Structure, prediction, evolution and genome wide studies of membrane proteins
... Figure 1. A. An example of a single lipid molecule. The two long, fatty acid hydrocarbon chains are green lines and the atoms belonging to the polar headgroup are depicted as balls. Carbon is colored green, oxygen red, phosphorus orange and oxygen blue. B. A snapshot of a computer simulation of a p ...
... Figure 1. A. An example of a single lipid molecule. The two long, fatty acid hydrocarbon chains are green lines and the atoms belonging to the polar headgroup are depicted as balls. Carbon is colored green, oxygen red, phosphorus orange and oxygen blue. B. A snapshot of a computer simulation of a p ...
Intersubunit contacts are often facilitated by specificity
... The LacI family of bacterial transcription factors ...
... The LacI family of bacterial transcription factors ...
Multivalent cross-linking of actin filaments and microtubules through
... synaptic impairment in Alzheimer’s disease. Here we provide insight into the nature of interaction between actin filaments and microtubule-associated proteins and the actin/microtubule crosstalk. We show that Tau uses several short helical segments to bind in a dynamic, multivalent process to the hy ...
... synaptic impairment in Alzheimer’s disease. Here we provide insight into the nature of interaction between actin filaments and microtubule-associated proteins and the actin/microtubule crosstalk. We show that Tau uses several short helical segments to bind in a dynamic, multivalent process to the hy ...
Increased MS Protein Identifi cation Rates Using 75 cm Long nano
... mammalian cell lysate. More importantly, longer columns showed better reproducibility as seen by increased correlation among technical replicates, higher numbers of quantifiable peptides, and a smaller coefficient of variance (CV), resulting in improved protein quantification for complex lysates by ...
... mammalian cell lysate. More importantly, longer columns showed better reproducibility as seen by increased correlation among technical replicates, higher numbers of quantifiable peptides, and a smaller coefficient of variance (CV), resulting in improved protein quantification for complex lysates by ...
Sequence Searching and Alignments
... Primary or archived databases contain information and annotation of DNA and protein sequences, DNA and protein structures and DNA and protein expression profiles straight from experimental results. Secondary or derived databases are so called because they contain the results of analysis on the prima ...
... Primary or archived databases contain information and annotation of DNA and protein sequences, DNA and protein structures and DNA and protein expression profiles straight from experimental results. Secondary or derived databases are so called because they contain the results of analysis on the prima ...
Advances in Natural and Applied Sciences Aedes aegypti Aulanni’am
... people in endemic area i.e. protein with MW of 31 kDa and 56 kDa. Sera sample from individuals living in non endemic area (sub tropical country) and who have never traveled to tropical countries, did not show an immunogenic reaction with SGE of Ae. Aegypti. These individuals were very likely never e ...
... people in endemic area i.e. protein with MW of 31 kDa and 56 kDa. Sera sample from individuals living in non endemic area (sub tropical country) and who have never traveled to tropical countries, did not show an immunogenic reaction with SGE of Ae. Aegypti. These individuals were very likely never e ...
Package `signalHsmm`
... A single prediction of signalHsmm. A stochastic model of signal peptide produced by signalHsmm. Details Always a named list of five elements 1. sp_probability is a probability of signal peptide presence. 2. sp_start is a start of potential signal peptide (naively 1 aminoacid). 3. sp_end is a positio ...
... A single prediction of signalHsmm. A stochastic model of signal peptide produced by signalHsmm. Details Always a named list of five elements 1. sp_probability is a probability of signal peptide presence. 2. sp_start is a start of potential signal peptide (naively 1 aminoacid). 3. sp_end is a positio ...
SCJ4600048 - Sigma
... buffer. The procedure may be scaled up or down for any amount of protein as long as the ratios of the reagents are maintained. One µmole of CF647 SE (dark blue solid) is provided, which is sufficient for labeling 8–12 mg of IgG. ...
... buffer. The procedure may be scaled up or down for any amount of protein as long as the ratios of the reagents are maintained. One µmole of CF647 SE (dark blue solid) is provided, which is sufficient for labeling 8–12 mg of IgG. ...
The Structural Basis of Molecular Adaptation
... which was rooted with a large number of related serine proteases of diverse function (fig. 1). Unfortunately, the phylogeny gave no clue as to the specificity of the ancestral chymase. The sequence of the ancestral chymase protein was inferred by maximum parsimony. Assignments at 15 sites in the anc ...
... which was rooted with a large number of related serine proteases of diverse function (fig. 1). Unfortunately, the phylogeny gave no clue as to the specificity of the ancestral chymase. The sequence of the ancestral chymase protein was inferred by maximum parsimony. Assignments at 15 sites in the anc ...
