Strong and weak hydrogen bonds in the protein
... and acceptors agree with Lipinski’s rule-of-five that predicts drug-like properties. Hydrogen bonds formed by water were also seen to be relevant in ligand binding and ligand C HOw interactions are abundant when compared to N HOw and O HOw. Among the limitations of our earlier study w ...
... and acceptors agree with Lipinski’s rule-of-five that predicts drug-like properties. Hydrogen bonds formed by water were also seen to be relevant in ligand binding and ligand C HOw interactions are abundant when compared to N HOw and O HOw. Among the limitations of our earlier study w ...
Functional and quantitative proteomics using SILAC
... Mass spectrometry is not inherently quantitative, as different molecules have different mass spectrometric responses. Stable-isotope analogues of the molecule to be quantified have therefore been used for many years for accurate quantitation in small-molecule mass spectrometry. To differentially qua ...
... Mass spectrometry is not inherently quantitative, as different molecules have different mass spectrometric responses. Stable-isotope analogues of the molecule to be quantified have therefore been used for many years for accurate quantitation in small-molecule mass spectrometry. To differentially qua ...
Machine learning methods for Protein Secondary Structure Prediction
... x-fold cross-validation (N-N/x ; N/x) Leave-one-out (N-1 ; 1), ...
... x-fold cross-validation (N-N/x ; N/x) Leave-one-out (N-1 ; 1), ...
Cloning, Purification, and Partial Characterization of the
... more slowly than predicted from their calculated molecular mass. The protein with intein migrates as a 123 kDa instead of 90 kDa molecule and the recombinant protein without intein migrates as 98 kDa instead of 71 kDa molecule. To confirm that the purified proteins are indeed the MCM proteins MALDI- ...
... more slowly than predicted from their calculated molecular mass. The protein with intein migrates as a 123 kDa instead of 90 kDa molecule and the recombinant protein without intein migrates as 98 kDa instead of 71 kDa molecule. To confirm that the purified proteins are indeed the MCM proteins MALDI- ...
An Expression and Bioinformatics Analysis of the Arabidopsis
... carboxypeptidases. Based on their sequences, these serine carboxypeptidase-like (SCPL) proteins can be divided into several major clades. The first group consists of 21 proteins which, despite the function implied by their annotation, includes two that have been shown to function as acyltransferases ...
... carboxypeptidases. Based on their sequences, these serine carboxypeptidase-like (SCPL) proteins can be divided into several major clades. The first group consists of 21 proteins which, despite the function implied by their annotation, includes two that have been shown to function as acyltransferases ...
Systems Biology of Biological Nitrogen Fixation
... reactive oxygen species (ROSs) such as chromosomally-localized superoxide dismutase SodB (RHE_CH01203), the disruption of the sodA gene previously was shown to affect symbiotic efficiency of in alfalfa [17]. In addition, ypch00606, a probable anti-oxidant protein from AhpCTSA family and ypch00400 a ...
... reactive oxygen species (ROSs) such as chromosomally-localized superoxide dismutase SodB (RHE_CH01203), the disruption of the sodA gene previously was shown to affect symbiotic efficiency of in alfalfa [17]. In addition, ypch00606, a probable anti-oxidant protein from AhpCTSA family and ypch00400 a ...
capitolo 1 - Structural Biology
... without disrupting the structural and functional properties of the protein. There are others that can be substituted, but only maintaining the chemical and physical characteristics of the side chain. Sometimes substitutions are compensatory in the sense that we must consider at least pairs of amino ...
... without disrupting the structural and functional properties of the protein. There are others that can be substituted, but only maintaining the chemical and physical characteristics of the side chain. Sometimes substitutions are compensatory in the sense that we must consider at least pairs of amino ...
`Hybrid Protein Model`for optimally defining 3D protein structure
... of these three databases shows that they classify similarly only two thirds of all proteins (Hadley and Jones, 1999). Describing and classifying protein structures are thus not easy tasks. The ‘hybrid protein model’ (HPM) attempts to tackle some of these issues. Because proteins have common local st ...
... of these three databases shows that they classify similarly only two thirds of all proteins (Hadley and Jones, 1999). Describing and classifying protein structures are thus not easy tasks. The ‘hybrid protein model’ (HPM) attempts to tackle some of these issues. Because proteins have common local st ...
A Simple Lattice Model That Captures Protein Folding, Aggregation
... The ability of many proteins to convert from their functional soluble state to amyloid fibrils can be attributed to intermolecular beta strand formation. Such amyloid formation is associated with neurodegenerative disorders like Alzheimer’s and Parkinson’s. Molecular modelling can play a key role in ...
... The ability of many proteins to convert from their functional soluble state to amyloid fibrils can be attributed to intermolecular beta strand formation. Such amyloid formation is associated with neurodegenerative disorders like Alzheimer’s and Parkinson’s. Molecular modelling can play a key role in ...
Bio/CS 251 Bioinformatics
... The Oxygen atom attracts electrons much more forcefully than does a Hydrogen atom. In this way, oxygen is a strongly electronegative atom. As a result the O-H bond is said to be polarized, such that one of the atoms has a partial negative charge, and the other a partial positive charge. Molecules, s ...
... The Oxygen atom attracts electrons much more forcefully than does a Hydrogen atom. In this way, oxygen is a strongly electronegative atom. As a result the O-H bond is said to be polarized, such that one of the atoms has a partial negative charge, and the other a partial positive charge. Molecules, s ...
