BIOINFORMATICS ORIGINAL PAPER Going from where to why—interpretable prediction of protein subcellular localization
... locations, YLoc employs a simple heuristic. After sorting the locations by probability, YLoc reports the locations with probability better than chance, i.e. P(Li |F) > 1/|L|, where L is the set of locations. To report only relevant locations with reasonable probability, YLoc stops reporting location ...
... locations, YLoc employs a simple heuristic. After sorting the locations by probability, YLoc reports the locations with probability better than chance, i.e. P(Li |F) > 1/|L|, where L is the set of locations. To report only relevant locations with reasonable probability, YLoc stops reporting location ...
Basic Structure of Proteins
... • Another way of saying this is that peptide bonds are formed by a condensation reaction between the amine group of one amino acid and the carboxyl group of another resulting in an amide group. The elements of water are removed as a by product of this reaction. Water (HOH) forms from the -OH of the ...
... • Another way of saying this is that peptide bonds are formed by a condensation reaction between the amine group of one amino acid and the carboxyl group of another resulting in an amide group. The elements of water are removed as a by product of this reaction. Water (HOH) forms from the -OH of the ...
as a PDF
... previously described above. Fd was further purified by gel filtration on a pre-packed Superdex 75 HR 10/30 column coupled to a HiLoad 26/10 ‘‘Fast flow column’’, both from Amersham Biosciences and previously equilibrated with 50 mM Phosphate buffer (pH 7.6) containing 150 mM NaCl. Fd fractions were ...
... previously described above. Fd was further purified by gel filtration on a pre-packed Superdex 75 HR 10/30 column coupled to a HiLoad 26/10 ‘‘Fast flow column’’, both from Amersham Biosciences and previously equilibrated with 50 mM Phosphate buffer (pH 7.6) containing 150 mM NaCl. Fd fractions were ...
Proteomic Mapping of Mitochondria in Living Cells
... detect this labeling (fig. S2), and HRP is inactive when expressed in the mammalian cytosol (5). We recently introduced engineered ascorbate peroxidase (APEX) as a genetic tag for electron microscopy (EM) (5). Unlike HRP, APEX is active within all cellular compartments. In addition to catalyzing the ...
... detect this labeling (fig. S2), and HRP is inactive when expressed in the mammalian cytosol (5). We recently introduced engineered ascorbate peroxidase (APEX) as a genetic tag for electron microscopy (EM) (5). Unlike HRP, APEX is active within all cellular compartments. In addition to catalyzing the ...
Teacher Notes - 3D Molecular Designs
... for valine, a hydrophobic residue. The normal amino acid at this position is a glutamic acid, a negatively charged amino acid located on the surface of the protein. In both normal (HbB) and sickle cell (HbS) hemoglobin, there is an uncharged patch of amino acids that is exposed to the surface in deo ...
... for valine, a hydrophobic residue. The normal amino acid at this position is a glutamic acid, a negatively charged amino acid located on the surface of the protein. In both normal (HbB) and sickle cell (HbS) hemoglobin, there is an uncharged patch of amino acids that is exposed to the surface in deo ...
outlines
... interactions, hydrogen bonding and covalent bonding (Disulfide bridges between cysteine residues) Quaternary Structure (same interactions involved as in tertiary structure) Interaction of multiple subunits (separate peptide chains) as in hemoglobin -Cooperativity Classes of Proteins 1) Globular Prot ...
... interactions, hydrogen bonding and covalent bonding (Disulfide bridges between cysteine residues) Quaternary Structure (same interactions involved as in tertiary structure) Interaction of multiple subunits (separate peptide chains) as in hemoglobin -Cooperativity Classes of Proteins 1) Globular Prot ...
SecStAnT: secondary structure analysis tool for data selection
... and space scales, needing large parallelism. This problem is not likely to be simply resolved by the increase of the processors power and of parallelism, becoming increasingly harder as the system complexity grows. Recent efforts have focused on the development of dedicated hardware. An example is t ...
... and space scales, needing large parallelism. This problem is not likely to be simply resolved by the increase of the processors power and of parallelism, becoming increasingly harder as the system complexity grows. Recent efforts have focused on the development of dedicated hardware. An example is t ...
Gilbert Ling Lecture 21
... In most proteins, each CO- group is joined (or hydrogen-bonded, or H-bonded) to the H+ atom of the NH+ group of the third amino acid down the chain. In this way, the protein chains assumes what is known as the alpha-helix structure. Both the polar NH+ and CO- groups also have affinity for water mol ...
... In most proteins, each CO- group is joined (or hydrogen-bonded, or H-bonded) to the H+ atom of the NH+ group of the third amino acid down the chain. In this way, the protein chains assumes what is known as the alpha-helix structure. Both the polar NH+ and CO- groups also have affinity for water mol ...
gln.val.tyr.ala lys.arg.glu.trp met.his.leu.asp cys.pro.gly.asn F-A-D
... (amino terminal or carboxyl terminal?) is then removed in _______________ (acid or alkaline?) conditions, and the resulting amino acid derivative, known as a ___________________, is analyzed by chromatography. ...
