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1.
Backgrounds
It is increasingly recognized that protein functions often require intricate conformational dynamics, which involves a network of key amino acid residues that couple spatially separated functional sites. Tremendous efforts have been made to identify these key residues by experimental and computational means. 相似文献2.
Background
Concepts of orthology and paralogy are become increasingly important as whole-genome comparison allows their identification in complete genomes. Functional specificity of proteins is assumed to be conserved among orthologs and is different among paralogs. We used this assumption to identify residues which determine specificity of protein-DNA and protein-ligand recognition. Finding such residues is crucial for understanding mechanisms of molecular recognition and for rational protein and drug design. 相似文献3.
Background
A great deal is known about the qualitative aspects of the sequence-structure relationship, for example that buried residues are usually more conserved between structurally similar homologues, but no attempts have been made to quantitate the relationship between evolutionary conservation at a sequence position and change to global tertiary structure. In this paper we demonstrate that the Spearman correlation between sequence and structural change is suitable for this purpose. 相似文献4.
Background
The mechanisms underlying protein function and associated conformational change are dominated by a series of local entropy fluctuations affecting the global structure yet are mediated by only a few key residues. Transitional Dynamic Analysis (TDA) is a new method to detect these changes in local protein flexibility between different conformations arising from, for example, ligand binding. Additionally, Positional Impact Vertex for Entropy Transfer (PIVET) uses TDA to identify important residue contact changes that have a large impact on global fluctuation. We demonstrate the utility of these methods for Cyclin-dependent kinase 2 (CDK2), a system with crystal structures of this protein in multiple functionally relevant conformations and experimental data revealing the importance of local fluctuation changes for protein function. 相似文献5.
Background
The secondary structure of an RNA must be known before the relationship between its structure and function can be determined. One way to predict the secondary structure of an RNA is to identify covarying residues that maintain the pairings (Watson-Crick, Wobble and non-canonical pairings). This "comparative approach" consists of identifying mutations from homologous sequence alignments. The sequences must covary enough for compensatory mutations to be revealed, but comparison is difficult if they are too different. Thus the choice of homologous sequences is critical. While many possible combinations of homologous sequences may be used for prediction, only a few will give good structure predictions. This can be due to poor quality alignment in stems or to the variability of certain sequences. This problem of sequence selection is currently unsolved. 相似文献6.
Rates of woody encroachment in African savannas reflect water constraints and fire disturbance
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Aim
The aims of this study were to (1) estimate current rates of woody encroachment across African savannas; (2) identify relationships between change in woody cover and potential drivers, including water constraints, fire frequency and livestock density. The found relationships led us to pursue a third goal: (3) use temporal dynamics in woody cover to estimate potential woody cover.Location
Sub‐Saharan African savannas.Methods
The study used very high spatial resolution satellite imagery at sites with overlapping older (2002–2006) and newer (2011–2016) imagery to estimate change in woody cover. We sampled 596 sites in 38 separate areas across African savannas. Areas with high anthropogenic impact were avoided in order to more clearly identify the influence of environmental factors. Relationships between woody cover change and potential drivers were identified using linear regression and simultaneous autoregression, where the latter accounts for spatial autocorrelation.Results
The mean annual change in woody cover across our study areas was 0.25% per year. Although we cannot explain the general trend of encroachment based on our data, we found that change rates were positively correlated with the difference between potential woody cover and actual woody cover (a proxy for water availability; p < .001), and negatively correlated with fire frequency (p < .01). Using the relationship between rates of encroachment and initial cover, we estimated potential woody cover at different rainfall levels.Main conclusions
The results indicate that woody encroachment is ongoing and widespread across African savannas. The fact that the difference between potential and actual cover was the most significant predictor highlights the central role of water availability and tree–tree competition in controlling change in woody populations, both in water‐limited and mesic savannas. Our approach to derive potential woody cover from the woody cover change trajectories demonstrates that temporal dynamics in woody populations can be used to infer resource limitations. 相似文献7.
Felix Eckstein Wolfgang Wirth Martin I Hudelmaier Susanne Maschek Wolfgang Hitzl Bradley T Wyman Michael Nevitt Marie-Pierre Hellio Le Graverand David Hunter 《Arthritis research & therapy》2009,11(3):R90-10
Introduction
The aim was to investigate the relationship of cartilage loss (change in medial femorotibial cartilage thickness measured with magnetic resonance imaging (MRI)) with compartment-specific baseline radiographic findings and MRI cartilage morphometry features, and to identify which baseline features can be used for stratification of fast progressors. 相似文献8.
Lucy Rutten Cecile Ribot Blanca Trejo-Aguilar Han AB Wösten Ronald P de Vries 《BMC microbiology》2009,9(1):166-7
Background
L-arabitol dehydrogenase (LAD) and xylitol dehydrogenase (XDH) are involved in the degradation of L-arabinose and D-xylose, which are among the most abundant monosaccharides on earth. Previous data demonstrated that LAD and XDH not only differ in the activity on their biological substrate, but also that only XDH has significant activity on D-sorbitol and may therefore be more closely related to D-sorbitol dehydrogenases (SDH). In this study we aimed to identify residues involved in the difference in substrate specificity. 相似文献9.
Background
The aim of this paper is to demonstrate the application of watermarks based on DNA sequences to identify the unauthorized use of genetically modified organisms (GMOs) protected by patents. Predicted mutations in the genome can be corrected by the DNA-Crypt program leaving the encrypted information intact. Existing DNA cryptographic and steganographic algorithms use synthetic DNA sequences to store binary information however, although these sequences can be used for authentication, they may change the target DNA sequence when introduced into living organisms. 相似文献10.
