Lo, Frederick: Three Recently Developed Algorithms for Aligning Distantly Related Proteins
... of whether residue i is exposed to solvent or buried. The residue is considered buried if less than 20% of its surface area is exposed to solvent. The weighting parameter f for the log-odds probability should ideally have a value of 1 but is present to allow flexibility to improve alignment accuracy ...
... of whether residue i is exposed to solvent or buried. The residue is considered buried if less than 20% of its surface area is exposed to solvent. The weighting parameter f for the log-odds probability should ideally have a value of 1 but is present to allow flexibility to improve alignment accuracy ...
Characterization of Low Molecular Weight Glutenin Subunits by
... Wheat grain of the cultivar Yecora Rojo, lot CWC-141, was obtained from the California Wheat Commission. IE-purified glutenin was prepared from the endosperm fraction. Flour was milled in a Brabender Quadrumat Senior mill (C. W. Brabender, South Hackensack, NJ), and flour protein was 11.0% on a 13% ...
... Wheat grain of the cultivar Yecora Rojo, lot CWC-141, was obtained from the California Wheat Commission. IE-purified glutenin was prepared from the endosperm fraction. Flour was milled in a Brabender Quadrumat Senior mill (C. W. Brabender, South Hackensack, NJ), and flour protein was 11.0% on a 13% ...
HRP - WordPress.com
... protein purification steps in order to isolate the peroxidase enzyme from a horseradish root. Horseradish peroxidase (HRP) has important clinical and industrial applications including: waste water treatment, reagent for organic synthesis, immunoassays, and diagnostic kits. Prior work shows the prote ...
... protein purification steps in order to isolate the peroxidase enzyme from a horseradish root. Horseradish peroxidase (HRP) has important clinical and industrial applications including: waste water treatment, reagent for organic synthesis, immunoassays, and diagnostic kits. Prior work shows the prote ...
Local homology recognition and distance
... the difference seen in other common k-mers, but we do not consider these ideas further here. k-mer extension All identical subsequences of length >k between two sequences can be identi®ed using the following procedure: assign a unique integer 0 ¼ (Nk ± 1) to a k-mer by interpreting letters as digits ...
... the difference seen in other common k-mers, but we do not consider these ideas further here. k-mer extension All identical subsequences of length >k between two sequences can be identi®ed using the following procedure: assign a unique integer 0 ¼ (Nk ± 1) to a k-mer by interpreting letters as digits ...
Identification of Pexl3p, a Peroxisomal Membrane Receptor for the
... netic approaches (for review see Rachubinski and Subramani, 1995). By analogy to the signal recognition- and targeting systems of other cellular membranes, binding of PTS1 and PTS2 to PTS1R and PTS2R is presumably followed by targeting of PTS1R and PTS2R to the peroxisomal membrane. The cognate pero ...
... netic approaches (for review see Rachubinski and Subramani, 1995). By analogy to the signal recognition- and targeting systems of other cellular membranes, binding of PTS1 and PTS2 to PTS1R and PTS2R is presumably followed by targeting of PTS1R and PTS2R to the peroxisomal membrane. The cognate pero ...
Local homology recognition and distance measures in linear time
... groups in relation to alignments, and Wu and Brutlag (11) identi®ed conserved amino acid groups in multiple sequence alignment databases; however, these groups are not required to be disjoint. In this work, the central observation is that ...
... groups in relation to alignments, and Wu and Brutlag (11) identi®ed conserved amino acid groups in multiple sequence alignment databases; however, these groups are not required to be disjoint. In this work, the central observation is that ...
The Amino Acid Sequence Contains Leucine-Rich
... many dialysis steps using various buffers before each chromatography. W e used only one buffer system through all chromatographies, and all the procedures can be easily done within 4 days. As to the yield, we can easily purify 200 pg of GPV from 10l2platelets. This high yield also seems to have an a ...
... many dialysis steps using various buffers before each chromatography. W e used only one buffer system through all chromatographies, and all the procedures can be easily done within 4 days. As to the yield, we can easily purify 200 pg of GPV from 10l2platelets. This high yield also seems to have an a ...
Full-Text PDF
... examples to date are the generation of usable fuels by modification of both yeast and bacteria, including direct synthesis of alkanes from free fatty acids by introduction of the key enzymes fatty acid reductase and aldehyde decarbonylase [1]. Others include the production of alcohols with examples ...
... examples to date are the generation of usable fuels by modification of both yeast and bacteria, including direct synthesis of alkanes from free fatty acids by introduction of the key enzymes fatty acid reductase and aldehyde decarbonylase [1]. Others include the production of alcohols with examples ...
Lecture 7 Notes CH.7
... structure of the plasma membrane • 7.1 Cellular membranes are fluid mosaics of lipids and proteins Descriptive term regarding the • 7.2 Membrane structure results in selective permeability ...
... structure of the plasma membrane • 7.1 Cellular membranes are fluid mosaics of lipids and proteins Descriptive term regarding the • 7.2 Membrane structure results in selective permeability ...
