Abstract：
:Tissue softening accompanies the ripening of many fruits and initiates the processes of irreversible deterioration. Expansins are plant cell wall proteins that have been proposed to disrupt hydrogen bonds within the cell wall polymer matrix. Several authors have shown that FaEXPA2 is a key gene that shows an increased expression level during ripening and softening of the strawberry fruit. For this reason, FaEXPA2 is frequently used as a molecular marker of softening in strawberry fruit, and changes in its relative expression have been related to changes in fruit firmness. In this context, we previously reported that FaEXPA2 has a high accumulation rate during fruit ripening in four different strawberry cultivars; however, the molecular mechanism of FaEXPA2 or expansins in general is not yet clear. Herein, a 3D model of the FaEXPA2 protein was built by comparative modeling to understand how FaEXPA2 interacts with different cell wall components at the molecular level. First, the structure was shown to display two domains characteristic of the other expansins that were previously described. The protein-ligand interaction was evaluated by molecular dynamic (MD) simulation using four different long ligands (a cellulose fiber, two of the more important xyloglucan (XG) fibers found in strawberry (XXXG and XXFG type), and a pectin (homogalacturonic acid type)). The results showed that FaEXPA2 formed a more stable complex with cellulose than other ligands via the different residues present in the open groove surface of its two domains, while FaEXPA2 did not interact with the pectin ligand.
journal_name
Comput Biol Chemjournal_title
Computational biology and chemistryauthors
Valenzuela-Riffo F,Morales-Quintana Ldoi
10.1016/j.compbiolchem.2020.107279subject
Has Abstractpub_date
2020-05-30 00:00:00pages
107279eissn
1476-9271issn
1476-928Xpii
S1476-9271(20)30050-5journal_volume
87pub_type
杂志文章abstract：:Klebsiella pneumoniae is declared as antibiotic resistant by WHO, with the critical urgency of developing novel antimicrobial therapeutics as drug resistance is the second most dangerous threat after terrorism. Besides many attempts still, there is no effective vaccine available against K. pneumoniae. By utilizing all...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2020.107380
更新日期：2020-12-01 00:00:00
abstract：:In process of creating genetic maps different labs/research groups obtain overlapping parts of the map. Merging these parts into one integrative map is based on looking for maximum shared marker orders among the maps. Really, not all shared markers of such maps have consensus order that obstructs building of the integ...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2005.09.007
更新日期：2006-02-01 00:00:00
abstract：:The long perceived notion that G-Protein Coupled Receptors (GPCRs) function in monomeric form has recently been changed by the description of a number of GPCRs that are found in oligomeric states. The mechanism of GPCR oligomerization, and its effect on receptor function, is not well understood. In the present study, ...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2013.11.002
更新日期：2014-02-01 00:00:00
abstract：:Alzheimer's disease (AD) is a progressive neurodegenerative disease of central nervous system among elderly people. Human acetylcholinesterase (hAChE), an important enzyme in neuronal signaling, is responsible for the degradation of acetylcholine which in turn prevents the post synaptic signal transmissions. hAChE has...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2017.04.002
更新日期：2017-06-01 00:00:00
abstract：:Real-time RT-PCR has been frequently used in quantitative research in molecular biology and bioinformatics. It provides remarkably useful technology to assess expression of genes. Although mathematical models for gene amplification process have been studied, statistical models and methods for data analysis in real-tim...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2005.10.005
更新日期：2006-02-01 00:00:00
abstract：:The growth and spread of drug resistance in bacteria have been well established in both mankind and beasts and thus is a serious public health concern. Due to the increasing problem of drug resistance, control of infectious diseases like diarrhea, pneumonia etc. is becoming more difficult. Hence, it is crucial to unde...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2015.07.011
更新日期：2015-10-01 00:00:00
abstract：:Developments of novel inhibitors to prevent the function of 5-lipoxygenase (5-LOX) proteins that are responsible for a variety of inflammatory and allergic disease are a major challenge in the scientific community. In this study, robust QSAR classification models for predicting 5-LOX activity were developed using mach...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2018.10.002
更新日期：2018-12-01 00:00:00
abstract：:Bacterial MocR transcriptional regulators possess an N-terminal DNA-binding domain containing a conserved helix-turn-helix module and an effector-binding and/or oligomerization domain at the C-terminus, homologous to fold type-I pyridoxal 5'-phosphate (PLP) enzymes. Since a comprehensive structural analysis of the Moc...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2015.05.003
更新日期：2015-10-01 00:00:00
abstract：:We have developed a computational technique refereed to as complex phylogenetic profiling. Our approach combines logic analyses of gene phylogenetic profiles and phenotype data. Logic analysis of phylogenetic profiles identifies sets of proteins whose presence or absence follows certain logic relationships. Our approa...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2008.07.003
