Structural insight into the thermostable NADP+-dependentmeso-diaminopimelate dehydrogenase fromUreibacillus thermosphaericus

Crystal structures of the thermostablemeso-diaminopimelate dehydrogenase (DAPDH) fromUreibacillus thermosphaericuswere determined for the enzyme in the apo form and in complex with NADP+andN-tris(hydroxymethyl)methyl-2-aminoethanesulfonic acid. The main-chain coordinates of the enzyme showed notable similarity to those ofSymbiobacterium thermophilumDAPDH. However, the subunit arrangement ofU. thermosphaericusDAPDH (a dimer) was totally different from that of theS. thermophilumenzyme (a hexamer). Structural comparison with the dimeric enzyme from the mesophileCorynebacterium glutamicumrevealed that the presence of large numbers of intrasubunit and intersubunit hydrophobic interactions, as well as the extensive formation of intersubunit ion-pair networks, were likely to be the main factors contributing to the higher thermostability ofU. thermosphaericusDAPDH. This differs fromS. thermophilumDAPDH, within which the unique hexameric assembly is likely to be responsible for its high thermostability. Analysis of the active site ofU. thermosphaericusDAPDH revealed the key factors responsible for the marked difference in substrate specificity between DAPDH and the D-amino acid dehydrogenase recently created from DAPDH by introducing five point mutations [Akitaet al.(2012).Biotechnol. Lett.34, 1693–1699; 1701–1702].

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Coaction of Electrostatic and Hydrophobic Interactions: Dynamic Constraints on Disordered TrkA Juxtamembrane Domain

10.26434/chemrxiv.9847190 ◽

2019 ◽

Author(s):

Zichen Wang ◽

Huaxun Fan ◽

Xiao Hu ◽

John Khamo ◽

Jiajie Diao ◽

...

Keyword(s):

Single Molecule ◽

Protein Function ◽

Hydrophobic Interactions ◽

Transmembrane Helix ◽

Point Mutations ◽

Salt Bridge ◽

Receptor Activation ◽

Membrane Dynamics ◽

Juxtamembrane Domain ◽

Joint Work

<p>The receptor tyrosine kinase family transmits signals into cell via a single transmembrane helix and a flexible juxtamembrane domain (JMD). Membrane dynamics makes it challenging to study the structural mechanism of receptor activation experimentally. In this study, we employ all-atom molecular dynamics with Highly Mobile Membrane-Mimetic to capture membrane interactions with the JMD of tropomyosin receptor kinase A (TrkA). We find that PIP<sub>2 </sub>lipids engage in lasting binding to multiple basic residues and compete with salt bridge within the peptide. We discover three residues insertion into the membrane, and perturb it through computationally designed point mutations. Single-molecule experiments indicate the contribution from hydrophobic insertion is comparable to electrostatic binding, and in-cell experiments show that enhanced TrkA-JMD insertion promotes receptor ubiquitination. Our joint work points to a scenario where basic and hydrophobic residues on disordered domains interact with lipid headgroups and tails, respectively, to restrain flexibility and potentially modulate protein function.</p>

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Insight into the HIV-1 Vif SOCS-box–ElonginBC interaction

Open Biology ◽

10.1098/rsob.130100 ◽

2013 ◽

Vol 3 (11) ◽

pp. 130100 ◽

Cited By ~ 7

Author(s):

Zhisheng Lu ◽

Julien R. C. Bergeron ◽

R. Andrew Atkinson ◽

Torsten Schaller ◽

Dennis A. Veselkov ◽

...

Keyword(s):

Solution Structure ◽

Hydrophobic Interactions ◽

Dynamic Information ◽

Ubiquitin Ligase Complex ◽

Biophysical Studies ◽

Viral Infectivity Factor ◽

Β Sheet ◽

Socs Box ◽

Insight Into ◽

Hiv 1

The HIV-1 viral infectivity factor (Vif) neutralizes cell-encoded antiviral APOBEC3 proteins by recruiting a cellular ElonginB (EloB)/ElonginC (EloC)/Cullin5-containing ubiquitin ligase complex, resulting in APOBEC3 ubiquitination and proteolysis. The suppressors-of-cytokine-signalling-like domain (SOCS-box) of HIV-1 Vif is essential for E3 ligase engagement, and contains a BC box as well as an unusual proline-rich motif. Here, we report the NMR solution structure of the Vif SOCS–ElonginBC (EloBC) complex. In contrast to SOCS-boxes described in other proteins, the HIV-1 Vif SOCS-box contains only one α-helical domain followed by a β-sheet fold. The SOCS-box of Vif binds primarily to EloC by hydrophobic interactions. The functionally essential proline-rich motif mediates a direct but weak interaction with residues 101–104 of EloB, inducing a conformational change from an unstructured state to a structured state. The structure of the complex and biophysical studies provide detailed insight into the function of Vif's proline-rich motif and reveal novel dynamic information on the Vif–EloBC interaction.

