Slide 1
... Let have Protein composed of 100 amino acids. Assume that each amino acid has only 3 possible conformations. Total number of conformations = 3100 ~= 5x1047 . If 100 psec (10-10 sec) were required to convert from a conformation to another one, a random search of all conformations would require ...
... Let have Protein composed of 100 amino acids. Assume that each amino acid has only 3 possible conformations. Total number of conformations = 3100 ~= 5x1047 . If 100 psec (10-10 sec) were required to convert from a conformation to another one, a random search of all conformations would require ...
The MOLECULES of LIFE
... might this be so? Approximately how many folds are there (hundreds, thousands, millions, or billions)? Answer: There are likely to be only thousands of folds because natural selection will favor protein sequences that will fold into stable structures. In order to fold into a stable structure, it is ...
... might this be so? Approximately how many folds are there (hundreds, thousands, millions, or billions)? Answer: There are likely to be only thousands of folds because natural selection will favor protein sequences that will fold into stable structures. In order to fold into a stable structure, it is ...
Solution Structure of Choline Binding Protein A of Streptococcus
... the non-ideality term (BM) in the fitting algorithm. Using this approach, it was possible to estimate weak (Kd up to 100 mM) interaction coefficients despite the inevitable presence of a non-ideality term of similar numerical magnitude. ...
... the non-ideality term (BM) in the fitting algorithm. Using this approach, it was possible to estimate weak (Kd up to 100 mM) interaction coefficients despite the inevitable presence of a non-ideality term of similar numerical magnitude. ...
Tecfa
... the patterns of lineage branching produced by the true evolutionary history of the organisms being considered. ...
... the patterns of lineage branching produced by the true evolutionary history of the organisms being considered. ...
A comprehensive investigation of ribosomal genes in complete
... Laboratoire de Biologie et Génomique Structurales, Institut de Génétique et de Biologie Moléculaire et Cellulaire (CNRS, INSERM, ULP), BP163, 67404 Illkirch Cedex, France ...
... Laboratoire de Biologie et Génomique Structurales, Institut de Génétique et de Biologie Moléculaire et Cellulaire (CNRS, INSERM, ULP), BP163, 67404 Illkirch Cedex, France ...
Genomics of Theileria parva
... query is protein or DNA. “local” means it searches and aligns sequence segments, rather than align the entire sequence. It’s able to detect relationships among sequences which share only isolated regions of similarity. Currently, it is the most popular and most accepted sequence analysis tool. ...
... query is protein or DNA. “local” means it searches and aligns sequence segments, rather than align the entire sequence. It’s able to detect relationships among sequences which share only isolated regions of similarity. Currently, it is the most popular and most accepted sequence analysis tool. ...
Chapter 5 Proteins: Primary Structure
... Energy transduction (Rhodopsin = light-absorbing membrane protein of rod cells in retina) It has been a long-standing goal in biochemistry to relate the structure of a protein to its function. Although a complete structural analysis of a protein is very complex, it begins with the sequence of amino ...
... Energy transduction (Rhodopsin = light-absorbing membrane protein of rod cells in retina) It has been a long-standing goal in biochemistry to relate the structure of a protein to its function. Although a complete structural analysis of a protein is very complex, it begins with the sequence of amino ...
Vragen voor tentamen Protein Engineering (8S080)
... Nuclear receptors are transcription factors that consist of a DNA binding domain and a ligand binding domain. The ligand binding domain (LBD) contains a binding site for estrogen. The activity of nuclear receptors is known to be regulated by post translational modifications such as acetylation of ly ...
... Nuclear receptors are transcription factors that consist of a DNA binding domain and a ligand binding domain. The ligand binding domain (LBD) contains a binding site for estrogen. The activity of nuclear receptors is known to be regulated by post translational modifications such as acetylation of ly ...
doc - Gogarten Lab
... ATPase? (0.5pt) In the catalytic cycle, do all of the catalytic subunits work in the same phase of the catalytic cycle at the same time? (0.5pt) Are the different ATP binding subunit types that form the hexamer of the F1- ATP synthase homologous to each other? (1pt) What may the ancestral ATPase hav ...