Background
Conservation and variation scores are used when evaluating sites in a multiple sequence alignment, in order to identify residues critical for structure or function. A variety of scores are available today but it is not clear how different scores relate to each other. 相似文献11.
Michelle I Portugal Adriane R Todeschini Cristiana S de Lima Carlos AM Silva Ronaldo Mohana-Borges Tom HM Ottenhoff Lucia Mendonça-Previato Jose O Previato Maria CV Pessolani 《BMC microbiology》2008,8(1):75
Background
The histone-like Hlp protein is emerging as a key component in mycobacterial pathogenesis, being involved in the initial events of host colonization by interacting with laminin and glycosaminoglycans (GAGs). In the present study, nuclear magnetic resonance (NMR) was used to map the binding site(s) of Hlp to heparan sulfate and identify the nature of the amino acid residues directly involved in this interaction. 相似文献12.
Background
In the research on protein functional sites, researchers often need to identify binding-site residues on a protein. A commonly used strategy is to find a complex structure from the Protein Data Bank (PDB) that consists of the protein of interest and its interacting partner(s) and calculate binding-site residues based on the complex structure. However, since a protein may participate in multiple interactions, the binding-site residues calculated based on one complex structure usually do not reveal all binding sites on a protein. Thus, this requires researchers to find all PDB complexes that contain the protein of interest and combine the binding-site information gleaned from them. This process is very time-consuming. Especially, combing binding-site information obtained from different PDB structures requires tedious work to align protein sequences. The process becomes overwhelmingly difficult when researchers have a large set of proteins to analyze, which is usually the case in practice. 相似文献13.
Background
Metagenomics, sequence analyses of genomic DNA isolated directly from the environments, can be used to identify organisms and model community dynamics of a particular ecosystem. Metagenomics also has the potential to identify significantly different metabolic potential in different environments. 相似文献14.
Andrew D Fernandes Benjamin P Kleinstiver David R Edgell Lindi M Wahl Gregory B Gloor 《Algorithms for molecular biology : AMB》2010,5(1):35
Background
Unigenic evolution is a large-scale mutagenesis experiment used to identify residues that are potentially important for protein function. Both currently-used methods for the analysis of unigenic evolution data analyze 'windows' of contiguous sites, a strategy that increases statistical power but incorrectly assumes that functionally-critical sites are contiguous. In addition, both methods require the questionable assumption of asymptotically-large sample size due to the presumption of approximate normality. 相似文献15.
Background
A multiple sequence alignment (MSA) generated for a protein can be used to characterise residues by means of a statistical analysis of single columns. In addition to the examination of individual positions, the investigation of co-variation of amino acid frequencies offers insights into function and evolution of the protein and residues. 相似文献16.
Drew H Bryant Mark Moll Brian Y Chen Viacheslav Y Fofanov Lydia E Kavraki 《BMC bioinformatics》2010,11(1):242
Background
Structural variations caused by a wide range of physico-chemical and biological sources directly influence the function of a protein. For enzymatic proteins, the structure and chemistry of the catalytic binding site residues can be loosely defined as a substructure of the protein. Comparative analysis of drug-receptor substructures across and within species has been used for lead evaluation. Substructure-level similarity between the binding sites of functionally similar proteins has also been used to identify instances of convergent evolution among proteins. In functionally homologous protein families, shared chemistry and geometry at catalytic sites provide a common, local point of comparison among proteins that may differ significantly at the sequence, fold, or domain topology levels. 相似文献17.
Hsiang Ho Tijana Milenković Vesna Memišević Jayavani Aruri Nataša Pržulj Anand K Ganesan 《BMC systems biology》2010,4(1):84
Background
RNA-mediated interference (RNAi)-based functional genomics is a systems-level approach to identify novel genes that control biological phenotypes. Existing computational approaches can identify individual genes from RNAi datasets that regulate a given biological process. However, currently available methods cannot identify which RNAi screen "hits" are novel components of well-characterized biological pathways known to regulate the interrogated phenotype. In this study, we describe a method to identify genes from RNAi datasets that are novel components of known biological pathways. We experimentally validate our approach in the context of a recently completed RNAi screen to identify novel regulators of melanogenesis. 相似文献18.
Background
Most methods for predicting functional sites in protein 3D structures, rely on information on related proteins and cannot be applied to proteins with no known relatives. Another limitation of these methods is the lack of a well annotated set of functional sites to use as benchmark for validating their predictions. Experimental findings and theoretical considerations suggest that residues involved in function often contribute unfavorably to the native state stability. We examine the possibility of systematically exploiting this intrinsic property to identify functional sites using an original procedure that detects destabilizing regions in protein structures. In addition, to relate destabilizing regions to known functional sites, a novel benchmark consisting of a diverse set of hand-curated protein functional sites is derived. 相似文献19.
Christian S Parry 《BMC structural biology》2008,8(1):44
Background
Eluted natural peptides from major histocompatibility molecules show patterns of conserved residues. Crystallographic structures show that the bound peptide in class II major histocompatibility complex adopts a near uniform polyproline II-like conformation. This way allele-specific favoured residues are able to anchor into pockets in the binding groove leaving other peptide side chains exposed for recognition by T cells. The anchor residues form a motif. This sequence pattern can be used to screen large sequences for potential epitopes. Quantitative matrices extend the motif idea to include the contribution of non-anchor peptide residues. This report examines two new matrices that extend the binding register to incorporate the polymorphic p10 pocket of human leukocyte antigen DR1. Their performance is quantified against experimental binding measurements and against the canonical nine-residue register matrix. 相似文献20.
Rebecca F Halperin Phillip Stafford Jack S Emery Krupa Arun Navalkar Stephen Albert Johnston 《BMC bioinformatics》2012,13(1):1