Abstract：
:Previous joint experimental and theoretical work demonstrates that typically soluble peptides will be rendered insoluble in the presence of saturated sodium ions in aqueous solution due to disruption of cation-π interactions between Trp and Lys. The present work utilizes quantum chemical methods including density functional theory, symmetry-adapted perturbation theory, and even coupled cluster theory to determine the strengths of cation-π interactions for the aromatic R groups of Trp, Tyr, and Phe (approximated as skatole, methyl phenol, and toluene) with both alkali and alkaline-Earth atomic cations and electron-accepting R groups from Lys, Arg, and His approximated as methyl ammonium, guanidinium, and imidazolium cations. This work shows that sodium ion is still the most likely disrupter of peptide folding built upon cation-π interactions, since Trp, Tyr, and Phe all bind more strongly to sodium ion than to any of the polyatomic cations. Additionally, the atomic cation complex binding energies decrease with an increase in partial charge on the atomic cation in the complex. However, as the average partial charge increases in the interacting hydrogen atoms in the polyatomic cations, the binding energy increases. The disruption of such peptide-peptide cation-π interactions is certainly relevant for peptide design in β-sheets or β-hairpin structures, but it could also have implications for astrobiology.
journal_name
Comput Biol Chemjournal_title
Computational biology and chemistryauthors
Scherer SL,Stewart AL,Fortenberry RCdoi
10.1016/j.compbiolchem.2017.12.009subject
Has Abstractpub_date
2018-02-01 00:00:00pages
11-15eissn
1476-9271issn
1476-928Xpii
S1476-9271(17)30768-5journal_volume
72pub_type
杂志文章abstract：:Non-specific lipid transfer proteins (nsLTPs) are common allergens and they are particularly widespread within the plant kingdom. They have a highly conserved three-dimensional structure that generate a strong cross-reactivity among the members of this family. In the last years several web tools for the prediction of ...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2015.11.006
更新日期：2016-02-01 00:00:00
abstract：:Multiple ligand simultaneous docking, a computational approach is used to study the concurrent interactions between substrate and the macromolecule binding together in the presence of an inhibitor. The present investigation deals with the study of the effect of different inhibitors on binding of substrate to the prote...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2015.09.008
更新日期：2015-12-01 00:00:00
abstract：:Recent studies suggest that protein folding should be revisited as the emergent property of a complex system and that the nature allows only a very limited number of folds that seem to be strongly influenced by geometrical properties. In this work we explore the principles underlying this new view and show how helical...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2008.03.015
更新日期：2008-08-01 00:00:00
abstract：:In this study, the structural and antioxidant behavior of the three lichen-derived natural compounds such as atranorin (AT), evernic acid (EV) and diffractaic acid (DF) has been investigated in the gas and water phase using both B3LYP and M06-2X functional level of density functional theory (DFT) with two different ba...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2019.03.009
更新日期：2019-06-01 00:00:00
abstract：:In order to extract phylogenetic information from DNA sequences, the new normalized k-word average relative distance is proposed in this paper. The proposed measure was tested by discriminate analysis and phylogenetic analysis. The phylogenetic trees based on the Manhattan distance measure are reconstructed with k ran...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2014.10.007
更新日期：2014-12-01 00:00:00
abstract：:Protein structure prediction is considered as one of the most challenging and computationally intractable combinatorial problem. Thus, the efficient modeling of convoluted search space, the clever use of energy functions, and more importantly, the use of effective sampling algorithms become crucial to address this pro...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2016.01.008
更新日期：2016-04-01 00:00:00
abstract：:Methylenetetrahydrofolate reductase (MTHFR) is a key enzyme involved in folate metabolism and plays a central role in DNA methylation and biosynthesis. MTHFR mutations may alter the cellular folate supply which in turn affects nucleic acid synthesis, DNA methylation and chromosomal damage. The identification of number...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2018.02.022
更新日期：2018-06-01 00:00:00
abstract：:The shortest common supersequence (SCS) problem is a classical NP-hard problem, which is normally solved by heuristic algorithms. One important heuristic that is inspired by the process of chemical reactions in nature is the chemical reaction optimization (CRO) and its algorithm known as CRO_SCS. In this paper we prop...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2020.107327
更新日期：2020-10-01 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：:The concept of chaos being radically different from statistical randomness is introduced into chemometrics research. The chaotic system that is deterministic with underlying patterns and inherent ability in searching the space of interest has been employed to improve the performance of chemometric algorithms. In this ...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/s1476-9271(02)00083-x
更新日期：2003-07-01 00:00:00
abstract：:There is a large gap between the number of discovered proteins and the number of functionally annotated ones. Due to the high cost of determining protein function by wet-lab research, function prediction has become a major task for computational biology and bioinformatics. Some researches utilize the proteins interact...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2012.12.003
更新日期：2013-04-01 00:00:00
