scholarly journals Tricarboxylate Citrate Transporter of an Oleaginous Fungus Mucor circinelloides WJ11: From Function to Structure and Role in Lipid Production

2021 ◽  
Vol 8 ◽  
Author(s):  
Wu Yang ◽  
Aabid Manzoor Shah ◽  
Shiqi Dong ◽  
Caili Sun ◽  
Huaiyuan Zhang ◽  
...  
Keyword(s):  
Structure Function ◽  
Structural Characteristics ◽  
Lipid Production ◽  
3D Structure ◽  
Kinetic Studies ◽  
Structural Data ◽  
Mucor Circinelloides ◽  
Dynamics Simulation ◽  
Citrate Transporter ◽  
Citrate Efflux

The citrate transporter protein (CTP) plays an important role in citrate efflux from the mitochondrial matrix to cytosol that has great importance in oleaginous fungi. The cytoplasmic citrate produced after citrate efflux serves as the primary carbon source for the triacylglycerol and cholesterol biosynthetic pathways. Because of the CTP's importance, our laboratory has extensively studied its structure/function relationships in Mucor circinelloides to comprehend its molecular mechanism. In the present study, the tricarboxylate citrate transporter (Tct) of M. circinelloides WJ11 has been cloned, overexpressed, purified, kinetically, and structurally characterized. The Tct protein of WJ11 was expressed in Escherichia coli, isolated, and functionally reconstituted in a liposomal system for kinetic studies. Our results showed that Tct has a high affinity for citrate with Km 0.018 mM. Furthermore, the tct overexpression and knockout plasmids were created and transformed into M. circinelloides WJ11. The mitochondria of the tct-overexpressing transformant of M. circinelloides WJ11 showed a 49% increase in citrate efflux, whereas the mitochondria of the tct-knockout transformant showed a 39% decrease in citrate efflux compared to the mitochondria of wild-type WJ11. To elucidate the structure-function relationship of this biologically important transporter a 3D model of the mitochondrial Tct protein was constructed using homology modeling. The overall structure of the protein is V-shaped and its 3D structure is dimeric. The transport stability of the structure was also assessed by molecular dynamics simulation studies. The activity domain was identified to form hydrogen bond and stacking interaction with citrate and malate upon docking. Tricarboxylate citrate transporter has shown high binding energy of −4.87 kcal/mol to citric acid, while −3.80 kcal/mol to malic acid. This is the first report of unraveling the structural characteristics of WJ11 mitochondrial Tct protein and understanding the approach of the transporting toward its substrate. In conclusion, the present findings support our efforts to combine functional and structural data to better understand the Tct of M. circinelloides at the molecular level and its role in lipid accumulation.

scholarly journals Molecular Mechanism of Citrate Efflux by the Mitochondrial Citrate Transporter CT in Filamentous Fungus Mucor circinelloides WJ11

2021 ◽  
Vol 12 ◽  
Author(s):  
Wu Yang ◽  
Shiqi Dong ◽  
Junhuan Yang ◽  
Hassan Mohamed ◽  
Aabid Manzoor Shah ◽  
...  
Keyword(s):  
Molecular Mechanism ◽  
Filamentous Fungus ◽  
Lipid Accumulation ◽  
High Efficiency ◽  
Mucor Circinelloides ◽  
Transport Activity ◽  
Citrate Transport ◽  
Citrate Transporter ◽  
High Lipid ◽  
Citrate Efflux

