Another refinement in the C36m FF concerns improved description of salt bridge interactions involving guanidinium and carboxylate functional groups with a pair-specific non-bonded LJ parameter (NBFIX term in CHARMM) between the guanidinium nitrogen in arginine and the carboxylate oxygen in glutamate, aspartate as well as the C terminus. This salt bridge interaction was found to be too favorable in the CHARMM protein force fields as indicated by the overestimation of the equilibrium association constant of a guanidinium-acetate solution ,33 , 34 as well as the underestimation of its osmotic pressure (personal communication, Benoit Roux). The added NBFIX term increases the Rmin from the 3.55 Å based on the Lorentz-Berthelot rule to a larger value of 3.637 Å (Shen and Roux, personal communication), which we subsequently showed to improve the agreement with the experimental osmotic pressure of guanidinium acetate solutions (Supplementary Figure 19 ). We noted that the NBFIX approach employed here differs from Piana et al’s work27 where the CHARMM22 charges of the Arg, Asp and Glu side chains were reduced in magnitude, with both approaches leading to weaker and more realistic salt-bridge interactions. The NBFIX term makes sure only the specific interaction between Arg and Asp/Glu is modified, while the interaction of these residues with other amino acids, water, or ions are kept the same as in the C36 FF. Again, our aim is to improve the C36 FF with minimal changes in the model.
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Arginine
Arginine
Arginine is a semi-essential amino acid that plays a crucial role in various physiological processes.
It is involved in protein synthesis, nitric oxide production, and the urea cycle.
Arginine has been studied for its potential benefits in cardiovascular health, wound healing, and immune function.
Researchers can optimize their arginine-related studies by using the PubCompare.ai tool, which helps identify the most reliable and reproducible protocols from the literature, pre-prints, and patents.
This AI-driven platform provides data-driven insights to enhance the accuracy and efficiency of arginine research.
It is involved in protein synthesis, nitric oxide production, and the urea cycle.
Arginine has been studied for its potential benefits in cardiovascular health, wound healing, and immune function.
Researchers can optimize their arginine-related studies by using the PubCompare.ai tool, which helps identify the most reliable and reproducible protocols from the literature, pre-prints, and patents.
This AI-driven platform provides data-driven insights to enhance the accuracy and efficiency of arginine research.
Most cited protocols related to «Arginine»
Acetate
Amino Acids
Arginine
Aspartate
aspartylglutamate
Glutamate
Guanidine
Ions
Nitrogen
Osmotic Pressure
Oxygen
Proteins
Sodium Chloride
We defined the task of learning SP regions as a multilabel classification problem at each sequence position. Multilabel differs from multiclass in the sense that more than one label can be true at a given position. This approach was motivated by the fact that there is no strict definition of region borders that is commonly agreed upon, making it impossible to establish ground-truth region labels for models to train on. We thus used the multilabel framework as a method for training with weak supervision, allowing us to use overlapping region labels during the learning phase that could be generated from the sequence data using rules. For inference, we did not make use of the multilabel framework, as we only predicted the single most probable label at each position using Viterbi decoding, yielding a single unambiguous solution.
We defined a set of three rules based on known properties of the n-, h-, and c-regions. The initial n-region must have a minimum length of two residues and the terminal c-region a minimum length of three residues. The most hydrophobic position, which is identified by sliding a seven-amino-acid window across the SP and computing the hydrophobicity using the Kyte–Doolittle scale29 (link), belongs to the h-region. All positions between these six labeled positions are labeled as either both n and h or h and c, yielding multitag labels.
This procedure was adapted for different SP classes, with only Sec/SPI completely following it. For Tat SPs, the n–h border was identified using the twin-arginine motif. All positions before the motif were labeled n, followed by two dedicated labels for the motif, again followed by a single position labeled n. For SPII SPs, we did not label a c-region, as the C-terminal positions cannot be considered as such30 (link). The last three positions were labeled as the lipobox, all positions before that as h only. For SPIII SPs, no region labels were generated within the SP.
We defined a set of three rules based on known properties of the n-, h-, and c-regions. The initial n-region must have a minimum length of two residues and the terminal c-region a minimum length of three residues. The most hydrophobic position, which is identified by sliding a seven-amino-acid window across the SP and computing the hydrophobicity using the Kyte–Doolittle scale29 (link), belongs to the h-region. All positions between these six labeled positions are labeled as either both n and h or h and c, yielding multitag labels.