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Combating the Coronavirus Pandemic in Small Schools

Sustainability ◽

10.3390/su13137086 ◽

2021 ◽

Vol 13 (13) ◽

pp. 7086

Author(s):

Martina Maněnová ◽

Janet Wolf ◽

Martin Skutil ◽

Jitka Vítová

Keyword(s):

Distance Education ◽

Primary Schools ◽

Small Schools ◽

Research Question ◽

Phenomenological Approach ◽

Key Factors ◽

Result Section ◽

School Directors ◽

Ict Competence ◽

Insight Into

Due to the COVID-19 pandemic, the issue of distance education in primary schools has become a much-discussed topic. It is therefore no surprise that the issues related to it have come to the forefront of many researchers. There is, however, at least one group that has stayed relatively unnoticed, and it is so-called small schools. Thus, we conducted a qualitative study based on the phenomenological approach, searching for answers to our research question: What has been the experience of the directors of small schools with distance education during the pandemic? Our findings offer an in-depth insight into the life of six schools through the eyes of their directors. Semi-structural interviews with school directors helped us reveal three key factors that, in our opinion, had the greatest influence on the form of distance education. These are (1) the factor of ICT competence of all actors, (2) the factor of organization of educational settings, and (3) the factor of the teaching methods and forms used in education. Furthermore, we conclude the result section with a subchapter that captures the positive aspects of distance education as perceived by the addressed school directors.

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Genetics of Metabolic Variations between Yersinia pestis Biovars and the Proposal of a New Biovar, microtus

Journal of Bacteriology ◽

10.1128/jb.186.15.5147-5152.2004 ◽

2004 ◽

Vol 186 (15) ◽

pp. 5147-5152 ◽

Cited By ~ 143

Author(s):

Dongsheng Zhou ◽

Zongzhong Tong ◽

Yajun Song ◽

Yanping Han ◽

Decui Pei ◽

...

Keyword(s):

Yersinia Pestis ◽

Nitrate Reduction ◽

Gene Loss ◽

Point Mutations ◽

Genomic Profile ◽

Frameshift Deletion ◽

Potential Vaccine ◽

Negative Characteristic ◽

Insight Into ◽

Negative Phenotype

ABSTRACT Yersinia pestis has been historically divided into three biovars: antiqua, mediaevalis, and orientalis. On the basis of this study, strains from Microtus-related plague foci are proposed to constitute a new biovar, microtus. Based on the ability to ferment glycerol and arabinose and to reduce nitrate, Y. pestis strains can be assigned to one of four biovars: antiqua (glycerol positive, arabinose positive, and nitrate positive), mediaevalis (glycerol positive, arabinose positive, and nitrate negative), orientalis (glycerol negative, arabinose positive, and nitrate positive), and microtus (glycerol positive, arabinose negative, and nitrate negative). A 93-bp in-frame deletion in glpD gene results in the glycerol-negative characteristic of biovar orientalis strains. Two kinds of point mutations in the napA gene may cause the nitrate reduction-negative characteristic in biovars mediaevalis and microtus, respectively. A 122-bp frameshift deletion in the araC gene may lead to the arabinose-negative phenotype of biovar microtus strains. Biovar microtus strains have a unique genomic profile of gene loss and pseudogene distribution, which most likely accounts for the human attenuation of this new biovar. Focused, hypothesis-based investigations on these specific genes will help delineate the determinants that enable this deadly pathogen to be virulent to humans and give insight into the evolution of Y. pestis and plague pathogenesis. Moreover, there may be the implications for development of biovar microtus strains as a potential vaccine.

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The main reasons for substance formation and natural process manifestation

Domestic geology ◽

10.47765/0869-7175-2021-10007 ◽

2021 ◽

pp. 76-96

Author(s):

Alexander Likhachev

Keyword(s):

Thermodynamic Parameters ◽

World History ◽

Natural Process ◽

Natural Materials ◽

Main Factors ◽

Composition Structure ◽

The Impact ◽

Insight Into ◽

Structure Properties

Natural materials and processes represent the global substance reflecting and determining its formation and existence as a whole and in all its components. Revealing the reasons for their formation and manifestation is crucial. The paper highlights the two main factors: «influences» and «gradients». Influences are interpreted as the impact of some substances and events on other similar parameters, and gradients are vector changes and differences in systems composition, structure, properties, states, energy and thermodynamic parameters. To provide an insight into the role and significance of the above factors and reasons, an attempt was made to consider their potential manifestation throughout the general world history within the existing knowledge about it.

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Fish and other faunal remains from a Late Iron Age site on the Letaba River, Kruger National Park

Koedoe ◽

10.4102/koedoe.v34i1.407 ◽

1991 ◽

Vol 34 (1) ◽

Cited By ~ 1

Author(s):

Ina Plug ◽

Paul Skelton

Keyword(s):

Iron Age ◽

National Park ◽

Fish Population ◽

Faunal Remains ◽

Late Iron Age ◽

Hunting Strategies ◽

The People ◽

Large Numbers ◽

Fish Remains ◽

Insight Into

Fish remains from Late Iron Age sites in the Transvaal are relatively scarce. It seems as if the people did not utilize the riverine resources extensively. Therefore the unique assemblage of large numbers of fish bones on a Late Iron Age site, provides some insight into the fish population of a section of the Letaba River a few hundred years ago. The presence of other faunal remains provides some information on prehistoric utilization of the environment in general. Hunting strategies and aspects of herding can also be deduced from the faunal remains.

