TD11 Identification of in vivo substrates of GroEL Nature 1999, 402
... Figure 1c shows after anti-GroEL IP now there are only 250-300 spots- 10% compared to control (indicates proteins that interact with GroEL), notice the predominance of larger proteins Figures 1e and f show how pI (isoelectric point) and MW compare to total proteins -pI distribution is about the same ...
... Figure 1c shows after anti-GroEL IP now there are only 250-300 spots- 10% compared to control (indicates proteins that interact with GroEL), notice the predominance of larger proteins Figures 1e and f show how pI (isoelectric point) and MW compare to total proteins -pI distribution is about the same ...
Cloning and Mapping of Members of the MYM Family
... motif (designated the MYM motif for myeloproliferative and mental retardation motif), where X is any amino acid, although at certain positions there are distinct preferences for particular amino acids (Fig. 1). This motif closely resembles zinc-binding sequences, especially the RING, PHD/LAP, and LI ...
... motif (designated the MYM motif for myeloproliferative and mental retardation motif), where X is any amino acid, although at certain positions there are distinct preferences for particular amino acids (Fig. 1). This motif closely resembles zinc-binding sequences, especially the RING, PHD/LAP, and LI ...
Workshop: Protein Structure Introduction Learning Objectives
... We can distinguish four distinct organizational levels in the three-dimensional structures of proteins, which are referred to as the primary, secondary, tertiary, and quaternary structures. The questions in this section (which begin on the next page) will help you understand the differences between ...
... We can distinguish four distinct organizational levels in the three-dimensional structures of proteins, which are referred to as the primary, secondary, tertiary, and quaternary structures. The questions in this section (which begin on the next page) will help you understand the differences between ...
oL-Amylase of Clostridium thermosulfurogenes EMi:
... enzymatically functioning regions. The tentative Ca2+-binding site (consensus region I) of this Ca2+independent enzyme showed only limited homology. The deduced amino acid sequence of a second obviously truncated open reading frame showed significant homology to the malG gene product of E. coli. Com ...
... enzymatically functioning regions. The tentative Ca2+-binding site (consensus region I) of this Ca2+independent enzyme showed only limited homology. The deduced amino acid sequence of a second obviously truncated open reading frame showed significant homology to the malG gene product of E. coli. Com ...
Structural investigation of single biomolecules
... Structural investigation of single biomolecules NMR spectroscopy and X-ray crystallography are currently the most common techniques capable of determining the structures of biological macromolecules like proteins and nucleic acids at an atomic level of resolution. The atomic force microscope (AFM) i ...
... Structural investigation of single biomolecules NMR spectroscopy and X-ray crystallography are currently the most common techniques capable of determining the structures of biological macromolecules like proteins and nucleic acids at an atomic level of resolution. The atomic force microscope (AFM) i ...
Supporting text S1
... corresponding residues are Met24 and Met44, respectively, Figure S2A. These substitutions do not cause any significant conformational adjustments in surrounding residues as the two residues serve to fill the hydrophobic pocket around the indole. Apart from the buried L-tryptophan molecules bound bet ...
... corresponding residues are Met24 and Met44, respectively, Figure S2A. These substitutions do not cause any significant conformational adjustments in surrounding residues as the two residues serve to fill the hydrophobic pocket around the indole. Apart from the buried L-tryptophan molecules bound bet ...
Probe design for microarrays using OligoWiz
... target and non-target under hybridization is to design all the oligos on an array with similar affinity for their targets. This will allow the experimentalist to optimize the hybridization conditions for all oligos by choosing the right hybridization temperature and salt concentration. Commonly Melt ...
... target and non-target under hybridization is to design all the oligos on an array with similar affinity for their targets. This will allow the experimentalist to optimize the hybridization conditions for all oligos by choosing the right hybridization temperature and salt concentration. Commonly Melt ...
CHAPTER 3 STRUCTURAL ELEMENTS OF
... 1. helix-loop-helix: it is present in many Ca2+ binding proteins (calmodulin, parvalbumin, troponin C ) or DNA binding proteins 2. β hairpin : two antiparallel β-strands are kept together by a short loop of 2-5 residues. 3. greek key: four β strands (minimum), two short loops and one long loop are n ...
