Computational elucidation of phylogenetic, functional and structural features of Methioninase from Pseudomonas, Escherichia, Clostridium and Citrobacter strains

2021 ◽  
Vol 15 ◽  
Author(s):  
Cambyz Irajie ◽  
Milad Mohkam ◽  
Bahareh Vakili ◽  
Navid Nezafat
Keyword(s):  
Pyridoxal Phosphate ◽  
Three Dimensional ◽  
Structural Features ◽  
Dimensional Structure ◽  
Bacterial Strains ◽  
Alpha Helices ◽  
Random Coils ◽  
Physico Chemical ◽  
Wet Lab ◽  
Therapeutic Enzymes

Background: L-Methioninase (EC 4.4.1.11; MGL) is a pyridoxal phosphate (PLP)-dependent enzyme that is produced by a variety of bacteria, fungi, and plants. L-methioninase, especially from Pseudomonas and Citrobacter sp. is considered as the efficient therapeutic enzymes, particularly in cancers such as glioblastomas, medulloblastoma, and neuroblastoma that are more sensitive to methionine starvation. Objective: The low stability is one of the main drawbacks of the enzyme; in this regard, in the current study, different features of the enzyme, including phylogenetic, functional, and structural from Pseudomonas, Escherichia, Clostridium, and Citrobacter strains were evaluated to find the best bacterial L-Methioninase. Methods: After the initial screening of L-Methioninase sequences from the above-mentioned bacterial strains, the three-dimensional structure of enzymes from Escherichia fergusonii, Pseudomonas fluorescens, and Clostridium homopropionicum were determined through homology modeling via GalaxyTBM server and refined by GalaxyRefine server. Results & Conclusion: Afterwards, PROCHECK, verify 3D, and ERRAT servers were used for verification of the obtained models. Moreover, antigenicity, allergenicity, and physico-chemical analysis of enzymes were also carried out. In order to get insight into interaction of enzyme with other proteins the STRING server was used. The secondary structure of enzyme is mainly composed of random coils and alpha-helices. However, these outcomes should further be validated by wet lab investigations.

scholarly journals Fish antifreeze proteins: Computational analysis and physicochemical characterization

1970 ◽  
Vol 1 (2) ◽  
pp. 18-26 ◽  
Author(s):  
Md Musharaf Hossain
Keyword(s):  
Homology Modeling ◽  
Antifreeze Proteins ◽  
Three Dimensional ◽  
Physicochemical Characterization ◽  
Chemical Properties ◽  
Pharmaceutical Journal ◽  
Structural Features ◽  
Dimensional Structure ◽  
Physico Chemical ◽  
Model Visualization

Antifreeze proteins (AFPs) protect organisms from freezing and shows great diversity in structure, and they have been found in a variety of organisms. In this study, a total of 15 antifreeze proteins of fish were selected where they represent distinct physicochemical and structural features. The present paper uses bioinformatics approach to describe the physiochemical, functional and structural properties of Antifreeze proteins. Several Physico-chemical properties such as pI, EC, AI, GRAVY and instability index are computed and provide data about these proteins and their properties. The result of primary structure analysis infers that, fish antifreeze proteins are mostly hydrophobic. Disulfide bridges and secondary structures were analyzed using CYS_REC and SOPMA respectively. The three dimensional structure of Antifreeze proteins is predicted by using three homology modeling server Geno3D, Swiss-model and CPHmodels. The model was evaluated with PROCHECK, WHAT IF, and ProSA programs. Model visualization and analysis was done with Pymol. These structures will provide a good foundation for functional analysis of experimentally derived crystal structures.Key Words: Antifreeze Proteins; Computational tools; hydrophobicity; homology modeling; isoelectric point.DOI: http://dx.doi.org/10.3329/icpj.v1i2.9412International Current Pharmaceutical Journal 2012, 1(2): 18-26

scholarly journals Stability of alpha-helical and beta-structural blocks in proteins of four structural classes

2018 ◽  
Vol 63 (4) ◽  
pp. 391-400 ◽  
Author(s):  
V. V. Poboinev ◽  
V. V. Khrustalev ◽  
T. A. Khrustaleva ◽  
A. N. Stozharov
Keyword(s):  
Three Dimensional ◽  
Structural Features ◽  
Dimensional Structure ◽  
Structural Domain ◽  
Alpha Helices ◽  
Structural Class ◽  
Beta Proteins ◽  
Alpha Beta ◽  
Beta Hairpin ◽  
Structural Classes

