Large-scale genome comparison based on cumulative Fourier power and phase spectra: Central moment and covariance vector
In this study, we propose a novel alignment-free method based on the one-to-one correspondence between a DNA sequence and its complete central moment vector of the cumulative Fourier power and phase spectra. In addition, the covariance between the four nucleotides in the power and phase spectra is included. We use the cumulative Fourier power and phase spectra to define a 28-dimensional vector for each DNA sequence. Euclidean distances between the vectors can measure the dissimilarity between DNA sequences. We perform testing with datasets of different sizes and types including simulated DNA sequences, exon-intron and comp...
Source: Computational and Structural Biotechnology Journal - July 12, 2019 Category: Biotechnology Source Type: research

Binding and catalytic mechanisms of Veratryl alcohol oxidation by lignin peroxidase: A theoretical and experimental study
Publication date: Available online 10 July 2019Source: Computational and Structural Biotechnology JournalAuthor(s): Jefferson O. Romero, Elena Fernández-Fueyo, Fabián Avila-Salas, Rodrigo Recabarren, Jans Alzate-Morales, Angel T. MartínezAbstractLignin peroxidase (LiP) and its natural substrate veratryl alcohol (VA) play a crucial role in lignin degradation by white-rot fungi. Understanding the molecular determinants for the interaction of this enzyme with its substrates is essential in the rational design of engineered peroxidases for biotechnological application. Here, we combine computational and ex...
Source: Computational and Structural Biotechnology Journal - July 12, 2019 Category: Biotechnology Source Type: research

AtbPpred: A robust sequence-based prediction of anti-tubercular peptides using extremely randomized trees
Publication date: Available online 3 July 2019Source: Computational and Structural Biotechnology JournalAuthor(s): Balachandran Manavalan, Shaherin Basith, Tae Hwan Shin, Leyi Wei, Gwang LeeAbstractMycobacterium tuberculosis is one of the most dangerous pathogens in humans. It acts as an etiological agent of tuberculosis (TB), infecting almost one-third of the world's population. Owing to the high incidence of multidrug-resistant TB and extensively drug-resistant TB, there is an urgent need for novel and effective alternative therapies. Peptide-based therapy has several advantages, such as diverse mechanisms of action, low...
Source: Computational and Structural Biotechnology Journal - July 4, 2019 Category: Biotechnology Source Type: research

Structural Biology and Protein Engineering of Thrombolytics
Publication date: Available online 2 July 2019Source: Computational and Structural Biotechnology JournalAuthor(s): Jan Mican, Martin Toul, David Bednar, Jiri DamborskyAbstract:Myocardial infarction and ischemic stroke are the most frequent causes of death or disability worldwide. Due to their ability to dissolve blood clots, the thrombolytics are frequently used for their treatment. Improving the effectiveness of thrombolytics for clinical uses is of great interest. The knowledge of the multiple roles of the endogenous thrombolytics and the fibrinolytic system grows continuously. The effects of thrombolytics on the alterat...
Source: Computational and Structural Biotechnology Journal - July 3, 2019 Category: Biotechnology Source Type: research

A web tool for ranking candidate drugs against a selected disease based on a combination of functional and structural criteria
Publication date: Available online 29 June 2019Source: Computational and Structural Biotechnology JournalAuthor(s): Evangelos Karatzas, George Minadakis, George Kolios, Alex Delis, George M. SpyrouAbstractDrug repurposing techniques allow existing drugs to be tested against diseases outside their initial spectrum, resulting in reduced cost and eliminating the long time-frames of new drug development. In silico drug repurposing further speeds up the process either by proposing drugs suitable to invert the transcriptomic profile of a disease or by indicating drugs based on their common targets or structural similarity with o...
Source: Computational and Structural Biotechnology Journal - June 29, 2019 Category: Biotechnology Source Type: research

Spotting, transcription and in situ synthesis: Three routes for the fabrication of RNA microarrays
Publication date: Available online 27 June 2019Source: Computational and Structural Biotechnology JournalAuthor(s): Jory Lietard, Mark M. SomozaAbstractDNA microarrays have become commonplace in the last two decades, but the synthesis of other nucleic acids biochips, most importantly RNA, has only recently been developed to a similar extent. RNA microarrays can be seen as organized surfaces displaying a potentially very large number of unique sequences and are of invaluable help in understanding the complexity of RNA structure and function as they allow the probing and treatment of each of the many different sequences simu...
Source: Computational and Structural Biotechnology Journal - June 27, 2019 Category: Biotechnology Source Type: research