更新日期：2008-12-01 00:00:00
abstract：:The low molecular weight protein tyrosine phosphatase (LMW-PTP) could regulate many signaling pathways, and it had drawn attention as a potential target for cancer. As previous report has indicated that the aplidin could inhibit the LMW-PTP, and thus, the relevant cancer caused by the abnormal regulation of the LMW-PT...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2019.107123
更新日期：2019-12-01 00:00:00
abstract：:A computational inestigation on the difference in colors of two plants 'Peony' and 'Morning glory' by the same pigment 'Peonidin' has been performed by means of absorption characteristics. Peonidin imparts purple color to the flowers in Peony and blue to that in Morning glory. TDDFT tool in Gaussian 09 software packag...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2018.07.015
更新日期：2018-10-01 00:00:00
abstract：:Nodulation is one of the very important processes of legume plants as it is the initiating event of fixing nitrogen. Although ethylene has essential role in normal plant metabolism but it has also negative impact on plants particularly in nodule formation in legume plants. It is also produced due to a variety of bioti...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2017.02.005
更新日期：2017-06-01 00:00:00
abstract：:Polymerase chain reaction (PCR) is an important diagnostic tool for the amplification of DNA. The PCR process can be treated as a problem in biochemical engineering. This study focuses on the development of a mathematical model of the polymerase chain reaction. The PCR process consists of three steps: denaturation of ...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2004.03.001
更新日期：2004-07-01 00:00:00
abstract：:We introduce a method for ungapped local multiple alignment (ULMA) in a given set of amino acid or nucleotide sequences. This method explores two search spaces using a linked optimization strategy. The first search space M consists of all possible words of a given length W, defined on the residue alphabet. An evolutio...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2004.01.001
更新日期：2004-04-01 00:00:00
abstract：:Nanoscopic properties of TiO2 augmented with its physicochemical properties and biocompatibility make it a material interest in the biomedical field. Efficient methods to design of such materials require a thorough understanding of associated nano-bio interfaces. In the present study, density functional theory calcula...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2020.107236
更新日期：2020-06-01 00:00:00
abstract：:With the development of cancer research, various gene expression datasets containing cancer information show an explosive growth trend. In addition, due to the continuous maturity of single-cell RNA sequencing (scRNA-seq) technology, the protein information and pedigree information of a single cell are also continuous...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2020.107368
更新日期：2020-12-01 00:00:00
abstract：BACKGROUND:Recent studies have indicated that microRNA (miRNA) may play an oncogenic or tumor suppressor role in human cancer. To study the regulatory role of miRNAs in tumorigenesis, an integrated platform has been set up to provide a user friendly interface for query. The main advantage of the present platform is tha...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2013.02.001
更新日期：2013-06-01 00:00:00
abstract：:In this study, the dipeptidyl peptidase-IV (DPP-IV) inhibition activities of a series of novel aminomethyl-piperidones were investigated by molecular docking studies and modeled by quantitative structure-activity relationship (QSAR) methodology. Molecular docking studies were used to find the best conformations of the...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2016.08.003
更新日期：2016-10-01 00:00:00
abstract：:Pseudomonas aeruginosa is an opportunistic gram-negative bacterium that has the capability to acquire resistance under hostile conditions and become a threat worldwide. It is involved in nosocomial infections. In the current study, potential novel drug targets against P. aeruginosa have been identified using core prot...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2018.02.017
更新日期：2018-06-01 00:00:00
abstract：:An oscillation with a period of around 500 kb in guanine and cytosine content (GC%) is observed in the DNA sequence of human chromosome 21. This oscillation is localized in the rightmost one-eighth region of the chromosome, from 43.5 Mb to 46.5 Mb. Five cycles of oscillation are observed in this region with six GC-ric...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2004.09.011
更新日期：2004-12-01 00:00:00
abstract：:Often the quantitative data coming from proteomics and metabolomics studies have irregular distribution with a spike. None of the wide used methods for human QTL mapping are applicable to such traits. Researchers have to reduce the sample, excluding the spike, and analyze only continuous measurements. In this study, w...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2011.11.004
更新日期：2012-02-01 00:00:00
abstract：:Feature selection techniques have been used as the workhorse in biomarker discovery applications for a long time. Surprisingly, the stability of feature selection with respect to sampling variations has long been under-considered. It is only until recently that this issue has received more and more attention. In this ...