The Proteomic Code: a molecular recognition code for proteins
... Background: The Proteomic Code is a set of rules by which information in genetic material is transferred into the physico-chemical properties of amino acids. It determines how individual amino acids interact with each other during folding and in specific protein-protein interactions. The Proteomic C ...
... Background: The Proteomic Code is a set of rules by which information in genetic material is transferred into the physico-chemical properties of amino acids. It determines how individual amino acids interact with each other during folding and in specific protein-protein interactions. The Proteomic C ...
Protein profiling of the dimorphic, pathogenic fungus,Penicillium
... Background: Penicillium marneffei is a pathogenic fungus that afflicts immunocompromised individuals having lived or traveled in Southeast Asia. This species is unique in that it is the only dimorphic member of the genus. Dimorphism results from a process, termed phase transition, which is regulated ...
... Background: Penicillium marneffei is a pathogenic fungus that afflicts immunocompromised individuals having lived or traveled in Southeast Asia. This species is unique in that it is the only dimorphic member of the genus. Dimorphism results from a process, termed phase transition, which is regulated ...
Efficiency assay of detergent removal columns on - G
... fractions using the 3100 OFFGEL fractionator (Agilent). After applying 20 kV, fractions were collected and 1/3 was dried down and run via SDS‐PAGE. The gel was stained with Sypro. In solution digestion: Samples were reduced and alkylated before trypsin digestion. DI‐QTOF: Samples were resuspended in ...
... fractions using the 3100 OFFGEL fractionator (Agilent). After applying 20 kV, fractions were collected and 1/3 was dried down and run via SDS‐PAGE. The gel was stained with Sypro. In solution digestion: Samples were reduced and alkylated before trypsin digestion. DI‐QTOF: Samples were resuspended in ...
Leveraging SADI Semantic Web Services to Exploit Fish Ecotoxicology Data
... knowledge domains provide the subject for the example queries, described in the results. An important requirement for the analysis of a fish toxicological dataset is the ability to compare experimental results with existing published data. This has the potential to provide valuable insights into tra ...
... knowledge domains provide the subject for the example queries, described in the results. An important requirement for the analysis of a fish toxicological dataset is the ability to compare experimental results with existing published data. This has the potential to provide valuable insights into tra ...
MEDICAL BIOCHEMISTRY Problem Unit One 1999/2000 pH and
... A. This study guide is provided in two forms: printed and electronic. I strongly encourage you to obtain the electronic form as a pdf file and install it on your computer so that it can be read using Adobe Acrobat Reader. See Appendix II for an introduction on how to view a pdf file. The pdf file ca ...
... A. This study guide is provided in two forms: printed and electronic. I strongly encourage you to obtain the electronic form as a pdf file and install it on your computer so that it can be read using Adobe Acrobat Reader. See Appendix II for an introduction on how to view a pdf file. The pdf file ca ...
Eukaryotically Encoded and Chloroplast
... protein, which was thermolysin-resistant as long as the chloroplasts were intact but was digested if thermolysin and Triton X-100 were added to the reaction mixture. Therefore, the Nterminal extension of the nucleomorph-encoded rubredoxin represents a transit peptide, and nmRub has a plastid destina ...
... protein, which was thermolysin-resistant as long as the chloroplasts were intact but was digested if thermolysin and Triton X-100 were added to the reaction mixture. Therefore, the Nterminal extension of the nucleomorph-encoded rubredoxin represents a transit peptide, and nmRub has a plastid destina ...
Supporting Information
... densities were well defined except in a few segments that we predict interact with membranes and may become disordered on detergent solubilization. Weak electron density was observed for residues 1–2 and 109–126, so these regions were excluded from the final model. The final model consisted of 96.3% ...
... densities were well defined except in a few segments that we predict interact with membranes and may become disordered on detergent solubilization. Weak electron density was observed for residues 1–2 and 109–126, so these regions were excluded from the final model. The final model consisted of 96.3% ...
The extraction of collagen protein from pigskin
... there are fewer disease sources. Thus, we study how to extract collagen protein from pigskin. Commonly used methods are: salting out method, alkaline method, acid method, and enzyme method. The salting out method Similar to the general protein, collagen proteins also have the properties of salt solu ...
... there are fewer disease sources. Thus, we study how to extract collagen protein from pigskin. Commonly used methods are: salting out method, alkaline method, acid method, and enzyme method. The salting out method Similar to the general protein, collagen proteins also have the properties of salt solu ...
Document
... • Used with cellular component terms • To describe proteins that are transiently or peripherally associated with an organelle or complex ...