Human albumin impairs amyloid β-peptide fibrillation through its C-terminus: From docking Modeling to protection against neurotoxicity in Alzheimer's disease
Publication date: Available online 26 June 2019Source: Computational and Structural Biotechnology JournalAuthor(s): Pol Picón-Pagès, Jaume Bonet, Javier García-García, Joan Garcia-Buendia, Daniela Gutierrez, Javier Valle, Carmen E.S. Gómez-Casuso, Valeriya Sidelkivska, Alejandra Alvarez, Alex Perálvarez-Marín, Albert Suades, Xavier Fernàndez-Busquets, David Andreu, Rubén Vicente, Baldomero Oliva, Francisco J. MuñozAbstractAlzheimer's disease (AD) is a neurodegenerative process characterized by the accumulation of extracellular deposits of amyloid β-...
Source: Computational and Structural Biotechnology Journal - June 26, 2019 Category: Biotechnology Source Type: research

Evolutionary stability of salt bridges hints its contribution to stability of proteins
Publication date: Available online 26 June 2019Source: Computational and Structural Biotechnology JournalAuthor(s): Xiaofeng Ban, Pratik Lahiri, Abhishek S. Dhoble, Dan Li, Zhengbiao Gu, Caiming Li, Li Cheng, Yan Hong, Zhaofeng Li, Bhalerao KaustubhAbstractThe contribution of newly designed salt bridges to protein stabilization remains controversial even today. In order to solve this problem, we investigated salt bridges from two aspects: spatial distribution and evolutionary characteristics of salt bridges. Firstly, we analyzed spatial distribution of salt bridges in proteins, elucidating the basic requirements of forming...
Source: Computational and Structural Biotechnology Journal - June 26, 2019 Category: Biotechnology Source Type: research

Computational drug screening identifies compounds targeting renal age-associated molecular profiles
In this study we generated a signature of renal age-associated genes (RAAGs) based on six different data sources including transcriptomics data as well as data extracted from scientific literature and dedicated databases. Protein abundance in renal tissue of the 634 identified RAAGs was studied next to the analysis of affected molecular pathways. RAAG expression profiles were furthermore analysed in a cohort of 63 CKD patients with available follow-up data to determine association with CKD progression. 23 RAAGs were identified showing concordant regulation in renal aging and CKD progression. This set was used as input to c...
Source: Computational and Structural Biotechnology Journal - June 25, 2019 Category: Biotechnology Source Type: research

Insights into a crucial role of TRIP13 in human Cancer
Publication date: Available online 22 June 2019Source: Computational and Structural Biotechnology JournalAuthor(s): S. Lu, J. Qian, M. Guo, C. Gu, Y. YangAbstractThyroid Hormone Receptor Interacting Protein 13 (TRIP13) plays a key role in regulating mitotic processes, including spindle assembly checkpoint and DNA repair pathways, which may account for Chromosome instability (CIN). As CIN is a predominant hallmark of cancer, TRIP13 may act as a tumor susceptibility locus. Amplification of TRIP13 has been observed in various human cancers and implicated in several aspects of malignant transformation, including cancer cell pr...
Source: Computational and Structural Biotechnology Journal - June 22, 2019 Category: Biotechnology Source Type: research

Mechanism of Sulfate Activation Catalyzed by ATP Sulfurylase - Magnesium Inhibits the Activity
Publication date: Available online 18 June 2019Source: Computational and Structural Biotechnology JournalAuthor(s): Anna Wójcik-Augustyn, A. Johannes Johansson, Tomasz BorowskiAbstractATPS Sulfurylase (ATPS) is the first of three enzymes in the sulfate reduction pathway - one of the oldest metabolic pathways on Earth, utilized by Sulfate Reducing Bacteria (SRB). Due to the low redox potential of the sulfate ion, its reduction requires activation via formation of adenosine 5′-phosphosulfate (APS), which is catalyzed by ATPS. Dispersion-corrected hybrid density functional theory (DFT/B3LYP-D3) was used to test t...
Source: Computational and Structural Biotechnology Journal - June 21, 2019 Category: Biotechnology Source Type: research

Predicting the most stable aptamer/target molecule complex configuration using a stochastic-tunnelling basin-hopping discrete molecular dynamics method: A novel global minimum search method for a biomolecule complex
This study proposed a novel global minimum search method for predicting the most stable biomolecule complex, which combines the strengths of three global minimum search methods (stochastic tunnelling, basin hopping, and discrete molecular dynamics) to efficiently improve the spatial domain search ability of the stochastic tunnelling–basin hopping (STUN–BH) method from our previous study. The epithelial cell adhesion molecule (EpCAM, PDB code: 4MZV) was used as a benchmark target molecule for the EpCAM aptamer EpA (AptEpA). For the most stable AptEpA/EpCAM complex predicted by our new method, the AptEpA was atta...
Source: Computational and Structural Biotechnology Journal - June 21, 2019 Category: Biotechnology Source Type: research

