Lecture#5 File
... A simple illustration of the way eight b strands are arranged in a jelly roll motif. (a) The eight b strands are drawn as arrows along two edges of a strip of paper. The strands are arranged such that strand 1 is opposite strand 8, etc. The b strands are separated by loop regions. (b) The strip of p ...
... A simple illustration of the way eight b strands are arranged in a jelly roll motif. (a) The eight b strands are drawn as arrows along two edges of a strip of paper. The strands are arranged such that strand 1 is opposite strand 8, etc. The b strands are separated by loop regions. (b) The strip of p ...
The Three-dimensional Structure of 4-Hydroxybenzoyl
... thioesterase subunit delineated by Tyr24-Phe39, Trp47-Val51, and Ala134-Ser141. The thioesterase subunit is somewhat elongated with overall dimensions of 35 Å 3 48 Å 3 34 Å. The average B-value for the solvent is 44.3 Å2. Of the 64 water molecules positioned into the electron density map, 13 have te ...
... thioesterase subunit delineated by Tyr24-Phe39, Trp47-Val51, and Ala134-Ser141. The thioesterase subunit is somewhat elongated with overall dimensions of 35 Å 3 48 Å 3 34 Å. The average B-value for the solvent is 44.3 Å2. Of the 64 water molecules positioned into the electron density map, 13 have te ...
Predicting DNA-binding sites of proteins from amino acid sequence
... DNA binding and transcription activation by SoxS [8]. More recently, methods for precisely identifying proteinDNA contacts by coupling photochemical crosslinking with mass spectrometry have also been developed [9]. With increasing availability of protein sequence data, there is an urgent need for co ...
... DNA binding and transcription activation by SoxS [8]. More recently, methods for precisely identifying proteinDNA contacts by coupling photochemical crosslinking with mass spectrometry have also been developed [9]. With increasing availability of protein sequence data, there is an urgent need for co ...
Reivew, Hemoglobin
... Blood transports two forms of CO2 to the lungs: carbamino-hemoglobin and H2CO3/HCO3- (carbonic acidconjugate base pair) 1. Carbamino-hemoglobin: exposure to low pCO2 results in the reversal of the carbamination reaction by mass action and O2 binding is again favored. CO2 is expelled by the lungs. ...
... Blood transports two forms of CO2 to the lungs: carbamino-hemoglobin and H2CO3/HCO3- (carbonic acidconjugate base pair) 1. Carbamino-hemoglobin: exposure to low pCO2 results in the reversal of the carbamination reaction by mass action and O2 binding is again favored. CO2 is expelled by the lungs. ...
Substrate Specificity and Mechanism from the Structure of
... and Ser107 and by oxygen atoms from the a and b-phosphate groups of ADP (Figure 4(a)). Galactose binding The galactose sits in a cavity between the two domains, oriented with the phosphoryl acceptor oxygen atom (O1) towards the phosphate-binding loop and the position of the terminal phosphate of the ...
... and Ser107 and by oxygen atoms from the a and b-phosphate groups of ADP (Figure 4(a)). Galactose binding The galactose sits in a cavity between the two domains, oriented with the phosphoryl acceptor oxygen atom (O1) towards the phosphate-binding loop and the position of the terminal phosphate of the ...
RELIC – A bioinformatics server for combinatorial
... the binding partner being sought may not be in the library, only a low number of conservatively close sequences. Affinity selection of a combinatorial peptide library screen may therefore generate a group of closely related sequences which are functional homologs, but may contain no obvious consensu ...
... the binding partner being sought may not be in the library, only a low number of conservatively close sequences. Affinity selection of a combinatorial peptide library screen may therefore generate a group of closely related sequences which are functional homologs, but may contain no obvious consensu ...
Globins in Nonvertebrate Species: Dispersal by Horizontal Gene
... atmospheric 0, became available the acquisition of oxygen-binding properties was initiated, culminating in the various highly specialized functions known at present. During this evolutionary process, we suggest that (1) high oxygen affinity may have been acquired repeatedly and (2) the formation of ...