This procedure was adapted for different SP classes, with only Sec/SPI completely following it. For Tat SPs, the n–h border was identified using the twin-arginine motif. All positions before the motif were labeled n, followed by two dedicated labels for the motif, again followed by a single position labeled n. For SPII SPs, we did not label a c-region, as the C-terminal positions cannot be considered as such30 (link). The last three positions were labeled as the lipobox, all positions before that as h only. For SPIII SPs, no region labels were generated within the SP.
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Amino Acids
Arginine
Debility
Supervision
Twins
lDDT measures how well the environment in a reference structure is reproduced in a protein model. It is computed over all pairs of atoms in the reference structure at a distance closer than a predefined threshold Ro (called inclusion radius), and not belonging to the same residue. These atom pairs define a set of local distances L. A distance is considered preserved in the model M if it is, within a certain tolerance threshold, the same as the corresponding distance in . If one or both the atoms defining a distance in the set are not present in M, the distance is considered non-preserved. For a given threshold, the fraction of preserved distances is calculated. The final lDDT score is the average of four fractions computed using the thresholds 0.5 Å, 1 Å, 2 Å and 4 Å, the same ones used to compute the GDT-HA score (Battey et al., 2007 (link)). For partially symmetric residues, where the naming of chemically equivalent atoms can be ambiguous (glutamic acid, aspartic acid, valine, tyrosine, leucine, phenylalaine and arginine), two lDDTs, one for each of the two possible naming schemes, are computed using all non-ambiguous atoms in M in the reference. The naming convention giving the higher score in each case is used for the calculation of the final structure-wide lDDT score.
The lDDT score can be computed using all atoms in the prediction (the default choice), but also using only distances between Cα atoms, or between backbone atoms. Interactions between adjacent residues can be excluded by specifying a minimum sequence separation parameter. Unless explicitly specified, the calculation of the lDDT scores for all experiments described in this article has been performed using default parameters, i.e. Ro = 15 Å, using all atoms at zero sequence separation.
The lDDT score can be computed using all atoms in the prediction (the default choice), but also using only distances between Cα atoms, or between backbone atoms. Interactions between adjacent residues can be excluded by specifying a minimum sequence separation parameter. Unless explicitly specified, the calculation of the lDDT scores for all experiments described in this article has been performed using default parameters, i.e. Ro = 15 Å, using all atoms at zero sequence separation.
Arginine
Aspartic Acid
Conferences
Glutamic Acid
Immune Tolerance
Leucine
Radius
Staphylococcal Protein A
Tyrosine
Valine
Vertebral Column
HEK-293 cells were transfected with either empty pcDNA3 vector (Invitrogen, Carlsbad, CA, USA) or pcDNA3 vector containing full-length ABCG2 coding either an arginine, threonine or glycine for amino-acid 482. Expression of ABCG2 in the transfectants was enforced by selection in G418 (Invitrogen, Carlsbad, CA, USA). Stable transfectants were maintained in Eagle's minimum essential medium (ATCC, Manassas, VA, USA) supplemented with 10% FCS, penicillin, and streptomycin with G418 at a concentration of 2 mg ml−1. Clones were preliminarily screened for ABCG2 expression by examining the ability of the cells to efflux BODIPY-prazosin in a flow cytometry-based assay. The ABCG2 sequence was subsequently verified in the clones examined here.
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Amino Acids
antibiotic G 418
Arginine
Biological Assay
BODIPY
Clone Cells
Cloning Vectors
Flow Cytometry
Glycine
HEK293 Cells
Penicillins
Prazosin
Streptomycin
Threonine
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Amino Acids
Amino Acid Sequence
Arginine
Cytoplasmic Granules
DNA-Binding Proteins
Genes
Glycine
Phenylalanine
Polypeptides
Proteins
Proteome
RNA-Binding Proteins
Saccharomyces cerevisiae
Most recents protocols related to «Arginine»
Example 1
Ultrapure water was taken in a compounding vessel and arginine was added and stirred. Propylene glycol was added to the solution and stirred. pH of the solution was adjusted to 11±0.5 by the addition of sodium hydroxide solution. Then the bulk solution was cooled to 2° C. to 8° C. Levothyroxine sodium was added and stirred till a clear solution was obtained, while maintaining the temperature at 5±3° C. The solution was filtered, followed by filling into suitable containers.