... ATPase? (0.5pt) In the catalytic cycle, do all of the catalytic subunits work in the same phase of the catalytic cycle at the same time? (0.5pt) Are the different ATP binding subunit types that form the hexamer of the F1- ATP synthase homologous to each other? (1pt) What may the ancestral ATPase hav ...
Gene Section JARID1A (jumonji, AT rich interactive domain 1A (RBBP2-like))
... Bergh AR, van den Heuvel-Eibrink MM, Veronese A, Mecucci C, Negrini M, de Greef GE, Beverloo HB. Identification of NUP98 abnormalities in acute leukemia: JARID1A (12p13) as a new partner gene. Genes Chromosomes Cancer ...
... Bergh AR, van den Heuvel-Eibrink MM, Veronese A, Mecucci C, Negrini M, de Greef GE, Beverloo HB. Identification of NUP98 abnormalities in acute leukemia: JARID1A (12p13) as a new partner gene. Genes Chromosomes Cancer ...
Comparing Sequences of Fluorescent Proteins Using
... “mFruits,” referring to the names given to these fluorescent proteins, such as: • mBlueberry (Blue Fluorescent Protein, or BFP) • mLemon (Yellow Fluorescent Protein, or YFP) • mGrape1 (Cyan Fluorescent Protein, or CFP) • and many others, all with similarly ‘fruity’ names… ...
... “mFruits,” referring to the names given to these fluorescent proteins, such as: • mBlueberry (Blue Fluorescent Protein, or BFP) • mLemon (Yellow Fluorescent Protein, or YFP) • mGrape1 (Cyan Fluorescent Protein, or CFP) • and many others, all with similarly ‘fruity’ names… ...
407_lecture_9
... the disruption of a protein in the body. Typically, the harmful phenotype(s) of disease-causing lesions in a protein gene are caused by effects on (a) the level of expression of the protein, (b) the activity of the protein, or (c) the folding of the protein. [Note: Some effects may be different in d ...
... the disruption of a protein in the body. Typically, the harmful phenotype(s) of disease-causing lesions in a protein gene are caused by effects on (a) the level of expression of the protein, (b) the activity of the protein, or (c) the folding of the protein. [Note: Some effects may be different in d ...
NMR experiment-driven modeling of biological macromolecules
... Nuclear Magnetic Resonance Spectroscopy (NMR) is one of the more versatile experimental techniques that allow determining three-dimensional (3D) structures of biomacromolecules at atomic resolution, whether these are proteins, RNA, DNA, and their complexes. Knowledge of the 3D structure is vital for ...
... Nuclear Magnetic Resonance Spectroscopy (NMR) is one of the more versatile experimental techniques that allow determining three-dimensional (3D) structures of biomacromolecules at atomic resolution, whether these are proteins, RNA, DNA, and their complexes. Knowledge of the 3D structure is vital for ...
Example: search for regulatory binding sites
... • 18 DNA segments, each of length 105 bps. • There are at least one CRP binding sites, known experimentally, in each sequence. • The binding sites are about 16-19 base pairs long, with considerable variability in their contents. • Interested in seeing if we can find these sites computationally. ...
... • 18 DNA segments, each of length 105 bps. • There are at least one CRP binding sites, known experimentally, in each sequence. • The binding sites are about 16-19 base pairs long, with considerable variability in their contents. • Interested in seeing if we can find these sites computationally. ...
FoldIndex©: a simple tool to predict whether a given protein
... intrinsically unfolded. It is based solely on the average hydrophobicity of its amino acids and on the absolute value of its net charge. Using as axes these two parameters, proteins determined experimentally to be folded and intrinsically unfolded ones are separated by a straight line described by a ...