... atmospheric 0, became available the acquisition of oxygen-binding properties was initiated, culminating in the various highly specialized functions known at present. During this evolutionary process, we suggest that (1) high oxygen affinity may have been acquired repeatedly and (2) the formation of ...
Introduction to Protein Structure
... • Aminoacids form polypeptide chains • Chains fold into three-dimensional structure • Specific backbone angles are permitted or not: Ramachandran plot • Secundary structure elements: -helix, b-sheet • Common structural motifs: Helix-turn-helix, Calcium binding motif, Hairpin, Greek key motif, b--b ...
... • Aminoacids form polypeptide chains • Chains fold into three-dimensional structure • Specific backbone angles are permitted or not: Ramachandran plot • Secundary structure elements: -helix, b-sheet • Common structural motifs: Helix-turn-helix, Calcium binding motif, Hairpin, Greek key motif, b--b ...
Seven Zinc Finger transcription factors are novel regulators of the
... (2004). In that study, those TFs were shown to bind to the cis-element A(G/C)T-X3-4-A(G/C)T. For ZOS12-7, only the two first Zn Finger domains were considered in this analysis. Amino-acid residues conserved in all the proteins are shown in dark grey, while residues conserved in all proteins except o ...
... (2004). In that study, those TFs were shown to bind to the cis-element A(G/C)T-X3-4-A(G/C)T. For ZOS12-7, only the two first Zn Finger domains were considered in this analysis. Amino-acid residues conserved in all the proteins are shown in dark grey, while residues conserved in all proteins except o ...
mechanism of the flagellar export system and its potential
... characteristic of export substrates. Approximately the first 190 residues encompass the complete highly conserved N-terminal part of the molecule, and the first report demonstrating that the N-terminal part of flagellin contains the signal used about the same fragment size. These 18 constructs were ...
... characteristic of export substrates. Approximately the first 190 residues encompass the complete highly conserved N-terminal part of the molecule, and the first report demonstrating that the N-terminal part of flagellin contains the signal used about the same fragment size. These 18 constructs were ...
EMBL-EBI Powerpoint Presentation
... Adjust scoring matrix to suit length of query sequence Adjust gap penalties to match scoring matrix ...
... Adjust scoring matrix to suit length of query sequence Adjust gap penalties to match scoring matrix ...
Population Biology of the First Replicators: On
... discussed in detail by Bernstein etal.{\ 983), Eigen (1971) and Kuhn (1972) and so only the general phenotypic categories will be given here. First, the free energies of base pair formation will affect the accuracy of base pairing as have been calculated by Eigen (1971). Second, in a molecule simila ...
... discussed in detail by Bernstein etal.{\ 983), Eigen (1971) and Kuhn (1972) and so only the general phenotypic categories will be given here. First, the free energies of base pair formation will affect the accuracy of base pairing as have been calculated by Eigen (1971). Second, in a molecule simila ...
Protein Function and Classification (Cont.) - EMBL-EBI
... InterPro provides functional analysis of proteins by classifying them into families and predicting the presence of important domains and sites. It does this by combining predictive models known as protein signatures from a number of different databases (referred to as member databases) into a single ...
... InterPro provides functional analysis of proteins by classifying them into families and predicting the presence of important domains and sites. It does this by combining predictive models known as protein signatures from a number of different databases (referred to as member databases) into a single ...
Evolution and Function of the Plant Cell Wall
... their role(s) in plant cell wall synthesis. The apparent disparate functions of the GT8 family (i.e. the GAUTs and GATLs as proven and putative plant cell wall polysaccharide biosynthetic a-galacturonosyltransferases, the eukaryotic GolSs as a-galactosyltransferases that synthesize the first step in ...