... 1. helix-loop-helix: it is present in many Ca2+ binding proteins (calmodulin, parvalbumin, troponin C ) or DNA binding proteins 2. β hairpin : two antiparallel β-strands are kept together by a short loop of 2-5 residues. 3. greek key: four β strands (minimum), two short loops and one long loop are n ...
Introduction
... • try to find some function which often works • do not stick to real physics Will my drug dissolve in water or oil (lipid) ? (important) • sounds like chemistry • usually approached by machine learning • number of atoms, types of atoms, … http://www.cgl.ucsf.edu/chimera/ImageGallery/, bluetongue vir ...
... • try to find some function which often works • do not stick to real physics Will my drug dissolve in water or oil (lipid) ? (important) • sounds like chemistry • usually approached by machine learning • number of atoms, types of atoms, … http://www.cgl.ucsf.edu/chimera/ImageGallery/, bluetongue vir ...
Chapter 5 - Biology 210A - Introduction to the Biological Sciences
... • Collagen is a fibrous protein consisting of three polypeptides coiled like a rope • Hemoglobin is a globular protein consisting of four polypeptides: two alpha and two beta chains Animation: Quaternary Protein Structure Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummi ...
... • Collagen is a fibrous protein consisting of three polypeptides coiled like a rope • Hemoglobin is a globular protein consisting of four polypeptides: two alpha and two beta chains Animation: Quaternary Protein Structure Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummi ...
Assignments 3 Problem 1 Below is the protein melting data for a pair
... wild-type protein. b) Determine your signal for the fully folded and the fully unfolded form (both mutant and WT). c) Plot the melting curves as the fraction of folded protein vs. temp. d) What are the melting temperatures for the two proteins? e) Pick the appropriate plots to determine ΔH and ΔS of ...
... wild-type protein. b) Determine your signal for the fully folded and the fully unfolded form (both mutant and WT). c) Plot the melting curves as the fraction of folded protein vs. temp. d) What are the melting temperatures for the two proteins? e) Pick the appropriate plots to determine ΔH and ΔS of ...
Supplementary Methods and References
... 1mM DTT). Subsequently, 10 μg of each substrate and 5 μCi of [γ-32P]ATP were added to the matrix-bound immunoprecipitates in a final volume of 50 μl to perform kinase assays for 30 minutes at 30°C. Equal aliquots (15 μl) from the kinase assays were loaded on 10% SDSPAGE and, following electrophoresi ...
... 1mM DTT). Subsequently, 10 μg of each substrate and 5 μCi of [γ-32P]ATP were added to the matrix-bound immunoprecipitates in a final volume of 50 μl to perform kinase assays for 30 minutes at 30°C. Equal aliquots (15 μl) from the kinase assays were loaded on 10% SDSPAGE and, following electrophoresi ...
Protein design TOPS cartoon of Top7 Approach to designing Top7
... [Kuhlman, B., Dantas, G., Ireton, G.C., Varani, G., Stoddard, B.L. and Baker, D. (2003) Design of a novel globular protein fold with atomiclevel accuracy. Science, 302, 1364-1368] What about folds that are not seen in SCOP or CATH? Some are: • physically impossible; • not yet sampled by evolution; • ...
... [Kuhlman, B., Dantas, G., Ireton, G.C., Varani, G., Stoddard, B.L. and Baker, D. (2003) Design of a novel globular protein fold with atomiclevel accuracy. Science, 302, 1364-1368] What about folds that are not seen in SCOP or CATH? Some are: • physically impossible; • not yet sampled by evolution; • ...
Imaging cellular acylation Rami N. Hannoush Genentech, Inc
... Genentech, Inc., South San Francisco, USA ...
... Genentech, Inc., South San Francisco, USA ...
The Copines, a Novel Class of C2 Domain-containing, Calcium
... In an attempt to identify proteins that might underlie membrane trafficking processes in ciliates, calcium-dependent, phospholipid-binding proteins were isolated from extracts of Paramecium tetraurelia. The major protein obtained, named copine, had a mass of 55 kDa, bound phosphatidylserine but not ...