Oxidation state dependent conformational changes of HMGB1 regulate the formation of the CXCL12/HMGB1 heterocomplex
Publication date: Available online 21 June 2019Source: Computational and Structural Biotechnology JournalAuthor(s): Enrico M.A. Fassi, Jacopo Sgrignani, Gianluca D'Agostino, Valentina Cecchinato, Maura Garofalo, Giovanni Grazioso, Mariagrazia Uguccioni, Andrea CavalliAbstractHigh-mobility Group Box 1 (HMGB1) is an abundant protein present in all mammalian cells and involved in several processes. During inflammation or tissue damage, HMGB1 is released in the extracellular space and, depending on its redox state, can form a heterocomplex with CXCL12. The heterocomplex acts exclusively via the chemokine receptor CXCR4 enhanci...
Source: Computational and Structural Biotechnology Journal - June 21, 2019 Category: Biotechnology Source Type: research

Inferring protein-protein interaction networks from mass spectrometry-based proteomic approaches: A mini-review
Publication date: Available online 20 June 2019Source: Computational and Structural Biotechnology JournalAuthor(s): Kumar Yugandhar, Shagun Gupta, Haiyuan YuAbstractStudying protein-protein interaction networks provide key evidence for the underlying molecular mechanisms. Mass spectrometry-based proteomic approaches have been playing a pivotal role in deciphering these interaction networks, along with precise quantification for individual interactions. In this mini-review we discuss the available techniques and methods for qualitative and quantitative elucidation of protein-protein interaction networks. We then summarize t...
Source: Computational and Structural Biotechnology Journal - June 20, 2019 Category: Biotechnology Source Type: research

Avenues toward microRNA detection in vitro: A review of technical advances and challenges
Publication date: Available online 20 June 2019Source: Computational and Structural Biotechnology JournalAuthor(s): Chu-shu Zhu, Lingyun Zhu, De-an Tan, Xin-yuan Qiu, Chuan-yang Liu, Si-si Xie, Lv-yun ZhuAbstractOver the decades, the biological role of microRNAs (miRNAs) in the post-transcriptional regulation of gene expression has been discovered in many cancer types, thus initiating the tremendous expectation of their application as biomarkers in the diagnosis, prognosis, and treatment of cancer. Hence, the development of efficient miRNA detection methods in vitro is in high demand. Extensive efforts have been made based...
Source: Computational and Structural Biotechnology Journal - June 20, 2019 Category: Biotechnology Source Type: research

Mutations in the Global Transcription Factor CRP/CAP: Insights from Experimental Evolution and Deep Sequencing
Publication date: Available online 18 June 2019Source: Computational and Structural Biotechnology JournalAuthor(s): Pernille Ott Frendorf, Ida Lauritsen, Agnieszka Sekowska, Antoine Danchin, Morten H.H. NørholmAbstractThe Escherichia coli cyclic AMP receptor protein (CRP or catabolite activator protein, CAP) provides a textbook example of bacterial transcriptional regulation and is one of the best studied transcription factors in biology. For almost five decades a large number of mutants, evolved in vivo or engineered in vitro, have shed light on the molecular structure and mechanism of CRP. Here, we review previous...
Source: Computational and Structural Biotechnology Journal - June 19, 2019 Category: Biotechnology Source Type: research

Mechanism of sulfate activation catalyzed by ATP Sulfurylase - magnesium inhibits the activity.
Publication date: Available online 18 June 2019Source: Computational and Structural Biotechnology JournalAuthor(s): Anna Wójcik-Augustyn, A. Johannes Johansson, Tomasz BorowskiAbstractATPS Sulfurylase (ATPS) is the first of three enzymes in the sulfate reduction pathway - one of the oldest metabolic pathways on Earth, utilized by Sulfate Reducing Bacteria (SRB). Due to the low redox potential of the sulfate ion, its reduction requires activation via formation of adenosine 5′-phosphosulfate (APS), which is catalyzed by ATPS. Dispersion-corrected hybrid density functional theory (DFT/B3LYP-D3) was used to test t...
Source: Computational and Structural Biotechnology Journal - June 18, 2019 Category: Biotechnology Source Type: research

Early vascular ageing and cellular senescence in chronic kidney disease
Publication date: Available online 18 June 2019Source: Computational and Structural Biotechnology JournalAuthor(s): Lu Dai, Abdul Rashid Qureshi, Anna Witasp, Bengt Lindholm, Peter StenvinkelAbstractChronic kidney disease (CKD) is a clinical model of premature ageing characterized by progressive vascular disease, systemic inflammation, muscle wasting and frailty. The predominant early vascular ageing (EVA) process mediated by medial vascular calcification (VC) results in a marked discrepancy between chronological and biological vascular age in CKD. Though the exact underlying mechanisms of VC and EVA are not fully elucidat...
Source: Computational and Structural Biotechnology Journal - June 18, 2019 Category: Biotechnology Source Type: research