... their role(s) in plant cell wall synthesis. The apparent disparate functions of the GT8 family (i.e. the GAUTs and GATLs as proven and putative plant cell wall polysaccharide biosynthetic a-galacturonosyltransferases, the eukaryotic GolSs as a-galactosyltransferases that synthesize the first step in ...
1. Synthetic polyamides, such as nylon, contain the same link as
... In the boxes below, draw the displayed formulae of the two monomers that could be used to prepare polymer D. ...
... In the boxes below, draw the displayed formulae of the two monomers that could be used to prepare polymer D. ...
Functional and structural roles of parasite-specific inserts in the bifunctional S-adenosylmethionine decarboxylase/ornithine
... advantage of these inserts remain unclear. Some speculations for the functions of these inserts include possible interaction sites with as yet undefined regulatory proteins in the parasite, interaction sites with host proteins and a method to evade the host immune response (Li and Baker, 1998; Schof ...
... advantage of these inserts remain unclear. Some speculations for the functions of these inserts include possible interaction sites with as yet undefined regulatory proteins in the parasite, interaction sites with host proteins and a method to evade the host immune response (Li and Baker, 1998; Schof ...
Structure of ATP-Bound Human ATP:Cobalamin
... Information. The list of invariant residues as defined by this alignment is shown in Figure 2c and listed in Table 2. Of these structures, the most similar sequence (41% identical) to the human enzyme is for Bacillus subtilis YVQK, which was used for the molecular replacement solution. The rms devia ...
... Information. The list of invariant residues as defined by this alignment is shown in Figure 2c and listed in Table 2. Of these structures, the most similar sequence (41% identical) to the human enzyme is for Bacillus subtilis YVQK, which was used for the molecular replacement solution. The rms devia ...
BIOGRAPHICAL SKETCH Joanne I. Yeh joanneyeh Associate
... Yeh, J.I. and Mao, N. (2006). Prediction of Membrane Proteins in Mycobacterium tuberculosis using Support Vector Machine Algorithm. Journal of Computational Biology 13(1), 128-131. Yeh, J.I. (2006). Coordinated Biosensors: integrated systems for ultra sensitive detection. In Nanotechnologies for Lif ...
... Yeh, J.I. and Mao, N. (2006). Prediction of Membrane Proteins in Mycobacterium tuberculosis using Support Vector Machine Algorithm. Journal of Computational Biology 13(1), 128-131. Yeh, J.I. (2006). Coordinated Biosensors: integrated systems for ultra sensitive detection. In Nanotechnologies for Lif ...
NAD - SBI
... • The overall topologies of the NAD-binding domain show variations. Not all the 6 strands are essential to NAD- binding. • There is a minimum structure conserved in most proteins: first motif (βαβαβ) and β4. β1 and β4 are located in the center of the NAD-binding domain and are involved in cofactor b ...
... • The overall topologies of the NAD-binding domain show variations. Not all the 6 strands are essential to NAD- binding. • There is a minimum structure conserved in most proteins: first motif (βαβαβ) and β4. β1 and β4 are located in the center of the NAD-binding domain and are involved in cofactor b ...
Intrinsically Disordered Protein - Center for Data Analytics and
... energies in equilibrium with each other, and that, upon interacting with a given hydrophobic anion, the best-fitting configuration becomes selected from albumin’s structural ensemble. Karush called this phenomenon configurational adaptability. Studies on albumin binding to the present support Karush ...
... energies in equilibrium with each other, and that, upon interacting with a given hydrophobic anion, the best-fitting configuration becomes selected from albumin’s structural ensemble. Karush called this phenomenon configurational adaptability. Studies on albumin binding to the present support Karush ...
Formate Dehydrogenase, Molecular Modeling and Docking with
... accurate method to generate trusted three dimensional (3D) protein structure models and has been recently used in many practical applications. It is also known as comparative modeling of protein, which is designed to construct the amino acid in form of protein structure. It has been emerged over rec ...