In this article we showed the characteristic structural features of the groups of interacting alpha-helices and beta-strands (blocks) in four sets of nonhomologous proteins from different structural classes. Stability of each element of secondary structure has been checked with help of the PentaFOLD algorithm that finds intrinsic alpha-helical and beta-structural sequences of amino acid residues. We proved that the most frequent blocks of “alpha + beta” and “alpha/beta” proteins are 2 interacting alpha helices, and they demonstrate the highest level of stability. In alpha-helical proteins the most frequent blocks contain 4 alpha-helices. In beta-structural proteins alpha-helices most frequently do not interact with other helices and demonstrate the lowest level of stability. The most stable type of beta-structure is a block made from three interacting beta-strands, while the less stable one is a beta-hairpin. There is a characteristic distribution of stable alpha-helices in “alpha + beta” proteins: they are usually situated in the beginning of a block while stable beta-strands are usually situated in the end of the block. This type of distribution of stable alpha-helices and beta-strands helps the protein to form its stable three-dimensional structure in case  it begins from beta-structural domain which is the most frequent case for the structural class of proteins. 

Crystal structure of the hinge domain of Smchd1 reveals its dimerization mode and nucleic acid–binding residues

2020 ◽  
Vol 13 (636) ◽  
pp. eaaz5599 ◽  
Author(s):  
Kelan Chen ◽  
Richard W. Birkinshaw ◽  
Alexandra D. Gurzau ◽  
Iromi Wanigasuriya ◽  
Ruoyun Wang ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Muscular Dystrophy ◽  
Three Dimensional ◽  
Underlying Mechanism ◽  
Structural Features ◽  
Facioscapulohumeral Muscular Dystrophy ◽  
Dimensional Structure ◽  
Nucleic Acid Binding ◽  
X Ray Crystallography ◽  
Hinge Domain

Structural maintenance of chromosomes flexible hinge domain containing 1 (SMCHD1) is an epigenetic regulator in which polymorphisms cause the human developmental disorder, Bosma arhinia micropthalmia syndrome, and the degenerative disease, facioscapulohumeral muscular dystrophy. SMCHD1 is considered a noncanonical SMC family member because its hinge domain is C-terminal, because it homodimerizes rather than heterodimerizes, and because SMCHD1 contains a GHKL-type, rather than an ABC-type ATPase domain at its N terminus. The hinge domain has been previously implicated in chromatin association; however, the underlying mechanism involved and the basis for SMCHD1 homodimerization are unclear. Here, we used x-ray crystallography to solve the three-dimensional structure of the Smchd1 hinge domain. Together with structure-guided mutagenesis, we defined structural features of the hinge domain that participated in homodimerization and nucleic acid binding, and we identified a functional hotspot required for chromatin localization in cells. This structure provides a template for interpreting the mechanism by which patient polymorphisms within the SMCHD1 hinge domain could compromise function and lead to facioscapulohumeral muscular dystrophy.

scholarly journals PROTEIN TEACHING: AN APPROACH FOR TEACHER TRAINING APPLIED TO STUDENTS OF THE BIOLOGICAL SCIENCES COURSE AT UFRN

2015 ◽  
Vol 13 ◽  
pp. 34
Author(s):  
J. K.S. NASCIMENTO et al
Keyword(s):  
Biological Sciences ◽  
Teaching Practice ◽  
Basic Education ◽  
New Technologies ◽  
Lesson Plan ◽  
Three Dimensional ◽  
Structural Features ◽  
Dimensional Structure ◽  
Educational Models ◽  
Teaching Learning

Teaching biochemistry in higher education is increasingly becoming a challenge. It is notoriously difficult for students to assimilate the topic; in addition there are many complaints about the complexity of subjects and a lack of integration with the day-to-day. A recurrent problem in undergraduate courses is the absence of teaching practice in specific disciplines. This work aimed to stimulate students in the biological sciences course who were enrolled in the discipline of MOLECULAR DIVERSITY (MD), to create hypothetical classes focused on basic education highlighting the proteins topic. The methodology was applied in a class that contained 35 students. Seven groups were formed, and each group chose a protein to be used as a source of study for elementary school classes. A lesson plan was created focusing on the methodology that the group would use to manage a class. The class was to be presented orally. Students were induced to be creative and incorporate a teacher figure, and to propose teaching methodologies for research using the CTS approach (Science, Technology and Society). Each group presented a three-dimensional structure of the protein they had chosen, explained their structural features and functions and how they would develop the theme for a class of basic education, and what kind of methodology they would use for this purpose. At the end of the presentations, a questionnaire was given to students in order to evaluate the effectiveness of the methodology in the teaching-learning process. The activity improved the teacher’s training and developed skills and abilities, such as creativity, didactical planning, teaching ability, development of educational models and the use of new technologies. The methodology used in this work was extremely important to the training of future teachers, who were able to better understand the content covered in the discipline and relate it to day-to-day life.