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Closing up onto our sun: solar imaging

EPJ Web of Conferences ◽

10.1051/epjconf/202024007011 ◽

2020 ◽

Vol 240 ◽

pp. 07011

Author(s):

Kushagra Shrivastava ◽

Keith Wen Kai Chia ◽

Kang Jun Wong ◽

Alfred Yong Liang Tan ◽

Hwee Tiang Ning

Keyword(s):

Solar Activity ◽

The Sun ◽

Research Needs ◽

Large Numbers ◽

Wide Range ◽

Future Science ◽

Insight Into ◽

Term Data ◽

Made In

Solar activity research provides insight into the Sun’s past, future (Science Daily, 2018). The solar activity includes observations of large numbers of intense sunspots, flares, and other phenomena; and demands a wide range of techniques and measurements on the observations. This research needs long term data collection before critical analyses can occur, to generate meaningful learning and knowledge. In this project, we will use solar imaging to make observations of solar activity, and take our baby steps to make contributions in citizen science. Observations will be made in 3 wavelengths to gain a more thorough analysis by looking at different perspectives of the Sun, namely H-Alpha, Calcium-K, and white light.

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Key Factors of Enterprise Development: Evidence from Biogas Sector of Nepal

Journal of Advanced Academic Research ◽

10.3126/jaar.v3i1.16619 ◽

2017 ◽

Vol 3 (1) ◽

pp. 76-94

Author(s):

Maheshwar Prasad Yadav ◽

Radhe S. Pradhan

Keyword(s):

Renewable Energy ◽

Fiscal Year ◽

Annual Data ◽

Enterprise Development ◽

Key Factors ◽

Entire Study ◽

The Past ◽

Lag Model ◽

Biogas Plants ◽

Insight Into

This paper aims at determining key factors for enterprise development in biogas sector in Nepal. The variables are introduced via an extension of the econometric model, which explicitly includes Almon (1965) Polynomial Lag Model using SPSS. The number of biogas companies comprises as a dependent variable for the indicator of enterprise development while number of biogas plants, numbers of biogas plants constructed with loan, micro credit i.e., loan, and subsidy are included as independent variables. The empirical results were estimated using annual data of 22 years from fiscal year 1992/93 to 2013/14 with entire study period divided into different sub-periods. The study reveals that enterprise development is influenced not only by the current values of the key factors but also by the past values. The study also shows that number of biogas plants and subsidy play a very strong role while number of plants constructed with loan and loan play a weak role in enterprise development in the context of biogas sector of Nepal. The paper can be extended by investigating characteristics of renewable energy enterprises and renewable energy entrepreneurs to get a greater insight into the results.

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A family of T6SS antibacterial effectors related to L,D-transpeptidases targets the Peptidoglycan

Access Microbiology ◽

10.1099/acmi.ac2020.po0033 ◽

2020 ◽

Vol 2 (7A) ◽

Author(s):

Stephanie Sibinelli de Sousa ◽

Julia Takuno Hespanhol ◽

Bruno Matsuyama ◽

Stephane Mesnage ◽

Gianlucca Nicastro ◽

...

Keyword(s):

Cell Envelope ◽

Point Mutations ◽

Time Lapse ◽

Secretion Systems ◽

Bacterial Antagonism ◽

New Family ◽

Type Vi Secretion ◽

Altered Cell ◽

Bacterial Effectors ◽

Insight Into

Type VI secretion systems (T6SSs) are contractile nanomachines widely used by bacteria to intoxicate competitors. Salmonella Typhimurium encodes a T6SS within the Salmonella pathogenicity island 6 (SPI-6) that is used during competition against species of the gut microbiota. We characterized a new SPI-6 T6SS antibacterial effector named Tlde1 (type VI L,D-transpeptidase effector 1). Tlde1 is toxic in target-cell periplasm and its toxicity is neutralized by co-expression with immunity protein Tldi1 (type VI L,D-transpeptidase immunity 1). Time-lapse microscopy revealed that intoxicated cells display altered cell division and lose cell envelope integrity. Bioinformatics analysis showed that Tlde1 is evolutionarily related to L,D-transpeptidases. Point mutations on conserved histidine121 and cysteine131 residues eliminated toxicity. Co-incubation of purified recombinant Tlde1 and peptidoglycan tetrapeptides showed that Tlde1 displays both L,D-carboxypeptidase activity by cleaving GM-tetrapeptides between meso-diaminopimelic acid3 and D-alanine4, and L,D-transpeptidase exchange activity by replacing D-alanine4 for a non-canonical D-amino acid. Tlde1 constitutes a new family of T6SS effectors widespread in Proteobacteria. This work increases our knowledge about the bacterial effectors used in interbacterial competitions and provides molecular insight into a new mechanism of bacterial antagonism.

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