... accurate method to generate trusted three dimensional (3D) protein structure models and has been recently used in many practical applications. It is also known as comparative modeling of protein, which is designed to construct the amino acid in form of protein structure. It has been emerged over rec ...
the elastin gene
... significance of "acidic" and "basic" keratins in this respect? 6. What are the main crosslinks in keratin? How can they be broken to partially solubilise the protein? How does increased crosslinking affect keratin's properties? 7. Keratin is the main component of hair. How are individual keratin mol ...
... significance of "acidic" and "basic" keratins in this respect? 6. What are the main crosslinks in keratin? How can they be broken to partially solubilise the protein? How does increased crosslinking affect keratin's properties? 7. Keratin is the main component of hair. How are individual keratin mol ...
Characterization of Phosphorylation Sites from the Activation Loop
... Reversible protein phosphorylation catalyzed by protein kinases is universally employed by eukaryotes to regulate enzyme activity, protein-protein interactions, subcelluar localization and protein turnover. The catalytic domains of most eukaryotic protein kinases are conserved in their primary seque ...
... Reversible protein phosphorylation catalyzed by protein kinases is universally employed by eukaryotes to regulate enzyme activity, protein-protein interactions, subcelluar localization and protein turnover. The catalytic domains of most eukaryotic protein kinases are conserved in their primary seque ...
The Enolase Superfamily: A General Strategy for Enzyme
... were determined from their structures; the boundaries of the putative β-barrel domains of the remaining superfamily members were assigned from comparisons to those structures. Where gaps had to be introduced to resolve conflicts among different PILEUP alignments, they were introduced systematically ...
... were determined from their structures; the boundaries of the putative β-barrel domains of the remaining superfamily members were assigned from comparisons to those structures. Where gaps had to be introduced to resolve conflicts among different PILEUP alignments, they were introduced systematically ...
Citrate synthase proteins in extremophilic organisms: Studies within
... features into account, but these features lead to a particular structure of the native conformation. Therefore, such models can tell the thermophilic and cryophilic proteins apart even if they belong to the same fold. We shall inquire here – to what extent. These models also identify properties that ...
... features into account, but these features lead to a particular structure of the native conformation. Therefore, such models can tell the thermophilic and cryophilic proteins apart even if they belong to the same fold. We shall inquire here – to what extent. These models also identify properties that ...
Structural alignment
Structural alignment attempts to establish homology between two or more polymer structures based on their shape and three-dimensional conformation. This process is usually applied to protein tertiary structures but can also be used for large RNA molecules. In contrast to simple structural superposition, where at least some equivalent residues of the two structures are known, structural alignment requires no a priori knowledge of equivalent positions. Structural alignment is a valuable tool for the comparison of proteins with low sequence similarity, where evolutionary relationships between proteins cannot be easily detected by standard sequence alignment techniques. Structural alignment can therefore be used to imply evolutionary relationships between proteins that share very little common sequence. However, caution should be used in using the results as evidence for shared evolutionary ancestry because of the possible confounding effects of convergent evolution by which multiple unrelated amino acid sequences converge on a common tertiary structure.Structural alignments can compare two sequences or multiple sequences. Because these alignments rely on information about all the query sequences' three-dimensional conformations, the method can only be used on sequences where these structures are known. These are usually found by X-ray crystallography or NMR spectroscopy. It is possible to perform a structural alignment on structures produced by structure prediction methods. Indeed, evaluating such predictions often requires a structural alignment between the model and the true known structure to assess the model's quality. Structural alignments are especially useful in analyzing data from structural genomics and proteomics efforts, and they can be used as comparison points to evaluate alignments produced by purely sequence-based bioinformatics methods.The outputs of a structural alignment are a superposition of the atomic coordinate sets and a minimal root mean square deviation (RMSD) between the structures. The RMSD of two aligned structures indicates their divergence from one another. Structural alignment can be complicated by the existence of multiple protein domains within one or more of the input structures, because changes in relative orientation of the domains between two structures to be aligned can artificially inflate the RMSD.