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Arginine
Blood Vessel
Dietary Fiber
hydroxide ion
Levothyroxine Sodium
Propylene Glycol
Sodium Hydroxide
Thyroxine
Example 4
Ultrapure water was taken in a compounding vessel and L-Arginine was added and stirred. Propylene glycol was added to the solution and stirred. Methyl paraben was added. pH of the solution was adjusted to 11±0.5 by the addition of sodium hydroxide solution. The solution was cooled to 2° C. to 8° C. Levothyroxine sodium was added and stirred till a clear solution was obtained. The solution was filtered, followed by filling into suitable containers.
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Arginine
Blood Vessel
hydroxide ion
Levothyroxine
Levothyroxine Sodium
methylparaben
Parabens
Propylene Glycol
Sodium Hydroxide
Example 5
Ultrapure water was taken in a compounding vessel and L-Arginine was added and stirred. Propylene glycol was added to the solution and stirred. Propyl paraben was added. Sorbitol was added to the solution and stirred. pH of the solution was adjusted to 11±0.5 by the addition of sodium hydroxide solution. The solution was cooled to 2° C. to 8° C. Levothyroxine sodium was added and stirred till a clear solution was obtained. The solution was filtered, followed by filling into suitable containers.
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Arginine
Blood Vessel
hydroxide ion
Levothyroxine Sodium
Parabens
Propylene Glycol
propylparaben
Sodium Hydroxide
Sorbitol
Thyroxine
Example 2
Evaluation of 10 mM acetate, 75 mM L-arginine, 2.4% (w/v) sorbitol, 0.01% (w/v) polysorbate 20 excipients formulations and a 10 mM acetate, 5% (w/v) sorbitol, 0.01% (w/v) polysorbate 20 excipients formulation, each with high concentration (120 mg/mL) denosumab, at a temperature of 37° C. for up to 1 month revealed the effects of pH and amino acid aggregation inhibitor on the rate and extent of HMWS formation. The formulations tested are described in Table 2 below. All buffer and excipient values quoted are for the buffer and excipient concentrations that the antibody is diafiltered against.
To prepare test samples M-Q, a 3 mL aliquot of denosumab at 70 mg/mL in acetate, pH 5.2 was dialyzed against 500 mL of DF buffer described below, with a total of 3 buffer changes to achieve a 1 million fold dilution of the previous formulation to ensure complete buffer exchange. The material was then over-concentrated using centrifuge-concentrator, followed by a dilution to 120 mg/mL and the addition of polysorbate 20 to a final concentration of 0.01%.
As the solution pH decreased, there was an increase in formation of large aggregates. At pH below 4.8, and especially 4.5, large aggregates were the dominant HWMS, with a dramatic increase for the test formulation at pH 4.5. As shown in
However, as the pH was increased, there was generally a resulting increase in the dimer species. As shown in
The presence of arginine in formulation O at a concentration of 75 mM resulted in approximately 0.3% and 25% reductions in the amounts of the dimer species and its kinetic rate of formation, respectively, after 1 month at 37° C. when compared to formulation P having the same pH, but without arginine.
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Acetate
Amino Acids
Anti-Antibodies
Arginine
Arginine Hydrochloride
Aromatic Amino Acids
Buffers
Denosumab
Dosage Forms
Excipients
Immunoglobulins
indole
Kinetics
Polysorbate 20
Retention (Psychology)
Sorbitol
Technique, Dilution
TNFSF11 protein, human
Example 9
The compound of Formula 1 (50 mg) was dissolved in MEK (20 vol, 1 ml) at 50° C. To the sample was added 1 mol eq of counterion L-arginine and H2O (5% w/w, 100 μl) The samples were then cooled from 50° C. to 5° C. at a rate of 0.1° C./min. Suspensions were isolated using a filter canular and analysed by XRPD. The material is a crystalline sample (99.0% purity) and the 1H-NMR was consistent with the proposed structure. The TGA analysis showed a 4.68% w/w loss between 30° C. and 100° C., corresponding to 2.1 mol eq of water. The DSC contained endotherm at 75.8° C. (153 J/g), an endotherm at 165.2° C. (41 J/g) and the endothermic melt at 205.9° C. (27 J/g).