Progress and challenges: Development and implementation of CRISPR/Cas9 technology in filamentous fungi
Publication date: Available online 13 June 2019Source: Computational and Structural Biotechnology JournalAuthor(s): Qiang Wang, Jeffrey J. ColemanAbstractWidely distributed in various environmental niches, filamentous fungi play an important role in industry, drug development, and plant/animal health. Manipulation of the genome and the coding sequences are essential for a better understanding of the function of genes and their regulation, but traditional genetic approaches in some filamentous fungi are either inefficient or nonfunctional. The rapid development and wide implementation of CRISPR/Cas9 (Clustered Regularly Int...
Source: Computational and Structural Biotechnology Journal - June 14, 2019 Category: Biotechnology Source Type: research

FOXO3 on the road to longevity: Lessons from SNPs and chromatin hubs
Publication date: Available online 13 June 2019Source: Computational and Structural Biotechnology JournalAuthor(s): Paola Sanese, Giovanna Forte, Vittoria Disciglio, Valentina Grossi, Cristiano SimoneAbstractHealth span is driven by a precise interplay between genes and the environment. Cell response to environmental cues is mediated by signaling cascades and genetic variants that affect gene expression by regulating chromatin plasticity. Indeed, they can promote the interaction of promoters with regulatory elements by forming active chromatin hubs.FOXO3 encodes a transcription factor with a strong impact on aging and age-...
Source: Computational and Structural Biotechnology Journal - June 14, 2019 Category: Biotechnology Source Type: research

The progress of CRISPR/Cas9-mediated gene editing in generating mouse/zebrafish models of human skeletal diseases
Publication date: Available online 13 June 2019Source: Computational and Structural Biotechnology JournalAuthor(s): Nan Wu, Bowen Liu, Huakang Du, Sen Zhao, Yaqi Li, Xi Cheng, Shengru Wang, Jiachen Lin, Junde Zhou, Guixing Qiu, Jianguo Zhang, Zhihong WuAbstractGenetic factors play a substantial role in the etiology of skeletal diseases, which involve 1) defects in skeletal development, including intramembranous ossification defects and endochondral ossification defects; 2) defects in skeletal metabolism, including late bone growth and bone remodeling; 3) defects in early developmental processes related to skeletal diseases...
Source: Computational and Structural Biotechnology Journal - June 14, 2019 Category: Biotechnology Source Type: research

Studies on molecular dynamics of intrinsically disordered proteins and their fuzzy complexes: A mini-review
Publication date: Available online 13 June 2019Source: Computational and Structural Biotechnology JournalAuthor(s): Kota Kasahara, Hiroki Terazawa, Takuya Takahashi, Junichi HigoAbstractThe molecular dynamics (MD) method is a promising approach toward elucidating the molecular mechanisms of intrinsically disordered regions (IDRs) of proteins and their fuzzy complexes. This mini-review introduces recent studies that apply MD simulations to investigate the molecular recognition of IDRs. Firstly, methodological issues by which MD simulations treat IDRs, such as developing force fields, treating periodic boundary conditions, a...
Source: Computational and Structural Biotechnology Journal - June 14, 2019 Category: Biotechnology Source Type: research

Base-pair opening dynamics of nucleic acids in relation to their biological function
Publication date: Available online 13 June 2019Source: Computational and Structural Biotechnology JournalAuthor(s): Seo-Ree Choi, Na-Hyun Kim, Ho-Seong Jin, Yeo-Jin Seo, Juhyun Lee, Joon-Hwa LeeAbstractBase-pair opening is a conformational transition that is required for proper biological function of nucleic acids. Hydrogen exchange, observed by NMR spectroscopic experiments, is a widely used method to study the thermodynamics and kinetics of base-pair opening in nucleic acids. The hydrogen exchange data of imino protons are analyzed based on a two-state (open/closed) model for the base-pair, where hydrogen exchange only o...
Source: Computational and Structural Biotechnology Journal - June 14, 2019 Category: Biotechnology Source Type: research

DNA nanostructures: A versatile lab-bench for interrogating biological reactions
Publication date: Available online 14 June 2019Source: Computational and Structural Biotechnology JournalAuthor(s): Andrew J. Lee, Christoph WältiAbstractAt its inception DNA nanotechnology was conceived as a tool for spatially arranging biological molecules in a programmable and deterministic way to improve their interrogation. To date, DNA nanotechnology has provided a versatile toolset of nanostructures and functional devices to augment traditional single molecule investigation approaches – including atomic force microscopy – by isolating, arranging and contextualising biological systems at the single m...
Source: Computational and Structural Biotechnology Journal - June 14, 2019 Category: Biotechnology Source Type: research

Computational biology solutions to identify enhancers-target gene pairs
Publication date: Available online 14 June 2019Source: Computational and Structural Biotechnology JournalAuthor(s): Judith Mary Hariprakash, Francesco FerrariAbstractEnhancers are non-coding regulatory elements that are distant from their target gene. Their characterization still remains elusive especially due to challenges in achieving a comprehensive pairing of enhancers and target genes. A number of computational biology solutions have been proposed to address this problem leveraging the increasing availability of functional genomics data and the improved mechanistic understanding of enhancer action.In this review we fo...
Source: Computational and Structural Biotechnology Journal - June 14, 2019 Category: Biotechnology Source Type: research