The mitochondrial citrate transporter (MCT) plays an important role in citrate efflux from the mitochondria in eukaryotes, and hence provides a direct correlation between carbohydrate metabolism and lipid synthesis. Our previous studies on transporters confirmed the presence of two MCTs (TCT and CT) in oleaginous Mucor circinelloides WJ11 associated with high lipid accumulation. However, the molecular mechanism of citrate efflux from the mitochondria by MCT in M. circinelloides is still unclear. To study the citrate transport mechanism of CT, the citrate transporter gene was expressed in Escherichia coli, and its product was purified. The citrate transport activity of the protein was studied in CT reconstituted liposomes. Our results showed high efficiency of CT for [14C] citrate/citrate exchange with Km 0.01 mM at 25°C. Besides citrate, other molecules such as oxaloacetate, malate, fumarate, succinate aconitate, oxoadipate, isocitrate, and glutamate also promote citrate transport. In addition, the ct overexpression and knockout plasmids were constructed and transferred into M. circinelloides WJ11, and the mitochondria were isolated, and the transport activity was studied. Our findings showed that in the presence of 10 mM malate, the mitochondria of ct-overexpressing transformant showed 51% increase in the efflux rate of [14C] citrate, whereas the mitochondria of the ct-knockout transformant showed 18% decrease in citrate efflux compared to the mitochondria of wild-type WJ11. This study provided the first mechanistic evidence of citrate efflux from the mitochondria by citrate transporter in oleaginous filamentous fungus M. circinelloides, which is associated with high lipid accumulation.

scholarly journals Modeling and Molecular Dynamics of the 3D Structure of the HPV16 E7 Protein and Its Variants

2021 ◽  
Vol 22 (3) ◽  
pp. 1400
Author(s):  
Ciresthel Bello-Rios ◽  
Sarita Montaño ◽  
Olga Lilia Garibay-Cerdenares ◽  
Lilian Esmeralda Araujo-Arcos ◽  
Marco Antonio Leyva-Vázquez ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
3D Structure ◽  
Epidemiological Studies ◽  
Dynamics Simulation ◽  
Structural Refinement ◽  
Oncogenic Potential ◽  
Structural Differences ◽  
Reference Protein ◽  
E6 And E7 ◽  
First Time

The oncogenic potential of high-risk human papillomavirus (HPV) is predicated on the production of the E6 and E7 oncoproteins, which are responsible for disrupting the control of the cell cycle. Epidemiological studies have proposed that the presence of the N29S and H51N variants of the HPV16 E7 protein is significantly associated with cervical cancer. It has been suggested that changes in the amino acid sequence of E7 variants may affect the oncoprotein 3D structure; however, this remains uncertain. An analysis of the structural differences of the HPV16 E7 protein and its variants (N29S and H51N) was performed through homology modeling and structural refinement by molecular dynamics simulation. We propose, for the first time, a 3D structure of the E7 reference protein and two of Its variants (N29S and H51N), and conclude that the mutations induced by the variants in N29S and H51N have a significant influence on the 3D structure of the E7 protein of HPV16, which could be related to the oncogenic capacity of this protein.

scholarly journals Dimer Interface Organization is a Main Determinant of Intermonomeric Interactions and Correlates with Evolutionary Relationships of Retroviral and Retroviral-Like Ddi1 and Ddi2 Proteases

2020 ◽  
Vol 21 (4) ◽  
pp. 1352 ◽  
Author(s):  
János András Mótyán ◽  
Márió Miczi ◽  
József Tőzsér
Keyword(s):  
Structural Characteristics ◽  
Limited Proteolysis ◽  
Structural Data ◽  
Data Bank ◽  
Life Cycles ◽  
Evolutionary Relationships ◽  
Multiple Sequence ◽  
Dimer Interface ◽  
Viral Proteases ◽  
Eukaryotic Organisms

The life cycles of retroviruses rely on the limited proteolysis catalyzed by the viral protease. Numerous eukaryotic organisms also express endogenously such proteases, which originate from retrotransposons or retroviruses, including DNA damage-inducible 1 and 2 (Ddi1 and Ddi2, respectively) proteins. In this study, we performed a comparative analysis based on the structural data currently available in Protein Data Bank (PDB) and Structural summaries of PDB entries (PDBsum) databases, with a special emphasis on the regions involved in dimerization of retroviral and retroviral-like Ddi proteases. In addition to Ddi1 and Ddi2, at least one member of all seven genera of the Retroviridae family was included in this comparison. We found that the studied retroviral and non-viral proteases show differences in the mode of dimerization and density of intermonomeric contacts, and distribution of the structural characteristics is in agreement with their evolutionary relationships. Multiple sequence and structure alignments revealed that the interactions between the subunits depend mainly on the overall organization of the dimer interface. We think that better understanding of the general and specific features of proteases may support the characterization of retroviral-like proteases.