scholarly journals Repeat elements organize 3D genome structure and mediate transcription in the filamentous fungusEpichloë festucae

2018 ◽  
Author(s):  
David J Winter ◽  
Austen RD Ganley ◽  
Carolyn A Young ◽  
Ivan Liachko ◽  
Christopher L Schardl ◽  
...  
Keyword(s):  
Genome Structure ◽  
Regulation Of Gene Expression ◽  
Three Dimensional ◽  
Structural Features ◽  
Dimensional Structure ◽  
In Planta ◽  
Repeat Elements ◽  
Symbiotic Relationships ◽  
3D Genome ◽  
Transcriptional Changes

AbstractStructural features of genomes, including the three-dimensional arrangement of DNA in the nucleus, are increasingly seen as key contributors to the regulation of gene expression. However, studies on how genome structure and nuclear organization influence transcription have so far been limited to a handful of model species. This narrow focus limits our ability to draw general conclusions about the ways in which three-dimensional structures are encoded, and to integrate information from three-dimensional data to address a broader gamut of biological questions. Here, we generate a complete and gapless genome sequence for the filamentous fungus,Epichloë festucae. Coupling it with RNAseq and HiC data, we investigate how the structure of the genome contributes to the suite of transcriptional changes that anEpichloëspecies needs to maintain symbiotic relationships with its grass host. Our results reveal a unique “patchwork” genome, in which repeat-rich blocks of DNA with discrete boundaries are interspersed by gene-rich sequences. In contrast to other species, the three-dimensional structure of the genome is anchored by these repeat blocks, which act to isolate transcription in neighbouring gene-rich regions. Genes that are differentially expressed in planta are enriched near the boundaries of these repeat-rich blocks, suggesting that their three-dimensional orientation partly encodes and regulates the symbiotic relationship formed by this organism.

scholarly journals Structural Features of a Bacteroidetes-Affiliated Cellulase Linked with a Polysaccharide Utilization Locus

2015 ◽  
Vol 5 (1) ◽  
Author(s):  
A.E. Naas ◽  
A.K. MacKenzie ◽  
B. Dalhus ◽  
V.G.H. Eijsink ◽  
P.B. Pope
Keyword(s):  
Active Site ◽  
Three Dimensional ◽  
Structural Features ◽  
Structure And Function ◽  
Dimensional Structure ◽  
Active Site Cleft ◽  
Polysaccharide Utilization Locus ◽  
And Function ◽  
Rumen Metagenome

Abstract Previous gene-centric analysis of a cow rumen metagenome revealed the first potentially cellulolytic polysaccharide utilization locus, of which the main catalytic enzyme (AC2aCel5A) was identified as a glycoside hydrolase (GH) family 5 endo-cellulase. Here we present the 1.8 Å three-dimensional structure of AC2aCel5A and characterization of its enzymatic activities. The enzyme possesses the archetypical (β/α)8-barrel found throughout the GH5 family and contains the two strictly conserved catalytic glutamates located at the C-terminal ends of β-strands 4 and 7. The enzyme is active on insoluble cellulose and acts exclusively on linear β-(1,4)-linked glucans. Co-crystallization of a catalytically inactive mutant with substrate yielded a 2.4 Å structure showing cellotriose bound in the −3 to −1 subsites. Additional electron density was observed between Trp178 and Trp254, two residues that form a hydrophobic “clamp”, potentially interacting with sugars at the +1 and +2 subsites. The enzyme’s active-site cleft was narrower compared to the closest structural relatives, which in contrast to AC2aCel5A, are also active on xylans, mannans and/or xyloglucans. Interestingly, the structure and function of this enzyme seem adapted to less-substituted substrates such as cellulose, presumably due to the insufficient space to accommodate the side-chains of branched glucans in the active-site cleft.