abstract：:Human Leukocyte Antigens (HLA) are highly polymorphic proteins that play a key role in the immune system. HLA molecule is present on the cell membrane of antigen-presenting cells of the immune system and presents short peptides, originating from the proteins of invading pathogens or self-proteins, to the T-cell Recept...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2016.02.019
更新日期：2016-06-01 00:00:00
abstract：:In this work we have studied the interaction of zervamicin IIB (ZrvIIB) with the model membranes of eukaryotes and prokaryotes using all-atom molecular dynamics. In all our simulations zervamicin molecule interacted only with lipid headgroups but did not penetrate the hydrophobic core of the bilayers. During the inter...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2010.12.005
更新日期：2011-02-01 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：:Zinc fingers are small protein domains in which zinc plays a structural role, contributing to the stability of the zinc-peptide complex. Zinc fingers are structurally diverse and are present in proteins that perform a broad range of functions in various cellular processes, such as replication and repair, transcription...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2018.03.005
更新日期：2018-06-01 00:00:00
abstract：BACKGROUND:Breast cancer remains the most lethal type of cancer for women. A significant proportion of breast cancer cases are characterised by overexpression of the human epidermal growth factor receptor 2 protein (HER2). These cancers are commonly treated by Herceptin (Trastuzumab), but resistance to drug treatment f...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2019.03.018
更新日期：2019-06-01 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：: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：:We report ligand field molecular mechanics, density functional theory and semi-empirical studies on the binding of Cu(II) to GlyHisLys (GHK) peptide. Following exhaustive conformational searching using molecular mechanics, we show that relative energy and geometry of conformations are in good agreement between GFN2-xT...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2020.107265
更新日期：2020-06-01 00:00:00
abstract：:Recent studies reported the involvement of JAK2/STAT3 pathway in various solid tumours including breast, ovarian, prostate and lung cancers. Clinical literature also reported the lowered burden in breast and ovarian cancers by targeting JAK2 pathway. In this study, a series of novel 2,4-disubstituted quinazolines (2a-...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2019.01.008
更新日期：2019-04-01 00:00:00
abstract：:Blood-feeding animals are known for their ability to produce bioactive compounds to impair haemostasis and suppress pain perception in the host. These compounds are extremely appealing for pharmacological development since they are generally very effective and specific for their molecular target. A preliminary RNA-Seq...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2018.05.014
更新日期：2018-08-01 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：:In this work, a framework is provided for identifying intracranial electroencephalography (iEEG) seizures based on discrete wavelet transform (DWT) analysis of iEEG signals using forward propagation and feedback neural networks. The performance of 5 different data sets combination classifications is studied using the ...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2020.107310
更新日期：2020-06-19 00:00:00
abstract：:Protein-ligand docking is an essential process that has accelerated drug discovery. How to accurately and effectively optimize the predominant position and orientation of ligands in the binding pocket of a target protein is a major challenge. This paper proposed a novel ligand binding pose search method called FWAVina...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2020.107363
更新日期：2020-10-01 00:00:00
abstract：:In many sequence data mining applications, the goal is to find frequent substrings. Some of these applications like extracting motifs in protein and DNA sequences are looking for frequently occurring approximate contiguous substrings called simple motifs. By approximate we mean that some mismatches are allowed during ...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2016.09.001
更新日期：2016-10-01 00:00:00
abstract：:Momordica charantia (bitter gourd, bitter melon) is a monoecious Cucurbitaceae with anti-oxidant, anti-microbial, anti-viral and anti-diabetic potential. Molecular studies on this economically valuable plant are very essential to understand its phylogeny and evolution. MicroRNAs (miRNAs) are conserved, small, non-codi...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2015.04.011
更新日期：2015-10-01 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：:Epigallocatechin gallate, a flavonoid from Camellia sinensis possess various pharmacological activities such as anticancer, antimicrobial and antioxidant etc. Adenosine deaminase, (ADA), is a key enzyme involved in the purine metabolism, the inhibitors of which is being considered as highly promising candidate for the...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2019.107111
更新日期：2019-12-01 00:00:00
abstract：:Protein methylation is a kind of post-translational modification (PTM), and typically takes place on lysine and arginine amino acid residues. Protein methylation is involved in many important biological processes, and most recent studies focused on lysine methylation of histones due to its critical roles in regulating...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2014.01.009
更新日期：2014-06-01 00:00:00
abstract：:MicroRNA (miRNA) plays an important role in life processes. In recent years, predicting the association between miRNAs and diseases has become a research hotspot. However, biological experiments take a lot of time and cost to identify pathogenic miRNAs. Computational biology-based methods can effectively improve accur...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2020.107369
更新日期：2020-12-01 00:00:00