Nutrients and Diet
... 13. Define of the terms: Anabolic and Catabolic. 14. Give an example of each 15. State carbohydrates role as cellulose in cell walls 16. State proteins role as fibrous protein e.g. keratin or as myosin 17. State the role of lipids as Phospholipids in cell membranes 18. State that carbohydrates & lip ...
... 13. Define of the terms: Anabolic and Catabolic. 14. Give an example of each 15. State carbohydrates role as cellulose in cell walls 16. State proteins role as fibrous protein e.g. keratin or as myosin 17. State the role of lipids as Phospholipids in cell membranes 18. State that carbohydrates & lip ...
Dissecting the protein–RNA interface
... complexes were selected based on the following criteria: (i) structural resolution better than 3.0 Å and (ii) polypeptides and polyribonucleotides longer than 20 amino acids and 5 nt, respectively. Ribosomal subunits were excluded from the data set because their component proteins include a large n ...
... complexes were selected based on the following criteria: (i) structural resolution better than 3.0 Å and (ii) polypeptides and polyribonucleotides longer than 20 amino acids and 5 nt, respectively. Ribosomal subunits were excluded from the data set because their component proteins include a large n ...
Dissecting protein function: an efficient protocol for
... analysis of genetic networks on a large scale, with the resulting information used to place genes in pathways, identify points of intersection between different pathways and assign gene function to novel ORFs (Tong et al. 2001; Dixon et al. 2009). However, an inherent caveat of these studies stems f ...
... analysis of genetic networks on a large scale, with the resulting information used to place genes in pathways, identify points of intersection between different pathways and assign gene function to novel ORFs (Tong et al. 2001; Dixon et al. 2009). However, an inherent caveat of these studies stems f ...
Bacterial Ribosomes and Protein Synthesis
... bacterial cell contains 10,000 or more ribosomes and makes perhaps 1000 different proteins, and it is important to know whether or not different proteins can be made on the same ribosome or whether a specific kind of ribosome is needed for each specific protein. If DNA in the nucleus transmits ‘info ...
... bacterial cell contains 10,000 or more ribosomes and makes perhaps 1000 different proteins, and it is important to know whether or not different proteins can be made on the same ribosome or whether a specific kind of ribosome is needed for each specific protein. If DNA in the nucleus transmits ‘info ...
template
... In figure 1, docking window of DockPro, where main actions take place, can be seen. In figure 1.a, DockPro’s regular docking view is shown. There are three view modes. In the default view, both proteins are fully visible, and they can be docked as anticipated. Each atom takes up space relative to th ...
... In figure 1, docking window of DockPro, where main actions take place, can be seen. In figure 1.a, DockPro’s regular docking view is shown. There are three view modes. In the default view, both proteins are fully visible, and they can be docked as anticipated. Each atom takes up space relative to th ...
Recognition of Nucleic Acid Bases and Base
... donates two hydrogen bonds to the O6 and N7 acceptor groups of guanine and a second in which the carboxamide group of Asn (or Gln) hydrogen bonds to the N7 acceptor and N6 donor groups of adenine. These interactions are indeed the most commonly observed in protein –DNA complexes,4,7 – 9 and the impo ...
... donates two hydrogen bonds to the O6 and N7 acceptor groups of guanine and a second in which the carboxamide group of Asn (or Gln) hydrogen bonds to the N7 acceptor and N6 donor groups of adenine. These interactions are indeed the most commonly observed in protein –DNA complexes,4,7 – 9 and the impo ...
Young Innovators 2009
... Purpose: The highly polymorphic organic transport protein, OCT1; SLC22A1 is involved in the translocation of the hydrophilic anti-diabetic drug metformin from the blood into hepatocytes. Since many drugs are inhibitors of the OCT1 [1], this may lead to drug-drug interactions at the OCT1. The risk of ...
... Purpose: The highly polymorphic organic transport protein, OCT1; SLC22A1 is involved in the translocation of the hydrophilic anti-diabetic drug metformin from the blood into hepatocytes. Since many drugs are inhibitors of the OCT1 [1], this may lead to drug-drug interactions at the OCT1. The risk of ...
Chapter 23: Meat Emulsions - FEA
... nonpolar regions within the same molecule (McClements 2005). The ability of fat emulsifier to form an emulsion is related to how easily it adsorbs to the water-in-oil interface. Emulsifiers reduce surface tension and work necessary to create new surfaces (Zhang and others 2009). They are not only n ...
... nonpolar regions within the same molecule (McClements 2005). The ability of fat emulsifier to form an emulsion is related to how easily it adsorbs to the water-in-oil interface. Emulsifiers reduce surface tension and work necessary to create new surfaces (Zhang and others 2009). They are not only n ...
Interactome
In molecular biology, an interactome is the whole set of molecular interactions in a particular cell. The term specifically refers to physical interactions among molecules (such as those among proteins, also known as protein-protein interactions) but can also describe sets of indirect interactions among genes (genetic interactions). Mathematically, interactomes are generally displayed as graphs.The word ""interactome"" was originally coined in 1999 by a group of French scientists headed by Bernard Jacq. Though interactomes may be described as biological networks, they should not be confused with other networks such as neural networks or food webs.