Structural basis for plant MADS transcription factor oligomerization
Publication date: Available online 14 June 2019Source: Computational and Structural Biotechnology JournalAuthor(s): Xuelei Lai, Hussein Daher, Antonin Galien, Veronique Hugouvieux, Chloe ZubietaAbstractMADS transcription factors (TFs) are DNA binding proteins found in almost all eukaryotes that play essential roles in diverse biological processes. While present in animals and fungi as a small TF family, the family has dramatically expanded in plants over the course of evolution, with the model flowering plant, Arabidopsis thaliana, possessing over 100 type I and type II MADS TFs. All MADS TFs contain a core and highly cons...
Source: Computational and Structural Biotechnology Journal - June 14, 2019 Category: Biotechnology Source Type: research

Endogenous and Foreign Nucleoid-Associated Proteins of Bacteria: occurrence, interactions and effects on Mobile Genetic Elements and host´s biology
Publication date: Available online 14 June 2019Source: Computational and Structural Biotechnology JournalAuthor(s): Rodrigo Flores-Ríos, Raquel Quatrini, Alejandra LoyolaAbstractMobile Genetic Elements (MGEs) are mosaics of functional gene modules of diverse evolutionary origin and are generally divergent from the hosts´ genetic background. Existing biases in base composition and codon usage of these elements` genes impose transcription and translation limitations that may affect the physical and regulatory integration of MGEs in new hosts. Stable appropriation of the foreign DNA depends on a number of host fa...
Source: Computational and Structural Biotechnology Journal - June 14, 2019 Category: Biotechnology Source Type: research

A collaborative platform for Management of Chronic Diseases via guideline-driven individualized care plans
Publication date: Available online 12 June 2019Source: Computational and Structural Biotechnology JournalAuthor(s): Gokce B. Laleci Erturkmen, Mustafa Yuksel, Bunyamin Sarigul, Theodoros N. Arvanitis, Pontus Lindman, Rong Chen, Lei Zhao, Eric Sadou, Jacques Bouaud, Lamine Traore, Alper Teoman, Sarah N. Lim Choi Keung, George Despotou, Esteban de Manuel, Dolores Verdoy, Antonio de Blas, Nicolas Gonzalez, Mikael Liljaj, Malte von Tottleben, Marie BeachAbstractOlder age is associated with an increased accumulation of multiple chronic conditions. The clinical management of patients suffering from multiple chronic conditions is...
Source: Computational and Structural Biotechnology Journal - June 12, 2019 Category: Biotechnology Source Type: research

Prediction of ligand transport along hydrophobic enzyme Nanochannels
Publication date: Available online 11 June 2019Source: Computational and Structural Biotechnology JournalAuthor(s): Diego E. Escalante, Alptekin AksanAbstractBuried active sites of enzymes are connected to the bulk solvent through a network of hydrophobic channels. We developed a discretized model that can accurately predict ligand transport along hydrophobic channels up to six orders of magnitude faster than any other existing method. The non-dimensional nature of the model makes it applicable to any hydrophobic channel/ligand combination. (57 words). (Source: Computational and Structural Biotechnology Journal)
Source: Computational and Structural Biotechnology Journal - June 11, 2019 Category: Biotechnology Source Type: research

Applications of genome editing technology in animal disease modeling and gene therapy
Publication date: Available online 8 June 2019Source: Computational and Structural Biotechnology JournalAuthor(s): Qian Li, Zhou Qin, Qingnan Wang, Ting Xu, Yang Yang, Zhiyao HeAbstractGenome editing technology is a technique for targeted genetic modifications, enabling the knockout and addition of specific DNA fragments. This technology has been widely used in various types of biomedical research, clinics and agriculture. In terms of disease research, constructing appropriate animal models is necessary. Combining reproductive technology with genome editing, many animal disease models have been generated for basic and clin...
Source: Computational and Structural Biotechnology Journal - June 8, 2019 Category: Biotechnology Source Type: research

An evaluation of machine learning approaches for the prediction of essential genes in eukaryotes using protein sequence-derived features
Publication date: Available online 8 June 2019Source: Computational and Structural Biotechnology JournalAuthor(s): Tulio L. Campos, Pasi K. Korhonen, Robin B. Gasser, Neil D. YoungAbstractThe availability of whole-genome sequences and associated multi-omics data sets, combined with advances in gene knockout and knockdown methods, has enabled large-scale annotation and exploration of gene and protein functions in eukaryotes. Knowing which genes are essential for the survival of eukaryotic organisms is paramount for an understanding of the basic mechanisms of life, and could assist in identifying intervention targets in euka...
Source: Computational and Structural Biotechnology Journal - June 8, 2019 Category: Biotechnology Source Type: research