scholarly journals Identification and Characterization of a Novel Thermostable and Salt-Tolerant β-1,3 Xylanase from Flammeovirga pacifica Strain WPAGA1

Biomolecules ◽  
2020 ◽  
Vol 10 (9) ◽  
pp. 1287
Author(s):  
Zhiwei Yi ◽  
Zhengwen Cai ◽  
Bo Zeng ◽  
Runying Zeng ◽  
Guangya Zhang
Keyword(s):  
Thermal Stability ◽  
Salt Tolerance ◽  
3D Structure ◽  
Catalytic Efficiency ◽  
Dynamics Simulation ◽  
Carbohydrate Binding ◽  
Salt Tolerant ◽  
Excellent Thermal Stability ◽  
Moderately Thermophilic

β-1,3 xylanase is an important enzyme in the biorefinery process for some algae. The discovery and characterization of new β-1,3 xylanase is a hot research topic. In this paper, a novel β-1,3 xylanase (Xyl88) is revealed from the annotated genome of Flammeovirga pacifica strain WPAGA1. Bioinformatic analysis shows that Xyl88 belongs to the glycoside hydrolase 26 (GH26) with a suspected CBM (carbohydrate-binding module) sequence. The activity of rXyl88 is 75% of the highest enzyme activity (1.5 mol/L NaCl) in 3 mol/L NaCl buffer, which suggests good salt tolerance of rXy188. The optimum reaction temperature in the buffer without NaCl and with 1.5 mol/L NaCl is 45 °C and 55 °C, respectively. Notably, the catalytic efficiency of rXyl88 (kcat/Km) is approximately 20 higher than that of the thermophilic β-1,3 xylanase that has the highest catalytic efficiency. Xyl88 in this study becomes the most efficient enzyme ever found, and it is also the first reported moderately thermophilic and salt-tolerant β-1,3 xylanase. Results of molecular dynamics simulation further prove the excellent thermal stability of Xyl88. Moreover, according to the predicted 3D structure of the Xyl88, the surface of the enzyme is distributed with more negative charges, which is related to its salt tolerance, and significantly more hydrogen bonds and Van der Waals force between the intramolecular residues, which is related to its thermal stability.

scholarly journals Electrostatics of Tau Protein by Molecular Dynamics

Biomolecules ◽  
2019 ◽  
Vol 9 (3) ◽  
pp. 116 ◽  
Author(s):  
Tarsila Castro ◽  
Florentina-Daniela Munteanu ◽  
Artur Cavaco-Paulo
Keyword(s):  
Molecular Dynamics ◽  
3D Structure ◽  
Three Dimensional ◽  
Dynamics Simulation ◽  
Microtubule Assembly ◽  
Interaction Sites ◽  
Disordered Protein ◽  
Fluid Environment ◽  
Function Relationship ◽  
Insight Into

Tau is a microtubule-associated protein that promotes microtubule assembly and stability. This protein is implicated in several neurodegenerative diseases, including Alzheimer’s. To date, the three-dimensional (3D) structure of tau has not been fully solved, experimentally. Even the most recent information is sometimes controversial in regard to how this protein folds, interacts, and behaves. Predicting the tau structure and its profile sheds light on the knowledge about its properties and biological function, such as the binding to microtubules (MT) and, for instance, the effect on ionic conductivity. Our findings on the tau structure suggest a disordered protein, with discrete portions of well-defined secondary structure, mostly at the microtubule binding region. In addition, the first molecular dynamics simulation of full-length tau along with an MT section was performed, unveiling tau structure when associated with MT and interaction sites. Electrostatics and conductivity were also examined to understand how tau affects the ions in the intracellular fluid environment. Our results bring a new insight into tau and tubulin MT proteins, their characteristics, and the structure–function relationship.

scholarly journals Three-Dimensional (3D) Vertical Resistive Random-Access Memory (VRRAM) Synapses for Neural Network Systems

Materials ◽  
2019 ◽  
Vol 12 (20) ◽  
pp. 3451 ◽  
Author(s):  
Wookyung Sun ◽  
Sujin Choi ◽  
Bokyung Kim ◽  
Junhee Park
Keyword(s):  
Neural Network ◽  
Structural Characteristics ◽  
3D Structure ◽  
Random Access ◽  
Random Access Memory ◽  
Resistive Random Access Memory ◽  
Operating Principle ◽  
Access Memory ◽  
Network Systems ◽  
Crossbar Array