... (amino terminal or carboxyl terminal?) is then removed in _______________ (acid or alkaline?) conditions, and the resulting amino acid derivative, known as a ___________________, is analyzed by chromatography. ...
Acetylcholine Receptor-associated 43K Protein Contains Covalently
... with both proteins accumulating at newly forming nervemuscle synapses at the same rate (8). Skeletal muscle 43K protein also resembles the Torpedo protein in being associated with nAchR clusters on receptor-rich membrane fragments and because redistribution of these nAchRs occurs upon its removal wi ...
... with both proteins accumulating at newly forming nervemuscle synapses at the same rate (8). Skeletal muscle 43K protein also resembles the Torpedo protein in being associated with nAchR clusters on receptor-rich membrane fragments and because redistribution of these nAchRs occurs upon its removal wi ...
A presentation of Dr. Gilbert Ling`s Association
... In most proteins, each CO- group is joined (or hydrogen-bonded, or H-bonded) to the H+ atom of the NH+ group of the third amino acid down the chain. In this way, the protein chains assumes what is known as the alpha-helix structure. Both the polar NH+ and CO- groups also have affinity for water mol ...
... In most proteins, each CO- group is joined (or hydrogen-bonded, or H-bonded) to the H+ atom of the NH+ group of the third amino acid down the chain. In this way, the protein chains assumes what is known as the alpha-helix structure. Both the polar NH+ and CO- groups also have affinity for water mol ...
Systematically Assessing the Influence of 3
... notion is readily assumed by many investigators (Bao and Cui 2005; Karchin et al. 2005; Porto et al. 2005), only a few studies have directly examined the influence of 3D structural context on selective constraint (Goldman et al. 1998; Bustamante et al. 2000; Mintseris and Weng 2005). Given that thes ...
... notion is readily assumed by many investigators (Bao and Cui 2005; Karchin et al. 2005; Porto et al. 2005), only a few studies have directly examined the influence of 3D structural context on selective constraint (Goldman et al. 1998; Bustamante et al. 2000; Mintseris and Weng 2005). Given that thes ...
Usha`s project - The University of Texas at Dallas
... Individual structures provide explanations of specific biochemical functions and mechanisms, whereas comparisons of structures give insight to general principles governing these molecules, the interactions they make and their biological roles. The three-dimensional structures form the foundation of ...
... Individual structures provide explanations of specific biochemical functions and mechanisms, whereas comparisons of structures give insight to general principles governing these molecules, the interactions they make and their biological roles. The three-dimensional structures form the foundation of ...
CHAPTER 4: CELLULAR METABOLISM
... 1. CR is how animal cells use chemical energy stored in food to make cellular energy (ATP). 2. The chemical reactions in CR must occur in a particular sequence, with each reaction being catalyzed by a different (specific) enzyme. There are three major series of reactions: a. glycolysis b. citric aci ...
... 1. CR is how animal cells use chemical energy stored in food to make cellular energy (ATP). 2. The chemical reactions in CR must occur in a particular sequence, with each reaction being catalyzed by a different (specific) enzyme. There are three major series of reactions: a. glycolysis b. citric aci ...
Cell Death and Differentiation
... but can be transiently elevated with complex forms of amplitude, frequency and duration by specific external stimuli.1,2 Transiently elevated [Ca2 þ ]cyt in the cell leads to binding of Ca2 þ to intracellular regulatory proteins, initiating a wide variety of cellular processes.3 Calmodulin (CaM) is ...
... but can be transiently elevated with complex forms of amplitude, frequency and duration by specific external stimuli.1,2 Transiently elevated [Ca2 þ ]cyt in the cell leads to binding of Ca2 þ to intracellular regulatory proteins, initiating a wide variety of cellular processes.3 Calmodulin (CaM) is ...
Chapter 4 Outline
... 1. CR is how animal cells use chemical energy stored in food to make cellular energy (ATP). 2. The chemical reactions in CR must occur in a particular sequence, with each reaction being catalyzed by a different (specific) enzyme. There are three major series of reactions: a. glycolysis b. citric aci ...
... 1. CR is how animal cells use chemical energy stored in food to make cellular energy (ATP). 2. The chemical reactions in CR must occur in a particular sequence, with each reaction being catalyzed by a different (specific) enzyme. There are three major series of reactions: a. glycolysis b. citric aci ...
Career of Tom Muir
... ■ First example of protein splicing by small molecule ■ MBP and His are model protein ■ No structural or sequence restrictions to exteins ...
... ■ First example of protein splicing by small molecule ■ MBP and His are model protein ■ No structural or sequence restrictions to exteins ...