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1H NMR
Arginine
Cannula
Carboxylic Acids
diphenyl
piperidine
Top products related to «Arginine»
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L-arginine is an amino acid that plays a crucial role in various physiological processes. It serves as a substrate for the production of nitric oxide, which is essential for maintaining healthy blood flow and cardiovascular function. This lab equipment product can be utilized for research and scientific applications related to the study of L-arginine and its associated biological functions.
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Fetal Bovine Serum (FBS) is a cell culture supplement derived from the blood of bovine fetuses. FBS provides a source of proteins, growth factors, and other components that support the growth and maintenance of various cell types in in vitro cell culture applications.
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L-lysine is an essential amino acid that is commonly used in various lab equipment and applications. It serves as a building block for proteins and plays a crucial role in various biological processes. The core function of L-lysine is to provide the necessary amino acid for protein synthesis and maintenance.
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Penicillin/streptomycin is a commonly used antibiotic solution for cell culture applications. It contains a combination of penicillin and streptomycin, which are broad-spectrum antibiotics that inhibit the growth of both Gram-positive and Gram-negative bacteria.
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DMEM (Dulbecco's Modified Eagle's Medium) is a cell culture medium formulated to support the growth and maintenance of a variety of cell types, including mammalian cells. It provides essential nutrients, amino acids, vitamins, and other components necessary for cell proliferation and survival in an in vitro environment.
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Bovine serum albumin (BSA) is a common laboratory reagent derived from bovine blood plasma. It is a protein that serves as a stabilizer and blocking agent in various biochemical and immunological applications. BSA is widely used to maintain the activity and solubility of enzymes, proteins, and other biomolecules in experimental settings.
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Penicillin is a type of antibiotic used in laboratory settings. It is a broad-spectrum antimicrobial agent effective against a variety of bacteria. Penicillin functions by disrupting the bacterial cell wall, leading to cell death.
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Formic acid is a colorless, pungent-smelling liquid chemical compound. It is the simplest carboxylic acid, with the chemical formula HCOOH. Formic acid is widely used in various industrial and laboratory applications.
More about "Arginine"
Arginine, also known as L-arginine, is a semi-essential amino acid that plays a crucial role in various physiological processes.
It is involved in protein synthesis, nitric oxide production, and the urea cycle.
Arginine has been studied for its potential benefits in cardiovascular health, wound healing, and immune function.
Researchers can optimize their arginine-related studies by using the PubCompare.ai tool, which helps identify the most reliable and reproducible protocols from the literature, pre-prints, and patents.
This AI-driven platform provides data-driven insights to enhance the accuracy and efficiency of arginine research.
Arginine can be supplemented in various forms, including L-arginine and L-lysine, which are commonly used in cell culture media along with other components like fetal bovine serum (FBS), penicillin/streptomycin, and bovine serum albumin (BSA).
These supplements and media components are essential for maintaining cell growth and viability in arginine-related experiments.
By utilizing the PubCompare.ai tool, researchers can access a wealth of information on the most effective and reproducible arginine-related protocols, helping to improve the quality and reliability of their research.
This can lead to a better understanding of arginine's physiological functions and its potential therapeutic applications in areas like cardiovascular health, wound healing, and immune function.
It is involved in protein synthesis, nitric oxide production, and the urea cycle.
Arginine has been studied for its potential benefits in cardiovascular health, wound healing, and immune function.
Researchers can optimize their arginine-related studies by using the PubCompare.ai tool, which helps identify the most reliable and reproducible protocols from the literature, pre-prints, and patents.
This AI-driven platform provides data-driven insights to enhance the accuracy and efficiency of arginine research.
Arginine can be supplemented in various forms, including L-arginine and L-lysine, which are commonly used in cell culture media along with other components like fetal bovine serum (FBS), penicillin/streptomycin, and bovine serum albumin (BSA).
These supplements and media components are essential for maintaining cell growth and viability in arginine-related experiments.
By utilizing the PubCompare.ai tool, researchers can access a wealth of information on the most effective and reproducible arginine-related protocols, helping to improve the quality and reliability of their research.
This can lead to a better understanding of arginine's physiological functions and its potential therapeutic applications in areas like cardiovascular health, wound healing, and immune function.