Memristor devices are generally suitable for incorporation in neuromorphic systems as synapses because they can be integrated into crossbar array circuits with high area efficiency. In the case of a two-dimensional (2D) crossbar array, however, the size of the array is proportional to the neural network’s depth and the number of its input and output nodes. This means that a 2D crossbar array is not suitable for a deep neural network. On the other hand, synapses that use a memristor with a 3D structure are suitable for implementing a neuromorphic chip for a multi-layered neural network. In this study, we propose a new optimization method for machine learning weight changes that considers the structural characteristics of a 3D vertical resistive random-access memory (VRRAM) structure for the first time. The newly proposed synapse operating principle of the 3D VRRAM structure can simplify the complexity of a neuron circuit. This study investigates the operating principle of 3D VRRAM synapses with comb-shaped word lines and demonstrates that the proposed 3D VRRAM structure will be a promising solution for a high-density neural network hardware system.

scholarly journals Optimization of coagulation-flocculation parameters using a photometric dispersion analyser

2014 ◽  
Vol 7 (2) ◽  
pp. 73-82 ◽  
Author(s):  
S. R. Ramphal ◽  
M. S. Sibiya
Keyword(s):  
Steady State ◽  
Structural Characteristics ◽  
Mixing Time ◽  
Kinetic Studies ◽  
Calcium Carbonate Precipitation ◽  
Additional Tool ◽  
Flocculation Efficiency ◽  
Jar Test ◽  
Slaked Lime ◽  
Photometric Dispersion

Abstract. The size and structural characteristics of floc particles are important design and control parameters in water treatment and should be rapidly monitored with a reasonable amount of accuracy. In this study, a photometric dispersion analyser (PDA) coupled to standard jar test experiments was used to optimize coagulation-flocculation parameters while monitoring floc size and structure as well as the rate of floc formation during coagulation using alum. The optimal coagulation conditions were as follows: sample pH 8; alum dosage, 3 mg L−1 as Al3+; G value, 172 s−1; rapid mixing time, 20 s. These conditions resulted in unstable treated water having a calcium carbonate precipitation potential (CCPP) of −15 mg L−1 as CaCO3 and required a slaked lime dosage of 17 mg L−1 as CaCO3 to equilibrate CCPP to acceptable levels. PDA data revealed that aggregation rate and steady-state variance are primary parameters as both have substantial influence on coagulation-flocculation efficiency. However, the average steady state ratio, although an important parameter, had a lessened impact on coagulation-flocculation efficiency. The results of this study showed that the PDA instrument is an important tool in coagulation kinetic studies and can be employed as an additional tool in the optimization of coagulation conditions.

TOPTMH: TOPOLOGY PREDICTOR FOR TRANSMEMBRANE α-HELICES

2010 ◽  
Vol 08 (01) ◽  
pp. 39-57 ◽  
Author(s):  
REZWAN AHMED ◽  
HUZEFA RANGWALA ◽  
GEORGE KARYPIS
Keyword(s):  
Markov Models ◽  
Structural Characteristics ◽  
Transmembrane Helix ◽  
3D Structure ◽  
Prediction Method ◽  
Support Vector ◽  
Svm Classifier ◽  
Sequence Information ◽  
Vector Machines ◽  
Prediction Approach

Alpha-helical transmembrane proteins mediate many key biological processes and represent 20%–30% of all genes in many organisms. Due to the difficulties in experimentally determining their high-resolution 3D structure, computational methods to predict the location and orientation of transmembrane helix segments using sequence information are essential. We present TOPTMH, a new transmembrane helix topology prediction method that combines support vector machines, hidden Markov models, and a widely used rule-based scheme. The contribution of this work is the development of a prediction approach that first uses a binary SVM classifier to predict the helix residues and then it employs a pair of HMM models that incorporate the SVM predictions and hydropathy-based features to identify the entire transmembrane helix segments by capturing the structural characteristics of these proteins. TOPTMH outperforms state-of-the-art prediction methods and achieves the best performance on an independent static benchmark.

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