scholarly journals A novel thermostable aspartic protease fromTalaromyces leycettanusand its specific autocatalytic activation through an intermediate transition state

2019 ◽  
Author(s):  
Yujie Guo ◽  
Tao Tu ◽  
Yaxin Ren ◽  
Yaru Wang ◽  
Yingguo Bai ◽  
...  
Keyword(s):  
Specific Pattern ◽  
Aspartic Protease ◽  
Activation Process ◽  
Evolutionary Analysis ◽  
The Novel ◽  
Mature Protein ◽  
Aspartic Proteases ◽  
Family Based ◽  
Two Stages ◽  
Protease Precursor

ABSTRACTAspartic proteases exhibit optimum enzyme activity under acidic condition and have been extensively used in food, fermentation and leather industries. In this study, a novel aspartic protease precursor (proTlAPA1) fromTalaromyces leycettanuswas identified and successfully expressed inPichia pastoris. Subsequently, the auto-activation processing of the zymogen proTlAPA1 was studied by SDS-PAGE and N-terminal sequencing, under different processing conditions.TlAPA1 shared the highest identity of 70.3 % with the aspartic endopeptidase fromByssochlamys spectabilis(GAD91729) and was classified into a new subgroup of the aspartic protease A1 family, based on evolutionary analysis. MatureTlAPA1 protein displayed an optimal activity at 60 °C and remained stable at temperatures of 55 °C and below, indicating the thermostable nature ofTlAPA1 aspartic protease. During the auto-activation processing of proTlAPA1, a 45 kDa intermediate was identified that divided the processing mechanism into two steps: formation of intermediates, and activation of the mature protein (TlAPA1). The former step was completely induced by pH of the buffer, while the latter process depended on protease activity. The discovery of the novel aspartic proteaseTlAPA1 and study of its activation process will contribute to a better understanding of the mechanism of aspartic proteases auto-activation.IMPORTANCEThe novel aspartic proteaseTlAPA1 was identified fromT. leycettanusand expressed as a zymogen (proTlAPA1) inP. pastoris. Enzymatic characteristics of the mature protein were studied and the specific pattern of zymogen conversion was described. The auto-activation processing of proTlAPA1 proceeded in two stages and an intermediate was identified in this process. These results describe a new subgroup of aspartic protease A1 family and provide insights into a novel mode of activation processing in aspartic proteases.

Damage Identification of Multimember Structure using Improved Neural Networks

2013 ◽  
Vol 3 (3) ◽  
pp. 57-75
Author(s):  
M. Rajendra ◽  
K. Shankar
Keyword(s):  
Damage Identification ◽  
Latin Hypercube Sampling ◽  
Search Space ◽  
Computational Effort ◽  
Frequency Change ◽  
The Novel ◽  
Damage Prediction ◽  
Rbf Network ◽  
Accuracy And Precision ◽  
Two Stages

A novel two stage Improved Radial Basis Function (IRBF) neural network for the damage identification of a multimember structure in the frequency domain is presented. The improvement of the proposed IRBF network is carried out in two stages. Conventional RBF network is used in the first stage for preliminary damage prediction and in the second stage reduced search space moving technique is used to minimize the prediction error. The network is trained with fractional frequency change ratios (FFCs) and damage signature indices (DSIs) as effective input patterns and the corresponding damage severity values as output patterns. The patterns are searched at different damage levels by Latin hypercube sampling (LHS) technique. The performance of the novel IRBF method is compared with the conventional RBF and Genetic algorithm (GA) methods and it is found to be a good multiple member damage identification strategy in terms of accuracy and precision with less computational effort.

Cleavage Efficiency of the Novel Aspartic Protease Yapsin 1 (Yap3p) Enhanced for Substrates with Arginine Residues Flanking the P1 Site:  Correlation with Electronegative Active-Site Pockets Predicted by Molecular Modeling†,‡

Biochemistry ◽  
1998 ◽  
Vol 37 (9) ◽  
pp. 2768-2777 ◽  
Author(s):  
Vicki Olsen ◽  
Kunchur Guruprasad ◽  
Niamh X. Cawley ◽  
Hao-Chia Chen ◽  
Tom L. Blundell ◽  
...  
Keyword(s):  
Molecular Modeling ◽  
Active Site ◽  
Aspartic Protease ◽  
The Novel ◽  
Cleavage Efficiency ◽  
Arginine Residues

scholarly journals A new genus of the family Micromonosporaceae, Polymorphospora gen. nov., with description of Polymorphospora rubra sp. nov.