journal_title：Computational biology and chemistry
pub_type： 杂志文章,评审
doi：10.1016/j.compbiolchem.2010.07.002
更新日期：2010-08-01 00:00:00
abstract：:A translation (framing) code based on the circular code was proposed in Michel (2012) with the identification of X circular code motifs (X motifs shortly) in the bacterial rRNA of Thermus thermophilus, in particular in the ribosome decoding center. Three classes of X motifs are now identified in the rRNAs of bacteria ...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2014.08.001
更新日期：2014-10-01 00:00:00
abstract：:Selecting the values of parameters used by de novo genomic assembly programs, or choosing an optimal de novo assembly from several runs obtained with different parameters or programs, are tasks that can require complex decision-making. A key parameter that must be supplied to typical next generation sequencing (NGS) a...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2014.08.014
更新日期：2014-12-01 00:00:00
abstract：:A series of indole-derived methoxylated chalcones were described as anti-dermatophyte agents. The in vitro antifungal susceptibility testing against different dermatophytes revealed that most of compounds had potent activity against the dermatophyte strains. In particular, the 4-ethoxy derivative 4d with MIC values of...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2019.107189
更新日期：2020-02-01 00:00:00
abstract：:The channel blocker picrotoxinin has been studied with GABAA-ρ1 and GABAA-ρ2 homology models based on the GluCl crystal structure. Picrotoxinin is tenfold more potent for GABAA-ρ2 than for GABAA-ρ1 homomeric channels. This intra-subunit selectivity arises from the unconserved residues at the 2' sites, which are the es...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2016.07.003
更新日期：2016-10-01 00:00:00
abstract：:Proline is an important osmotic adjusting material greatly accumulated under drought stress and can help plant to adapt to osmotic stress. MicroRNAs (miRNAs) are small, endogenous RNAs that play important regulatory roles in plant development and stress response by negatively affecting gene expression at post-transcri...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2013.04.006
更新日期：2013-10-01 00:00:00
abstract：:Due to their lethal consequences and a relatively high probability of introduction of repair errors and mutations, single and double strand breaks are among the most important and dangerous DNA lesions. However, the mechanisms of their recognition and repair processes are only poorly known at present. This work define...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2005.12.001
更新日期：2006-04-01 00:00:00
abstract：:Inhibition of poly(ADP-ribose) polymerase-1 (PARP-1) has turned out an innovative approach for cancer therapy due to its involvement in DNA repair pathways. Although several potent PARP-1 inhibitors have been identified, they exhibit high toxicity, resistivity and diverse pharmacological profile in clinical trials, wh...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2019.04.018
更新日期：2019-06-01 00:00:00
abstract：:Monoamine oxidase (MAO) enzymes are one of the most promising targets for the treatment of neurological disorders. A series of phenylisoxazole carbohydrazides was designed, synthesized and screened for both MAO-A and MAO-B inhibition using Amplex Red assays. None of the compounds inhibited the MAO-A activity while mos...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2019.01.012
更新日期：2019-04-01 00:00:00