... In an attempt to identify proteins that might underlie membrane trafficking processes in ciliates, calcium-dependent, phospholipid-binding proteins were isolated from extracts of Paramecium tetraurelia. The major protein obtained, named copine, had a mass of 55 kDa, bound phosphatidylserine but not ...
Chapter 15. Recognition of foreign molecules by the immune system
... All immunoglobulin domains have similar three-dimensional structures – Immunoglobulin fold ...
... All immunoglobulin domains have similar three-dimensional structures – Immunoglobulin fold ...
Leukaemia Section t(5;9)(q33;q22) Atlas of Genetics and Cytogenetics in Oncology and Haematology
... regulating T-helper-cell differentiation. ITK is not required for Th2 differentiation per se, but effector Th2 cytokine production during recall responses is severely impaired in the absence of ITK. ...
... regulating T-helper-cell differentiation. ITK is not required for Th2 differentiation per se, but effector Th2 cytokine production during recall responses is severely impaired in the absence of ITK. ...
ppt file
... acceptors be hydrogen bonded to something, be it solvent, protein backbone, or protein side chains. Alan Fersht has called this concept “hydrogen bond inventory”. This is important when trying to understand the effect of mutations that impact hydrogen bonding, because removal of one partner of a hyd ...
... acceptors be hydrogen bonded to something, be it solvent, protein backbone, or protein side chains. Alan Fersht has called this concept “hydrogen bond inventory”. This is important when trying to understand the effect of mutations that impact hydrogen bonding, because removal of one partner of a hyd ...
The Case Against a Darwinian Origin of Protein Folds
... chances of confusing any one amino acid for any other during protein synthesis, and (as already noted) we see that the products of this tightly controlled process are long proteins. Lastly, we see that these long proteins perform an impressive variety of functions with equally impressive specificity ...
... chances of confusing any one amino acid for any other during protein synthesis, and (as already noted) we see that the products of this tightly controlled process are long proteins. Lastly, we see that these long proteins perform an impressive variety of functions with equally impressive specificity ...
Drosophila melanogaster
... Localization of cMyBP-C in transgenic Drosophila melanogaster flight muscle Cardiac myosin-binding protein C (cMyBP-C) is a thick filament protein that is critical for proper cardiac muscle function. cMyBP-C increases the stiffness of the thick filaments and aids in their assembly during development ...
... Localization of cMyBP-C in transgenic Drosophila melanogaster flight muscle Cardiac myosin-binding protein C (cMyBP-C) is a thick filament protein that is critical for proper cardiac muscle function. cMyBP-C increases the stiffness of the thick filaments and aids in their assembly during development ...
Scientists clarify structural basis for biosynthesis of mysterious 21st
... encoding mechanism offers clues about the origins of the genetic alphabet. The findings deepen our understanding of protein synthesis and lay the groundwork for advances in protein design. ...
... encoding mechanism offers clues about the origins of the genetic alphabet. The findings deepen our understanding of protein synthesis and lay the groundwork for advances in protein design. ...
the RbDe web service - Oxford Academic
... diagrams and the creation of stored diagram libraries. The service has been tuned for the construction of snake-like diagrams (for transmembrane proteins) but can be used to render any protein for which defined secondary structure data or hypotheses are available. RbDe is freely available through th ...
... diagrams and the creation of stored diagram libraries. The service has been tuned for the construction of snake-like diagrams (for transmembrane proteins) but can be used to render any protein for which defined secondary structure data or hypotheses are available. RbDe is freely available through th ...
Interactions, Tertiary Structures
... Fibrous Proteins, α- and β-Keratins Fibrous proteins consist of long, thin, fiber-like shapes, involved in the structure of cells and tissues. Two types of fibrous protein include • α-keratins, which make up hair, wool, skin, and nails and contain three α-helices linked by disulfide — S — S — linka ...
... Fibrous Proteins, α- and β-Keratins Fibrous proteins consist of long, thin, fiber-like shapes, involved in the structure of cells and tissues. Two types of fibrous protein include • α-keratins, which make up hair, wool, skin, and nails and contain three α-helices linked by disulfide — S — S — linka ...
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.