Validation of an HPLC method for the determination of
... determination of amino acids.4–26 Mostly, the methods were based on the technology developed by Moore and Stein,4 which includes post-column derivatisation and detection in the visible region on an amino acid analyser. These analyses are reliable, but costly and time-consuming.9 The HPLC technique, ...
... determination of amino acids.4–26 Mostly, the methods were based on the technology developed by Moore and Stein,4 which includes post-column derivatisation and detection in the visible region on an amino acid analyser. These analyses are reliable, but costly and time-consuming.9 The HPLC technique, ...
Protein S-nitrosylation in photosynthetic organisms: A
... 2 accumulates due to external signals or stress conditions, nitrate reduction is inhibited and NR preferentially produces NO from nitrite [27]. Nevertheless, nitrite-dependent NO production is not strictly dependent on the activity of NR. In roots, a plasma membrane-bound nitrite/ NO reductase (Ni-N ...
... 2 accumulates due to external signals or stress conditions, nitrate reduction is inhibited and NR preferentially produces NO from nitrite [27]. Nevertheless, nitrite-dependent NO production is not strictly dependent on the activity of NR. In roots, a plasma membrane-bound nitrite/ NO reductase (Ni-N ...
Defining the anabolic window of opportunity
... studies directly assessing this question makes it all but impossible to make solid conclusions about the optimal timing. Moreover, it appears that the optimal timing of protein and/or amino acid ingestion may differ depending on the type of amino acid source, as well as concurrent ingestion of other ...
... studies directly assessing this question makes it all but impossible to make solid conclusions about the optimal timing. Moreover, it appears that the optimal timing of protein and/or amino acid ingestion may differ depending on the type of amino acid source, as well as concurrent ingestion of other ...
Mapping allosteric connections from the receptor G proteins
... of Ophthalmology and Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095 ...
... of Ophthalmology and Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095 ...
Interdependence, Reflexivity, Fidelity, Impedance Matching
... Gene expression consists of interpreting symbolic information stored in nucleic acid sequences. This irreversible computational process creates intrinsically novel meaning, and is thus fundamentally different from the physical chemistry underlying other natural processes, dis ...
... Gene expression consists of interpreting symbolic information stored in nucleic acid sequences. This irreversible computational process creates intrinsically novel meaning, and is thus fundamentally different from the physical chemistry underlying other natural processes, dis ...
In-lab PDB Worksheet ()
... WEEK6: Examination of LDH Structure using PYMOL INTRODUCTION: (Adapted from CH11 from the Lab Manual) Molecular modeling and database searching have become essential parts of modern molecular sciences. It is important for anyone working in biochemistry and molecular biology today to be familiar with ...
... WEEK6: Examination of LDH Structure using PYMOL INTRODUCTION: (Adapted from CH11 from the Lab Manual) Molecular modeling and database searching have become essential parts of modern molecular sciences. It is important for anyone working in biochemistry and molecular biology today to be familiar with ...
Full-Text PDF
... racemate with homochiral membranes of the two enantiomers that are comprised by the same racemate, and it has indeed been confirmed for vesicles of 2-methyldodecanoic acid [18]. Other experimental results [17] are unfortunately inconclusive, because highly derived bipolar lipids of hyperthermophilic ...
... racemate with homochiral membranes of the two enantiomers that are comprised by the same racemate, and it has indeed been confirmed for vesicles of 2-methyldodecanoic acid [18]. Other experimental results [17] are unfortunately inconclusive, because highly derived bipolar lipids of hyperthermophilic ...
Interdependence, Reflexivity, Fidelity, Impedance Matching
... Gene expression consists of interpreting symbolic information stored in nucleic acid sequences. This irreversible computational process creates intrinsically novel meaning, and is thus fundamentally different from the physical chemistry underlying other natural processes, dis ...
... Gene expression consists of interpreting symbolic information stored in nucleic acid sequences. This irreversible computational process creates intrinsically novel meaning, and is thus fundamentally different from the physical chemistry underlying other natural processes, dis ...
Comparative mycobacterial genomics as a tool for drug S.T. Cole
... confer the ability to invade and survive within HeLa cells to Escherichia coli [25]. Of these candidates, isocitrate lyase, whose crystal structure is available [26], appears to be the most promising drug target as it intervenes in the glyoxylate shunt, a biochemical pathway confined to certain micr ...
... confer the ability to invade and survive within HeLa cells to Escherichia coli [25]. Of these candidates, isocitrate lyase, whose crystal structure is available [26], appears to be the most promising drug target as it intervenes in the glyoxylate shunt, a biochemical pathway confined to certain micr ...
life - MDPI
... racemate with homochiral membranes of the two enantiomers that are comprised by the same racemate, and it has indeed been confirmed for vesicles of 2-methyldodecanoic acid [18]. Other experimental results [17] are unfortunately inconclusive, because highly derived bipolar lipids of hyperthermophilic ...