The use of diffusion calculations and Monte Carlo simulations to understand the behavior of cells in Dictyostelium communities
Publication date: Available online 8 June 2019Source: Computational and Structural Biotechnology JournalAuthor(s): Richard H. GomerAbstractMicrobial communities are the simplest possible model of multicellular tissues, allowing studies of cell-cell interactions to be done with as few extraneous factors as possible. For instance, the eukaryotic microbe Dictyostelium discoideum proliferates as single cells, and when starved, the cells aggregate together and form structures of ~20,000 cells. The cells use a variety of signals to direct their movement, inform each other of their local cell density and whether they are starving...
Source: Computational and Structural Biotechnology Journal - June 8, 2019 Category: Biotechnology Source Type: research

Interfaces between alpha-helical integral membrane proteins: Characterization, prediction, and docking
Publication date: Available online 25 May 2019Source: Computational and Structural Biotechnology JournalAuthor(s): Bian Li, Jeffrey Mendenhall, Jens MeilerAbstractProtein-protein interactions (PPIs) are an essential mechanism by which proteins perform their biological functions. For globular proteins, the molecular characteristics of such interactions have been well analyzed, and many computational tools are available for predicting PPI sites and constructing structural models of the complex. In contrast, little is known about the molecular features of the interaction between integral membrane proteins (IMPs) and few metho...
Source: Computational and Structural Biotechnology Journal - May 25, 2019 Category: Biotechnology Source Type: research

Energetics of storage and diffusion of water and Cyclo-Octasulfur for a nonpolar cavity of RHCC Tetrabrachion by molecular dynamics simulations
Publication date: Available online 23 May 2019Source: Computational and Structural Biotechnology JournalAuthor(s): C. Harder-Viddal, M. McDougall, R.M. Roshko, J. StetefeldAbstractTetrabrachion forms the key component of the S-layer of Staphylothermus marinus. Molecular dynamics simulations have been used to study the energetics of occupancy of cavity 3 of the right-handed coiled-coil stalk of tetrabrachion by both water molecules and cyclooctasulfur S8 crowns, as well as to determine possible pathways and free energy barriers for the diffusion of both water and cyclooctasulfur through the peptide walls of RHCC tetrabrachi...
Source: Computational and Structural Biotechnology Journal - May 24, 2019 Category: Biotechnology Source Type: research

Application of PD-1 blockade in cancer immunotherapy
Publication date: Available online 23 May 2019Source: Computational and Structural Biotechnology JournalAuthor(s): Xiaomo Wu, Zhongkai Gu, Yang Chen, Borui Chen, Wei Chen, Liqiang Weng, Xiaolong LiuAbstractThe programmed cell death protein 1 (PD-1) pathway has received considerable attention due to its role in eliciting the immune checkpoint response of T cells, resulting in tumor cells capable of evading immune surveillance and being highly refractory to conventional chemotherapy. Application of anti-PD-1/PD-L1 antibodies as checkpoint inhibitors is rapidly becoming a promising therapeutic approach in treating tumors, and...
Source: Computational and Structural Biotechnology Journal - May 24, 2019 Category: Biotechnology Source Type: research

A rhizosphere-derived consortium of Bacillus subtilis and Trichoderma harzianum suppresses common scab of potato and increases yield
Publication date: Available online 15 May 2019Source: Computational and Structural Biotechnology JournalAuthor(s): Zhenshuo Wang, Yan Li, Lubo Zhuang, Yue Yu, Jia Liu, Lixia Zhang, Zhenjiang Gao, Yufeng Wu, Wa Gao, Guo-chun Ding, Qi WangAbstractThe ability of a rhizosphere-derived microbial product (composed of a consortium of a strain of Bacillus subtilis and a strain of Trichoderma harzianum) to suppress common scab disease in potato caused by Streptomyces spp. was examined over a two-year period. Relative to the condition in which 0 kg·ha−1 of the designated microbial product was applied (control), the di...
Source: Computational and Structural Biotechnology Journal - May 15, 2019 Category: Biotechnology Source Type: research

Cytochrome c: Surfing off of the mitochondrial membrane on the tops of complexes III and IV
Publication date: Available online 13 May 2019Source: Computational and Structural Biotechnology JournalAuthor(s): Gonzalo Pérez-Mejías, Alejandra Guerra-Castellano, Antonio Díaz-Quintana, Miguel A. De la Rosa, Irene Díaz-MorenoAbstractThe proper arrangement of protein components within the respiratory electron transport chain is nowadays a matter of intense debate, since altering it leads to cell aging and other related pathologies. Here, we discuss three current views—the so-called solid, fluid and plasticity models—which describe the organization of the main membrane-embedded mito...
Source: Computational and Structural Biotechnology Journal - May 15, 2019 Category: Biotechnology Source Type: research