... • Used with cellular component terms • To describe proteins that are transiently or peripherally associated with an organelle or complex ...
Amiito acid sequence of the testosterone
... single gene (2,10). Previous work has reported two different polyadenylatIon sites that are recognized to produce the 1450 and 1950 nt mRNAs in the kidney (9). In this paper we identify a third polyadenylation site, responsible for the generation of the 1350 nt species. The hormonal regulation and t ...
... single gene (2,10). Previous work has reported two different polyadenylatIon sites that are recognized to produce the 1450 and 1950 nt mRNAs in the kidney (9). In this paper we identify a third polyadenylation site, responsible for the generation of the 1350 nt species. The hormonal regulation and t ...
Intrinsically Disordered Protein - Center for Data Analytics and
... Partially folded intermediates: In contrast to the two-state view of protein folding and denaturation, partially-unfolded intermediates between the ordered state and the random coil have been observed as the major species in urea, guanidine, and pH titration studies for several (but not all) protein ...
... Partially folded intermediates: In contrast to the two-state view of protein folding and denaturation, partially-unfolded intermediates between the ordered state and the random coil have been observed as the major species in urea, guanidine, and pH titration studies for several (but not all) protein ...
STRUCTURAL INSIGHTS INTO NOVEL MICROBIAL METALLOENZYMES
... a metal ion influences both protein stability and function through structural, catalytic or regulatory roles. Discovery of a metal ion cofactor presents new insight into both the structural and functional aspects of a protein and can be essential for the elucidation of the functional and mechanistic ...
... a metal ion influences both protein stability and function through structural, catalytic or regulatory roles. Discovery of a metal ion cofactor presents new insight into both the structural and functional aspects of a protein and can be essential for the elucidation of the functional and mechanistic ...
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 ...
Homology modeling
Homology modeling, also known as comparative modeling of protein, refers to constructing an atomic-resolution model of the ""target"" protein from its amino acid sequence and an experimental three-dimensional structure of a related homologous protein (the ""template""). Homology modeling relies on the identification of one or more known protein structures likely to resemble the structure of the query sequence, and on the production of an alignment that maps residues in the query sequence to residues in the template sequence. It has been shown that protein structures are more conserved than protein sequences amongst homologues, but sequences falling below a 20% sequence identity can have very different structure.Evolutionarily related proteins have similar sequences and naturally occurring homologous proteins have similar protein structure.It has been shown that three-dimensional protein structure is evolutionarily more conserved than would be expected on the basis of sequence conservation alone.The sequence alignment and template structure are then used to produce a structural model of the target. Because protein structures are more conserved than DNA sequences, detectable levels of sequence similarity usually imply significant structural similarity.The quality of the homology model is dependent on the quality of the sequence alignment and template structure. The approach can be complicated by the presence of alignment gaps (commonly called indels) that indicate a structural region present in the target but not in the template, and by structure gaps in the template that arise from poor resolution in the experimental procedure (usually X-ray crystallography) used to solve the structure. Model quality declines with decreasing sequence identity; a typical model has ~1–2 Å root mean square deviation between the matched Cα atoms at 70% sequence identity but only 2–4 Å agreement at 25% sequence identity. However, the errors are significantly higher in the loop regions, where the amino acid sequences of the target and template proteins may be completely different.Regions of the model that were constructed without a template, usually by loop modeling, are generally much less accurate than the rest of the model. Errors in side chain packing and position also increase with decreasing identity, and variations in these packing configurations have been suggested as a major reason for poor model quality at low identity. Taken together, these various atomic-position errors are significant and impede the use of homology models for purposes that require atomic-resolution data, such as drug design and protein–protein interaction predictions; even the quaternary structure of a protein may be difficult to predict from homology models of its subunit(s). Nevertheless, homology models can be useful in reaching qualitative conclusions about the biochemistry of the query sequence, especially in formulating hypotheses about why certain residues are conserved, which may in turn lead to experiments to test those hypotheses. For example, the spatial arrangement of conserved residues may suggest whether a particular residue is conserved to stabilize the folding, to participate in binding some small molecule, or to foster association with another protein or nucleic acid. Homology modeling can produce high-quality structural models when the target and template are closely related, which has inspired the formation of a structural genomics consortium dedicated to the production of representative experimental structures for all classes of protein folds. The chief inaccuracies in homology modeling, which worsen with lower sequence identity, derive from errors in the initial sequence alignment and from improper template selection. Like other methods of structure prediction, current practice in homology modeling is assessed in a biennial large-scale experiment known as the Critical Assessment of Techniques for Protein Structure Prediction, or CASP.