... intrinsically unfolded. It is based solely on the average hydrophobicity of its amino acids and on the absolute value of its net charge. Using as axes these two parameters, proteins determined experimentally to be folded and intrinsically unfolded ones are separated by a straight line described by a ...
Creating Multiple Sequence Alignments
... BIT150 – Lab3 Multiple sequence alignment and Phylogenetics Copy 08_Lab3 from Z: to C:, and open the file ‘FT proteins for MEGA.doc’. Objective: Perform multiple sequence alignments, calculate distance matrices, and construct phylogenetic trees, to understand and interpret relationships between spec ...
... BIT150 – Lab3 Multiple sequence alignment and Phylogenetics Copy 08_Lab3 from Z: to C:, and open the file ‘FT proteins for MEGA.doc’. Objective: Perform multiple sequence alignments, calculate distance matrices, and construct phylogenetic trees, to understand and interpret relationships between spec ...
Molecular weight determination
... through the column quickly. • Molecules smaller than gel pores move thorough the column slowly. • Differences in movement rate make available for separate collection. ...
... through the column quickly. • Molecules smaller than gel pores move thorough the column slowly. • Differences in movement rate make available for separate collection. ...
Polypeptide: alpha-helix and beta
... Concept: Peptide chains tend to form orderly hydrogen-bonded arrangements. Materials: alpha-helix and beta-sheet models made by Prof. Ewing Procedure: Models may be used to help explain secondary protein structure. Related Information: Fibrous proteins are stringy, tough, and usually insoluble in ...
... Concept: Peptide chains tend to form orderly hydrogen-bonded arrangements. Materials: alpha-helix and beta-sheet models made by Prof. Ewing Procedure: Models may be used to help explain secondary protein structure. Related Information: Fibrous proteins are stringy, tough, and usually insoluble in ...
Poster - Protein Information Resource
... The PIRSF protein classification system reflects evolutionary relationship of full-length proteins and domains. PIRSF families are extensively curated using a bioinformatics infrastructure implemented in a J2EE framework. Expert manual curation includes membership, annotation of specific biological ...
... The PIRSF protein classification system reflects evolutionary relationship of full-length proteins and domains. PIRSF families are extensively curated using a bioinformatics infrastructure implemented in a J2EE framework. Expert manual curation includes membership, annotation of specific biological ...
Tag-ChIP-IT® Enables ChIP Without Protein
... protein of interest? No problem! Transcription factor ChIP is often challenging due to a lack of available antibodies that are capable of recognizing target-bound protein of interest post-fixation, or the inability of available antibodies to distinguish between protein isoforms. These limitations ma ...
... protein of interest? No problem! Transcription factor ChIP is often challenging due to a lack of available antibodies that are capable of recognizing target-bound protein of interest post-fixation, or the inability of available antibodies to distinguish between protein isoforms. These limitations ma ...
MAFFT: Multiple Sequence Alignment using Fast Fourier Transform
... Approx. O(NlogN) homology detection Simpler-to-compute scoring function ...
... Approx. O(NlogN) homology detection Simpler-to-compute scoring function ...
Bolsum and PAM Matrix
... Alignment Scoring methods • In general sequences are given a score at each matching position and the one with the largest score is optimal and is chosen; however suboptimal may also need to be considered. • The most basic approach is obtained by measuring the percentage of similarity. • Given that ...
... Alignment Scoring methods • In general sequences are given a score at each matching position and the one with the largest score is optimal and is chosen; however suboptimal may also need to be considered. • The most basic approach is obtained by measuring the percentage of similarity. • Given that ...
A1987J365500002
... In a contest initiated by G.E. Schultz in 1974, individuals were asked to submit predictions for adenylate kinase, which would be published together with the X-ray determined results that he had just completed. We were satisfied when we learned that we had tied for first place for the a- and fl-pred ...
... In a contest initiated by G.E. Schultz in 1974, individuals were asked to submit predictions for adenylate kinase, which would be published together with the X-ray determined results that he had just completed. We were satisfied when we learned that we had tied for first place for the a- and fl-pred ...