A viral T7 RNA polymerase ratcheting along DNA with fidelity control
Publication date: Available online 9 May 2019Source: Computational and Structural Biotechnology JournalAuthor(s): Chunhong Long, E. Chao, Lin-Tai Da, Jin YuAbstractRNA polymerase (RNAP) from bacteriophage T7 is a representative single-subunit viral RNAP that can transcribe with high promoter activities without assistances from transcription factors. We accordingly studied this small transcription machine computationally as a model system to understand underlying mechanisms of mechano-chemical coupling and fidelity control in the RNAP transcription elongation. Here we summarize our computational work from several recent pub...
Source: Computational and Structural Biotechnology Journal - May 10, 2019 Category: Biotechnology Source Type: research

Computational methods for mapping, assembly and quantification for coding and non-coding transcripts
Publication date: Available online 7 May 2019Source: Computational and Structural Biotechnology JournalAuthor(s): Isaac A. Babarinde, Yuhao Li, Andrew P. HutchinsAbstractThe measurement of gene expression has long provided significant insight into biological functions. The development of high-throughput short-read sequencing technology has revealed transcriptional complexity at an unprecedented scale, and informed almost all areas of biology. However, as researchers have sought to gather more insights from the data, these new technologies have also increased the computational analysis burden. In this review, we describe ty...
Source: Computational and Structural Biotechnology Journal - May 7, 2019 Category: Biotechnology Source Type: research

Analytical Py-GC/MS of genetically modified poplar for the increased production of bio-aromatics
This study manifests the applicability of PCA analysis in tracking the biological changes in biomass (poplar in this case) and their effects on pyrolysis-oil compositions.Graphical Abstract (Source: Computational and Structural Biotechnology Journal)
Source: Computational and Structural Biotechnology Journal - April 25, 2019 Category: Biotechnology Source Type: research

Accounting for biological variation with linear mixed-effects modelling improves the quality of clinical metabolomics data
Publication date: Available online 22 April 2019Source: Computational and Structural Biotechnology JournalAuthor(s): Kwanjeera Wanichthanarak, Saharuetai Jeamsripong, Natapol Pornputtapong, Sakda KhoomrungAbstractMetabolite profiles from biological samples suffer from both technical variations and subject-specific variants. To improve the quality of metabolomics data, conventional data processing methods can be employed to remove technical variations. These methods do not consider sources of subject variation as separate factors from biological factors of interest. This can be a significant issue when performing quantitati...
Source: Computational and Structural Biotechnology Journal - April 24, 2019 Category: Biotechnology Source Type: research

Computational simulations identified two candidate inhibitors of Cdk5/p25 to abrogate tau-associated neurological disorders
Publication date: Available online 22 April 2019Source: Computational and Structural Biotechnology JournalAuthor(s): Amir Zeb, Minky Son, Sanghwa Yoon, Ju Hyun Kim, Seok Ju Park, Keun Woo LeeAbstractDeregulation of Cdk5 is a hallmark in neurodegenerative diseases and its complex with p25 forms Cdk5/p25, thereby causes severe neuropathological insults. Cdk5/p25 abnormally phosphorylates tau protein, and induces tau-associated neurofibrillary tangles in neurological disorders. Therefore, the pharmacological inhibition of Cdk5/p25 alleviates tau-associated neurological disorders. Herein, computational simulations probed two c...
Source: Computational and Structural Biotechnology Journal - April 24, 2019 Category: Biotechnology Source Type: research

Modeling conformationally flexible proteins with X-ray scattering and molecular simulations
Publication date: Available online 22 April 2019Source: Computational and Structural Biotechnology JournalAuthor(s): Kyle T. Powers, Melissa S. Gildenberg, M. Todd WashingtonAbstractProteins and protein complexes with high conformational flexibility participate in a wide range of biological processes. These processes include genome maintenance, gene expression, signal transduction, cell cycle regulation, and many others. Gaining a structural understanding of conformationally flexible proteins and protein complexes is arguably the greatest problem facing structural biologists today. Over the last decade, some progress has b...
Source: Computational and Structural Biotechnology Journal - April 24, 2019 Category: Biotechnology Source Type: research

Tissue engineering: Understanding the role of biomaterials and biophysical forces on cell functionality through computational and structural biotechnology analytical methods
Publication date: Available online 17 April 2019Source: Computational and Structural Biotechnology JournalAuthor(s): Nour Almouemen, Helena M. Kelly, Cian O'LearyAbstractWithin the past 25 years, tissue engineering (TE) has grown enormously as a science and as an industry. Although classically concerned with the recapitulation of tissue and organ formation in our body for regenerative medicine, the evolution of TE research is intertwined with progress in other fields through the examination of cell function and behaviour in isolated biomimetic microenvironments. As such, TE applications now extend beyond the field of tis...
Source: Computational and Structural Biotechnology Journal - April 17, 2019 Category: Biotechnology Source Type: research