Structural characterization of intrinsically disordered proteins by the combined use of NMR and SAXS

2012 ◽  
Vol 40 (5) ◽  
pp. 955-962 ◽  
Author(s):  
Nathalie Sibille ◽  
Pau Bernadó
Keyword(s):  
Intrinsically Disordered Proteins ◽  
Dynamic Models ◽  
Dimensional Space ◽  
Three Dimensional ◽  
Main Tool ◽  
Structural Features ◽  
Disordered Proteins ◽  
Dimensional Structure ◽  
Intrinsically Disordered ◽  
Conformational Preferences

In recent years, IDPs (intrinsically disordered proteins) have emerged as pivotal actors in biology. Despite IDPs being present in all kingdoms of life, they are more abundant in eukaryotes where they are involved in the vast majority of regulation and signalling processes. The realization that, in some cases, functional states of proteins were partly or fully disordered was in contradiction to the traditional view where a well defined three-dimensional structure was required for activity. Several experimental evidences indicate, however, that structural features in IDPs such as transient secondary-structural elements and overall dimensions are crucial to their function. NMR has been the main tool to study IDP structure by probing conformational preferences at residue level. Additionally, SAXS (small-angle X-ray scattering) has the capacity to report on the three-dimensional space sampled by disordered states and therefore complements the local information provided by NMR. The present review describes how the synergy between NMR and SAXS can be exploited to obtain more detailed structural and dynamic models of IDPs in solution. These combined strategies, embedded into computational approaches, promise the elucidation of the structure–function properties of this important, but elusive, family of biomolecules.

Zona Pellucida Proteins, Fibrils, and Matrix

2020 ◽  
Vol 89 (1) ◽  
pp. 695-715
Author(s):  
Eveline S. Litscher ◽  
Paul M. Wassarman
Keyword(s):  
Extracellular Matrix ◽  
Zona Pellucida ◽  
Three Dimensional ◽  
Structural Features ◽  
Biological Properties ◽  
Preimplantation Development ◽  
Dimensional Structure ◽  
Three Dimensional Structure ◽  
Early Embryos ◽  
N Terminus

The zona pellucida (ZP) is an extracellular matrix that surrounds all mammalian oocytes, eggs, and early embryos and plays vital roles during oogenesis, fertilization, and preimplantation development. The ZP is composed of three or four glycosylated proteins, ZP1–4, that are synthesized, processed, secreted, and assembled into long, cross-linked fibrils by growing oocytes. ZP proteins have an immunoglobulin-like three-dimensional structure and a ZP domain that consists of two subdomains, ZP-N and ZP-C, with ZP-N of ZP2 and ZP3 required for fibril assembly. A ZP2–ZP3 dimer is located periodically along ZP fibrils that are cross-linked by ZP1, a protein with a proline-rich N terminus. Fibrils in the inner and outer regions of the ZP are oriented perpendicular and parallel to the oolemma, respectively, giving the ZP a multilayered appearance. Upon fertilization of eggs, modification of ZP2 and ZP3 results in changes in the ZP's physical and biological properties that have important consequences. Certain structural features of ZP proteins suggest that they may be amyloid-like proteins.

Development of a Quickly Erectable Prefabricated Collapsible Construction System for Temporary Accommodation

2018 ◽  
Vol 931 ◽  
pp. 411-416
Author(s):  
S.G. Abramyan ◽  
Vladimir G. Polyakov ◽  
Svetlana I. Lipatova ◽  
O.V. Oganesyan
Keyword(s):  
Three Dimensional ◽  
Environmental Safety ◽  
Structural Features ◽  
Dimensional Structure ◽  
Labor Costs ◽  
Scientific Publications ◽  
Space Planning ◽  
Covering Set ◽  
Temporary Accommodation ◽  
Construction System

This paper considers the importance of quickly erectable construction systems, as well as their main purpose and applicability in various situations. Based on the analysis of scientific publications and the results of patent search, the authors suggest the structural features and technological solutions for installation of a new small-size quickly erectable collapsible construction system. The system is designed for temporary accommodation of a group of people involved in construction, geological exploration and other works in hard-to-reach areas, for tourists etc. Such a collapsible construction system can be adapted to serve as a temporary shelter for people surviving natural calamities. The foundation of the suggested system is an enclosed three-dimensional structure (crate) where the necessary structural elements are kept pending the assembly of the construction system, including telescopic legs and other tubular framing structures, rolls of tent covering, set of coupling elements, and supports. The specific features of this new system, as compared to similar space planning solutions, are low labor costs involved in its assembly and dismantling, small weight ensuring transportability of a collapsed and packed system, and reusability. Other benefits of the new small-size construction system include its low overall cost, environmental safety and energy efficiency.

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