untuk mempersiapkan generasi-generasi yang nantinya lebih siap untuk masuk ke tahapan lanjutan seperti eksperimen yang dilaksanakan di Universitas-universitas atau lembaga penelitian lainnya. Oleh karena itu, proses sosialisasi yang direalisasikan dalam bentuk pelatihan atau workshop dilakukan bagi guru MGMP kimia sekolah menengah atas di kota Ternate. Tujuannya agar ketika diimplementasikan, pemahaman para siswa terkait dengan mekanisme reaksi dapat meningkat. Kegiatan ini, selain tergolong dalam kegiatan yang masih baru di Indonesia, juga merupakan kegiatan yang pertama kali diajukan untuk daerah provinsi Maluku Utara. Berdasarkan hasil evaluasi kegiatan, sebanyak 98% peserta dapat memahami, mengoperasikan, serta mengimplementasikan software komputasi kimia dalam bentuk reaksi sederhana.&nbsp

Understanding the role of oxygen-vacancy defects in Cu₂O(111) from first-principle calculations

The presence of defects, such as copper and oxygen vacancies, in cuprous oxide films determines their characteristic carrier conductivity and consequently their application as semiconducting systems. There are still open questions on the induced electronic re-distribution, including the formation of polarons. Indeed, to accurately reproduce the structural and electronic properties at the cuprous oxide surface, very large slab models and theoretical approaches that go beyond the standard generalized gradient corrected density functional theory are needed. In this work we investigate oxygen vacancies formed in proximity of a reconstructed Cu$_{2}$O(111) surface, where the outermost unsaturated copper atoms are removed, thus forming non-stoichiometric surface layers with copper vacancies. We address simultaneously surface and bulk properties by modelling a thick and symmetric slab, to find that hybrid exchange-correlation functionals are needed to describe the oxygen vacancy in this system. Our simulations show that the formation of oxygen vacancies is favoured in the sub-surface layer. Moreover, the oxygen vacancy leads to a splitting and left-shift of the shallow hole states in the gap, which are associated with the deficiency of copper at the surface. These findings suggest that surface electronic structure and reactivity are sensitive to the presence of oxygen vacancies, also when the latter are formed deeper within the film

Biochemical, Molecular, and Clinical Characterization of Patients With Primary Carnitine Deficiency via Large-Scale Newborn Screening in Xuzhou Area

Background: Primary carnitine deficiency (PCD) is attributed to a variation in the SLC22A5 (OCTN2) gene which encodes the key protein of the carnitine cycle, the OCTN2 carnitine transporter. PCD is typically identified in childhood by either hypoketotic hypoglycemia, or skeletal and cardiac myopathy. The aim of this study was to the clinical, biochemical, and molecular characteristics of PCD patients via newborn screening with tandem mass spectrometry (MS/MS).Methods: MS/MS was performed to screen newborns for inherited metabolic diseases. SLC22A5 gene mutations were detected in the individual and/or their family member by DNA mass array and next-generation sequencing (NGS).Results: Among the 236,368 newborns tested, ten exhibited PCD, and six others were diagnosed with low carnitine levels caused by their mothers, who had asymptomatic PCD. The incidence of PCD in the Xuzhou area is ~1:23,637. The mean initial free carnitine (C0) concentration of patients was 6.41 ± 2.01 μmol/L, and the follow-up screening concentration was 5.80 ± 1.29 μmol/L. After treatment, the concentration increased to 22.8 ± 4.13 μmol/L.Conclusion: This study demonstrates the important clinical value of combining MS/MS and NGS for the diagnosis of PCD and provides new insight into the diagnosis of PCD and maternal patients with PCD using C0 concentration and SLC22A5 mutations

The Substrate-Driven Transition to an Inward-Facing Conformation in the Functional Mechanism of the Dopamine Transporter