DNA i-motifs with guanidino-i-clamp residues: The counterplay between kinetics and thermodynamics and implications for the design of pH sensors
Publication date: Available online 13 April 2019Source: Computational and Structural Biotechnology JournalAuthor(s): Vladimir B. Tsvetkov, Timofei S. Zatsepin, Anton V. Turaev, Valentina M. Farzan, Galina E. Pozmogova, Andrey V. Aralov, Anna M. VarizhukAbstractI-motif structures, adopted by cytosine-rich DNA strands, have attracted considerable interest as possible regulatory elements in genomes. Applied science exploits the advantages of i-motif stabilization under acidic conditions: i-motif-based pH sensors and other biocompatible nanodevices are being developed. Two key characteristics of i-motifs as core elements of na...
Source: Computational and Structural Biotechnology Journal - April 13, 2019 Category: Biotechnology Source Type: research

Single-component bismuth nanoparticles as a theranostic agent for multimodal imaging-guided glioma therapy
Publication date: Available online 13 April 2019Source: Computational and Structural Biotechnology JournalAuthor(s): Shu-Ting Lu, Dan Xu, Ru-Fang Liao, Jia-Zhen Luo, Yu-Hang Liu, Zhen-Hua Qi, Cai-Ju Zhang, Nai-Li Ye, Bo Wu, Hai-Bo XuAbstractSingle-component nanomaterials such as bismuth (Bi) based on nanoparticles (NPs) intrinsically having both diagnostic and therapeutic capabilities are widely needed in biomedical fields. However, their design and fabrication still face enormous challenges. Here, a kind of pure Bi NPs with ultrahigh X-ray attenuation coeffcient was developed and evaluated as a simple but powerful therano...
Source: Computational and Structural Biotechnology Journal - April 13, 2019 Category: Biotechnology Source Type: research

Interrelations of sphingolipid and lysophosphatidate signaling with immune system in ovarian cancer
Publication date: Available online 10 April 2019Source: Computational and Structural Biotechnology JournalAuthor(s): Anastasia Meshcheryakova, Martin Svoboda, Markus Jaritz, Felicitas Mungenast, Martina Salzmann, Dietmar Pils, Dan Cacsire Castillo-Tong, Gudrun Hager, Andrea Wolf, Elena Ioana Braicu, Jalid Sehouli, Sandrina Lambrechts, Ignace Vergote, Sven Mahner, Peter Birner, Philip Zimmermann, David N. Brindley, Georg Heinze, Robert Zeillinger, Diana MechtcheriakovaAbstractThe sphingolipid and lysophosphatidate regulatory networks impact diverse mechanisms attributed to cancer cells and the tumor immune microenvironment....
Source: Computational and Structural Biotechnology Journal - April 10, 2019 Category: Biotechnology Source Type: research

Calling Variants in the Clinic: Informed Variant Calling Decisions Based on Biological, Clinical, and Laboratory Variables
Publication date: Available online 8 April 2019Source: Computational and Structural Biotechnology JournalAuthor(s): Zachary S. Bohannan, Antonina MitrofanovaAbstractDeep sequencing genomic analysis is becoming increasingly common in clinical research and practice, enabling accurate identification of diagnostic, prognostic, and predictive determinants. Variant calling, distinguishing between true mutations and experimental errors, is a central task of genomic analysis and often requires sophisticated statistical, computational, and/or heuristic techniques. Although variant callers seek to overcome noise inherent in biologic...
Source: Computational and Structural Biotechnology Journal - April 10, 2019 Category: Biotechnology Source Type: research

Recursive Motif Analyses Identify Brain Epigenetic Transcription Regulatory Modules
In this study, we conceived an algorithm to predict epigenetic regulatory modules through recursive motif analyses on differentially methylated loci. A two-step procedure was implemented to first group differentially methylated loci into clusters according to their correlations in methylation profiles and then to repeatedly identify the transcription factor binding motifs significantly enriched in each cluster. We applied this tool on methylome datasets generated for mouse brains which have a lack of DNA demethylation enzymes TET1 or TET2. Compared with wild type control, the differentially methylated CpG sites identified ...
Source: Computational and Structural Biotechnology Journal - April 10, 2019 Category: Biotechnology Source Type: research

Asymmetric spontaneous intercalation of lutein into a phospholipid bilayer, a computational study
Publication date: Available online 6 April 2019Source: Computational and Structural Biotechnology JournalAuthor(s): Krzysztof Makuch, Michal Markiewicz, Marta Pasenkiewicz-GierulaAbstractLutein, a hydroxylated carotenoid, is a pigment synthesised by plants and bacteria. Animals are unable to synthesise lutein nevertheless, it is present in animal tissues, where its only source is dietary intake. Both in plants and animals, carotenoids are associated mainly with membranes where they carry out important physiological functions. Their trafficking to and insertion into membranes are not well recognised due to experimental diff...
Source: Computational and Structural Biotechnology Journal - April 7, 2019 Category: Biotechnology Source Type: research