2006 ◽  
Vol 56 (8) ◽  
pp. 1959-1964 ◽  
Author(s):  
Tomohiko Tamura ◽  
Kazunori Hatano ◽  
Ken-ichiro Suzuki
Keyword(s):  
New Genus ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
The Novel ◽  
Phenotypic Properties ◽  
The Family ◽  
Isoprenoid Quinones ◽  
Mangrove Roots ◽  
Family Based ◽  
Distinct Taxon

Two actinomycete strains were isolated from soil surrounding mangrove roots. The isolates formed short spore chains with spores showing diverse shapes. The isolates contained glutamic acid, glycine, alanine and meso-diaminopimelic acid in the cell wall, 3-O-methylmannose, mannose, galactose and glucose as the whole-cell sugars and MK-10(H6), MK-10(H4), MK-9(H6) and MK-9(H4) as the predominant isoprenoid quinones. The isolates formed a distinct taxon in the phylogenetic tree of the Micromonosporaceae based on analysis of 16S rRNA gene sequences and showed chemical and phenotypic properties that were different from members of all of the other genera of this family. Based on these observations, it is proposed that the novel isolates belong to a new genus, Polymorphospora gen. nov. The type species of the genus is proposed as Polymorphospora rubra sp. nov., with strain TT 97-42T (=NBRC 101157T=DSM 44947T) as the type strain.

scholarly journals Hemoglobin degradation in the human malaria pathogen Plasmodium falciparum: a catabolic pathway initiated by a specific aspartic protease.

1991 ◽  
Vol 173 (4) ◽  
pp. 961-969 ◽  
Author(s):  
D E Goldberg ◽  
A F Slater ◽  
R Beavis ◽  
B Chait ◽  
A Cerami ◽  
...  
Keyword(s):  
Laser Desorption ◽  
Aspartic Protease ◽  
Digestive Vacuole ◽  
Catabolic Pathway ◽  
Nutrient Source ◽  
Aspartic Proteases ◽  
Laser Desorption Mass Spectrometry ◽  
Proteolytic Action ◽  
Hemoglobin Degradation

Hemoglobin is an important nutrient source for intraerythrocytic malaria organisms. Its catabolism occurs in an acidic digestive vacuole. Our previous studies suggested that an aspartic protease plays a key role in the degradative process. We have now isolated this enzyme and defined its role in the hemoglobinolytic pathway. Laser desorption mass spectrometry was used to analyze the proteolytic action of the purified protease. The enzyme has a remarkably stringent specificity towards native hemoglobin, making a single cleavage between alpha 33Phe and 34Leu. This scission is in the hemoglobin hinge region, unraveling the molecule and exposing other sites for proteolysis. The protease is inhibited by pepstatin and has NH2-terminal homology to mammalian aspartic proteases. Isolated digestive vacuoles make a pepstatin-inhibitable cleavage identical to that of the purified enzyme. The pivotal role of this aspartic hemoglobinase in initiating hemoglobin degradation in the malaria parasite digestive vacuoles is demonstrated.

scholarly journals Unravelling novel synergies between organometallic and biological partners: a quantum mechanics/molecular mechanics study of an artificial metalloenzyme

2014 ◽  
Vol 11 (96) ◽  
pp. 20140090 ◽  
Author(s):  
Elisabeth Ortega-Carrasco ◽  
Agustí Lledós ◽  
Jean-Didier Maréchal
Keyword(s):  
Quantum Mechanics ◽  
Molecular Mechanics ◽  
Resting State ◽  
Structural Features ◽  
Activation Process ◽  
Biological Macromolecules ◽  
The Novel ◽  
Molecular Mechanics Calculations ◽  
Artificial Metalloenzymes ◽  
Artificial Metalloenzyme

In recent years, the design of artificial metalloenzymes obtained by the insertion of homogeneous catalysts into biological macromolecules has become a major field of research. These hybrids, and the corresponding X-ray structures of several of them, are offering opportunities to better understand the synergy between organometallic and biological subsystems. In this work, we investigate the resting state and activation process of a hybrid inspired by an oxidative haemoenzyme but presenting an unexpected reactivity and structural features. An extensive series of quantum mechanics/molecular mechanics calculations show that the resting state and the activation processes of the novel enzyme differ from naturally occurring haemoenzymes in terms of the electronic state of the metal, participation of the first coordination sphere of the metal and the dynamic process. This study presents novel insights into the sensitivity of the association between organometallic and biological partners and illustrates the molecular challenge that represents the design of efficient enzymes based on this strategy.

scholarly journals A Two-Step Polynomial and Nonlinear Growth Approach for Modeling COVID-19 Cases in Mexico

Mathematics ◽  
2021 ◽  
Vol 9 (18) ◽  
pp. 2180
Author(s):  
Rafael Pérez Abreu C. ◽  
Samantha Estrada ◽  
Héctor de-la-Torre-Gutiérrez
Keyword(s):  
Predictive Models ◽  
Statistical Models ◽  
Inflection Point ◽  
The Novel ◽  
Safety Measures ◽  
Nonlinear Growth ◽  
Mexican Government ◽  
Novel Coronavirus ◽  
Two Stages ◽  
Growth Approach