The dopamine transporter (DAT), a member of the neurotransmitter:Na(+) symporter (NSS) family, terminates dopaminergic neurotransmission and is a major molecular target for psychostimulants such as cocaine and amphetamine, and for the treatment of attention deficit disorder and depression. The crystal structures of the prokaryotic NSS homolog of DAT, the leucine transporter LeuT, have provided critical structural insights about the occluded and outward-facing conformations visited during the substrate transport, but only limited clues regarding mechanism. To understand the transport mechanism in DAT we have used a homology model based on the LeuT structure in a computational protocol validated previously for LeuT, in which steered molecular dynamics (SMD) simulations guide the substrate along a pathway leading from the extracellular end to the intracellular (cytoplasmic) end.Key findings are (1) a second substrate binding site in the extracellular vestibule, and (2) models of the conformational states identified as occluded, doubly occupied, and inward-facing. The transition between these states involve a spatially ordered sequence of interactions between the two substrate-binding sites, followed by rearrangements in structural elements located between the primary binding site and the cytoplasmic end. These rearrangements are facilitated by identified conserved hinge regions and a reorganization of interaction networks that had been identified as gates.Computational simulations supported by information available from experiments in DAT and other NSS transporters have produced a detailed mechanistic proposal for the dynamic changes associated with substrate transport in DAT. This allosteric mechanism is triggered by the binding of substrate in the S2 site in the presence of the substrate in the S1 site. Specific structural elements involved in this mechanism, and their roles in the conformational transitions illuminated here describe, a specific substrate-driven allosteric mechanism that is directly amenable to experiment as shown previously for LeuT

The Energy Landscape Analysis of Cancer Mutations in Protein Kinases

The growing interest in quantifying the molecular basis of protein kinase activation and allosteric regulation by cancer mutations has fueled computational studies of allosteric signaling in protein kinases. In the present study, we combined computer simulations and the energy landscape analysis of protein kinases to characterize the interplay between oncogenic mutations and locally frustrated sites as important catalysts of allostetric kinase activation. While structurally rigid kinase core constitutes a minimally frustrated hub of the catalytic domain, locally frustrated residue clusters, whose interaction networks are not energetically optimized, are prone to dynamic modulation and could enable allosteric conformational transitions. The results of this study have shown that the energy landscape effect of oncogenic mutations may be allosteric eliciting global changes in the spatial distribution of highly frustrated residues. We have found that mutation-induced allosteric signaling may involve a dynamic coupling between structurally rigid (minimally frustrated) and plastic (locally frustrated) clusters of residues. The presented study has demonstrated that activation cancer mutations may affect the thermodynamic equilibrium between kinase states by allosterically altering the distribution of locally frustrated sites and increasing the local frustration in the inactive form, while eliminating locally frustrated sites and restoring structural rigidity of the active form. The energy landsape analysis of protein kinases and the proposed role of locally frustrated sites in activation mechanisms may have useful implications for bioinformatics-based screening and detection of functional sites critical for allosteric regulation in complex biomolecular systems

Biochemical, Structural and Molecular Dynamics Analyses of the Potential Virulence Factor RipA from Yersinia pestis

Human diseases are attributed in part to the ability of pathogens to evade the eukaryotic immune systems. A subset of these pathogens has developed mechanisms to survive in human macrophages. Yersinia pestis, the causative agent of the bubonic plague, is a predominately extracellular pathogen with the ability to survive and replicate intracellularly. A previous study has shown that a novel rip (required for intracellular proliferation) operon (ripA, ripB and ripC) is essential for replication and survival of Y. pestis in postactivated macrophages, by playing a role in lowering macrophage-produced nitric oxide (NO) levels. A bioinformatics analysis indicates that the rip operon is conserved among a distally related subset of macrophage-residing pathogens, including Burkholderia and Salmonella species, and suggests that this previously uncharacterized pathway is also required for intracellular survival of these pathogens. The focus of this study is ripA, which encodes for a protein highly homologous to 4-hydroxybutyrate-CoA transferase; however, biochemical analysis suggests that RipA functions as a butyryl-CoA transferase. The 1.9 Å X-ray crystal structure reveals that RipA belongs to the class of Family I CoA transferases and exhibits a unique tetrameric state. Molecular dynamics simulations are consistent with RipA tetramer formation and suggest a possible gating mechanism for CoA binding mediated by Val227. Together, our structural characterization and molecular dynamic simulations offer insights into acyl-CoA specificity within the active site binding pocket, and support biochemical results that RipA is a butyryl-CoA transferase. We hypothesize that the end product of the rip operon is butyrate, a known anti-inflammatory, which has been shown to lower NO levels in macrophages. Thus, the results of this molecular study of Y. pestis RipA provide a structural platform for rational inhibitor design, which may lead to a greater understanding of the role of RipA in this unique virulence pathway