... racemate with homochiral membranes of the two enantiomers that are comprised by the same racemate, and it has indeed been confirmed for vesicles of 2-methyldodecanoic acid [18]. Other experimental results [17] are unfortunately inconclusive, because highly derived bipolar lipids of hyperthermophilic ...
Adv. Protein Chem. Struct. Biol.
... and with atomic detail the conformational evolution of a protein. Detection of structural changes as small as 0.2–0.3 Å with a time resolution of 100 ps is possible. The time-resolved Laue diffraction experiments are of a pump-probe type. The reaction is triggered within the protein crystal by phot ...
... and with atomic detail the conformational evolution of a protein. Detection of structural changes as small as 0.2–0.3 Å with a time resolution of 100 ps is possible. The time-resolved Laue diffraction experiments are of a pump-probe type. The reaction is triggered within the protein crystal by phot ...
Amyotrophic lateral sclerosis: Protein
... 2-DE and bioinformatics. When used within the framework of proper experimental designs, proteomic technologies can be very powerful at providing clues or answers to many crucial biological questions, including changes in protein expression, PTM, protein-protein interactions and protein activities. T ...
... 2-DE and bioinformatics. When used within the framework of proper experimental designs, proteomic technologies can be very powerful at providing clues or answers to many crucial biological questions, including changes in protein expression, PTM, protein-protein interactions and protein activities. T ...
medbiochem exam, 1999
... 29. Which of the following processes could NOT change the primary sequence of a protein encoded by an mRNA? A. Alternative splicing within the coding region. B. A frameshift mutation in the start codon. C. Alternative splicing in the 5' UTR. D. An insertion mutation in the coding region. Answer: C 3 ...
... 29. Which of the following processes could NOT change the primary sequence of a protein encoded by an mRNA? A. Alternative splicing within the coding region. B. A frameshift mutation in the start codon. C. Alternative splicing in the 5' UTR. D. An insertion mutation in the coding region. Answer: C 3 ...
... The hydrophobic effect is the ordering of water around non-polar groups. It decreases the entropy of the system, which is unfavorable. (+3 pts) In the case of globular proteins, the hydrophobic effect 'drives' the non-polar residues into the core of the protein, releasing water. This is one of the m ...
Protein
Proteins (/ˈproʊˌtiːnz/ or /ˈproʊti.ɨnz/) are large biomolecules, or macromolecules, consisting of one or more long chains of amino acid residues. Proteins perform a vast array of functions within living organisms, including catalyzing metabolic reactions, DNA replication, responding to stimuli, and transporting molecules from one location to another. Proteins differ from one another primarily in their sequence of amino acids, which is dictated by the nucleotide sequence of their genes, and which usually results in protein folding into a specific three-dimensional structure that determines its activity.A linear chain of amino acid residues is called a polypeptide. A protein contains at least one long polypeptide. Short polypeptides, containing less than about 20-30 residues, are rarely considered to be proteins and are commonly called peptides, or sometimes oligopeptides. The individual amino acid residues are bonded together by peptide bonds and adjacent amino acid residues. The sequence of amino acid residues in a protein is defined by the sequence of a gene, which is encoded in the genetic code. In general, the genetic code specifies 20 standard amino acids; however, in certain organisms the genetic code can include selenocysteine and—in certain archaea—pyrrolysine. Shortly after or even during synthesis, the residues in a protein are often chemically modified by posttranslational modification, which alters the physical and chemical properties, folding, stability, activity, and ultimately, the function of the proteins. Sometimes proteins have non-peptide groups attached, which can be called prosthetic groups or cofactors. Proteins can also work together to achieve a particular function, and they often associate to form stable protein complexes.Once formed, proteins only exist for a certain period of time and are then degraded and recycled by the cell's machinery through the process of protein turnover. A protein's lifespan is measured in terms of its half-life and covers a wide range. They can exist for minutes or years with an average lifespan of 1–2 days in mammalian cells. Abnormal and or misfolded proteins are degraded more rapidly either due to being targeted for destruction or due to being unstable.Like other biological macromolecules such as polysaccharides and nucleic acids, proteins are essential parts of organisms and participate in virtually every process within cells. Many proteins are enzymes that catalyze biochemical reactions and are vital to metabolism. Proteins also have structural or mechanical functions, such as actin and myosin in muscle and the proteins in the cytoskeleton, which form a system of scaffolding that maintains cell shape. Other proteins are important in cell signaling, immune responses, cell adhesion, and the cell cycle. Proteins are also necessary in animals' diets, since animals cannot synthesize all the amino acids they need and must obtain essential amino acids from food. Through the process of digestion, animals break down ingested protein into free amino acids that are then used in metabolism.Proteins may be purified from other cellular components using a variety of techniques such as ultracentrifugation, precipitation, electrophoresis, and chromatography; the advent of genetic engineering has made possible a number of methods to facilitate purification. Methods commonly used to study protein structure and function include immunohistochemistry, site-directed mutagenesis, X-ray crystallography, nuclear magnetic resonance and mass spectrometry.