Since December 2019, the novel coronavirus (SARS-CoV-2) and its associated illness COVID-19 have rapidly spread worldwide. The Mexican government has implemented public safety measures to minimize the spread of the virus. In this paper, we used statistical models in two stages to estimate the total number of coronavirus (COVID-19) cases per day at the state and national levels in Mexico. In this paper, we propose two types of models. First, a polynomial model of the growth for the first part of the outbreak until the inflection point of the pandemic curve and then a second nonlinear growth model used to estimate the middle and the end of the outbreak. Model selection was performed using Vuong’s test. The proposed models showed overall fit similar to predictive models (e.g., time series and machine learning); however, the interpretation of parameters is simpler for decisionmakers, and the residuals follow the expected distribution when fitting the models without autocorrelation being an issue.

scholarly journals Recent Molecular Evolution of Human Metapneumovirus (HMPV): Subdivision of HMPV A2b Strains

2020 ◽  
Vol 8 (9) ◽  
pp. 1280
Author(s):  
Naganori Nao ◽  
Miwako Saikusa ◽  
Ko Sato ◽  
Tsuyoshi Sekizuka ◽  
Shuzo Usuku ◽  
...  
Keyword(s):  
Respiratory Infections ◽  
Epidemiological Studies ◽  
Human Metapneumovirus ◽  
Evolutionary Relationships ◽  
Acute Respiratory Infections ◽  
Evolutionary Analysis ◽  
The Novel ◽  
Genome Wide ◽  
A Genome

Human metapneumovirus (HMPV) is a major etiological agent of acute respiratory infections in humans. HMPV has been circulating worldwide for more than six decades and is currently divided into five agreed-upon subtypes: A1, A2a, A2b, B1, and B2. Recently, the novel HMPV subtypes A2c, A2b1, and A2b2 have been proposed. However, the phylogenetic and evolutionary relationships between these recently proposed HMPV subtypes are unclear. Here, we report a genome-wide phylogenetic and evolutionary analysis of 161 HMPV strains, including unique HMPV subtype A2b strains with a 180- or 111-nucleotide duplication in the G gene (nt-dup). Our data demonstrate that the HMPV A2b subtype contains two distinct subtypes, A2b1 and A2b2, and that the HMPV subtypes A2c and A2b2 may be different names for the same subtype. HMPV A2b strains with a nt-dup also belong to subtype A2b2. Molecular evolutionary analyses indicate that subtypes A2b1 and A2b2 diverged from subtype A2b around a decade after the subtype A2 was divided into the subtypes A2a and A2b. These data support the A2b1 and A2b2 subtypes proposed in 2012 and are essential for the unified classification of HMPV subtype A2 strains, which is important for future HMPV surveillance and epidemiological studies.

scholarly journals Evolutionary analysis of chloroplast tRNA of Gymnosperm revealed the novel structural variation and evolutionary aspect

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e10312
Author(s):  
Ting-Ting Zhang ◽  
Yi-Kun Hou ◽  
Ting Yang ◽  
Shu-Ya Zhang ◽  
Ming Yue ◽  
...  
Keyword(s):  
Structural Variation ◽  
Gene Loss ◽  
Evolutionary Analysis ◽  
The Novel ◽  
Comprehensive Understanding ◽  
Transfer Rnas ◽  
Evolutionary Aspect ◽  
Evolutionary Pattern ◽  
Information Level ◽  
Key Participants

Gymnosperms such as ginkgo, conifers, cycads, and gnetophytes are vital components of land ecosystems, and they have significant economic and ecologic value, as well as important roles as forest vegetation. In this study, we investigated the structural variation and evolution of chloroplast transfer RNAs (tRNAs) in gymnosperms. Chloroplasts are important organelles in photosynthetic plants. tRNAs are key participants in translation where they act as adapter molecules between the information level of nucleic acids and functional level of proteins. The basic structures of gymnosperm chloroplast tRNAs were found to have family-specific conserved sequences. The tRNAΨ -loop was observed to contain a conforming sequence, i.e., U-U-C-N-A-N2. In gymnosperms, tRNAIle was found to encode a “CAU” anticodon, which is usually encoded by tRNAMet. Phylogenetic analysis suggested that plastid tRNAs have a common polyphyletic evolutionary pattern, i.e., rooted in abundant common ancestors. Analyses of duplication and loss events in chloroplast tRNAs showed that gymnosperm tRNAs have experienced little more gene loss than gene duplication. Transition and transversion analysis showed that the tRNAs are iso-acceptor specific and they have experienced unequal evolutionary rates. These results provide new insights into the structural variation and evolution of gymnosperm chloroplast tRNAs, which may improve our comprehensive understanding of the biological characteristics of the tRNA family.

Sign in / Sign up

Export Citation Format

Share Document