Biology PBL
... Therefore the chicken chop meal offers an insufficient amount of fat (easily corrected) and carbohydrates. This is essential as the projected intake of carbohydrates is 19% short. This shortage of carbohydrates is important even though the overall calories output of the meal is in the recommended ...
... Therefore the chicken chop meal offers an insufficient amount of fat (easily corrected) and carbohydrates. This is essential as the projected intake of carbohydrates is 19% short. This shortage of carbohydrates is important even though the overall calories output of the meal is in the recommended ...
to the complete text
... Sorting of membrane cargo into a COPII prebudding complex has been described for several proteins in yeast [19••] and mammals [20,21••] and is believed to be mediated via an interaction with the Sec23p complex [21••], although no direct binding of these components has been demonstrated. Thus, sortin ...
... Sorting of membrane cargo into a COPII prebudding complex has been described for several proteins in yeast [19••] and mammals [20,21••] and is believed to be mediated via an interaction with the Sec23p complex [21••], although no direct binding of these components has been demonstrated. Thus, sortin ...
F factor conjugation is a true type IV secretion system
... revealing the versatility of this macromolecular secretion apparatus [4,5]. Despite the clinical and evolutionary importance of T4SS, the general mechanism by which they secrete or take up macromolecules remains unknown. The F factor remains a paradigm for understanding the mechanism by which T4SS t ...
... revealing the versatility of this macromolecular secretion apparatus [4,5]. Despite the clinical and evolutionary importance of T4SS, the general mechanism by which they secrete or take up macromolecules remains unknown. The F factor remains a paradigm for understanding the mechanism by which T4SS t ...
Identification and Characterization of cvHsp
... cvHsp were requested and fully sequenced on both strands using an ABI automatic sequencer. 59-Rapid amplification of cDNA ends experiments were performed using the Marathon Ready human heart cDNA (CLONTECH). The following primers were used: 59-CCGCTCGGAAGGTGGAAGAGGTTCT-39 and 59-CGAGGGCTGGACAGGAGAGG ...
... cvHsp were requested and fully sequenced on both strands using an ABI automatic sequencer. 59-Rapid amplification of cDNA ends experiments were performed using the Marathon Ready human heart cDNA (CLONTECH). The following primers were used: 59-CCGCTCGGAAGGTGGAAGAGGTTCT-39 and 59-CGAGGGCTGGACAGGAGAGG ...
Full Text
... region. In many instances the specificity and accuracy of profile-based methods for functional identification is sufficient to correctly annotate the majority of genes in a biological system. This is particularly important because the rate of gene sequencing is increasing exponentially, and annotati ...
... region. In many instances the specificity and accuracy of profile-based methods for functional identification is sufficient to correctly annotate the majority of genes in a biological system. This is particularly important because the rate of gene sequencing is increasing exponentially, and annotati ...
Protein S deficiency
... n 1977, three years after the discovery of the γ-carboxy glutamic acid,1 Richard DiScipio reported on the identification of a new vitamin K-dependent protein which was named protein S.2 Three years later, Frederick Walker reported that bovine protein S functioned as a cofactor to activated protein C ...
... n 1977, three years after the discovery of the γ-carboxy glutamic acid,1 Richard DiScipio reported on the identification of a new vitamin K-dependent protein which was named protein S.2 Three years later, Frederick Walker reported that bovine protein S functioned as a cofactor to activated protein C ...
Measurement of the synthesis of liver
... above these values. John & Miller (1969) added cortisol, amino acids, and insulin to their rat liver perfusions, but still failed to achieve a ‘normal’ in vivo rate. With incubated liver slices or isolated liver cells, synthesis rates for albumin are even lower, about 20 and 10% of the in vivo rates ...
... above these values. John & Miller (1969) added cortisol, amino acids, and insulin to their rat liver perfusions, but still failed to achieve a ‘normal’ in vivo rate. With incubated liver slices or isolated liver cells, synthesis rates for albumin are even lower, about 20 and 10% of the in vivo rates ...
Protein–protein interaction
Protein–protein interactions (PPIs) refer to physical contacts established between two or more proteins as a result of biochemical events and/or electrostatic forces.In fact, proteins are vital macromolecules, at both cellular and systemic levels, but they rarely act alone. Diverse essential molecular processes within a cell are carried out by molecular machines that are built from a large number of protein components organized by their PPIs. Indeed, these interactions are at the core of the entire interactomics system of any living cell and so, unsurprisingly, aberrant PPIs are on the basis of multiple diseases, such as Creutzfeld-Jacob, Alzheimer's disease, and cancer.PPIs have been studied from different perspectives: biochemistry, quantum chemistry, molecular dynamics, signal transduction, among others. All this information enables the creation of large protein interaction networks – similar to metabolic or genetic/epigenetic networks – that empower the current knowledge on biochemical cascades and disease pathogenesis, as well as provide putative new therapeutic targets.