Identification of fungal oxaloacetate hydrolyase within the
... used throughout this article. From this structural alignment we were able to segregate sequences into subclasses, one of which we named the OAH-like class of fungal proteins. The sequences of the members of this subclass from fungi with confirmed OAH activity12,16–19 were shown to be distinguished b ...
... used throughout this article. From this structural alignment we were able to segregate sequences into subclasses, one of which we named the OAH-like class of fungal proteins. The sequences of the members of this subclass from fungi with confirmed OAH activity12,16–19 were shown to be distinguished b ...
Thai Sports Supplements Co., Ltd.
... blood stream and muscle tissues extremely quickly. Despite this, whey protein concentrate will be enough to satisfy their daily protein requirements of most sports people. For those wanting to extract an extra advantage from their diet and training or drop that extra percentage of body-fat, then whe ...
... blood stream and muscle tissues extremely quickly. Despite this, whey protein concentrate will be enough to satisfy their daily protein requirements of most sports people. For those wanting to extract an extra advantage from their diet and training or drop that extra percentage of body-fat, then whe ...
PSI-BLAST is used for
... I. Friedberg and H. Margalit: Persistently Conserved Positions inStructurally-Similar, Sequence Dissimilar Proteins: Roles in PreservingProtein Fold and Function (2002) Protein Science 11(2):350-360 ...
... I. Friedberg and H. Margalit: Persistently Conserved Positions inStructurally-Similar, Sequence Dissimilar Proteins: Roles in PreservingProtein Fold and Function (2002) Protein Science 11(2):350-360 ...
Krogh, A., Brown, M., Mian, I.S., Sjolander, K., and Haussler, D. Hidden Markov Models in Computational Biology. J. Mol. Biol. , 235. pp. 1501-1531, 1994.
... SWISS-PROT 22 databaseforother sequences. thatare members of the givenprotein family, or contain the givendomain. The Hi" producesmultiplealignments of good quality that agree closely with the alignmentsproduced by programsthat incorporate threedimensional structural information. When employed in di ...
... SWISS-PROT 22 databaseforother sequences. thatare members of the givenprotein family, or contain the givendomain. The Hi" producesmultiplealignments of good quality that agree closely with the alignmentsproduced by programsthat incorporate threedimensional structural information. When employed in di ...
Short hydrogen bonds in proteins - Molecular Biophysics Unit
... Fig. 2A, which indicates that SHBs are possible between neutral species. A greater proportion of these BB-BB SHBs occur in the distance range of about 2.6– 2.7 Å. The distribution of the SC-SC SHBs is also high, and increases gradually from 2.3 Å to 2.65 Å. The distribution of the BB-SC and the S ...
... Fig. 2A, which indicates that SHBs are possible between neutral species. A greater proportion of these BB-BB SHBs occur in the distance range of about 2.6– 2.7 Å. The distribution of the SC-SC SHBs is also high, and increases gradually from 2.3 Å to 2.65 Å. The distribution of the BB-SC and the S ...
Disorder Prediction Methods, Their Applicability to Different Protein
... adopted. A protein with high levels of disorder (most of the length) would likely prove to be difficult to crystallise even with major sequence edits. In that case, solution based methods, such as CD, NMR or small angle X-ray scattering (SAXS) would be sensible techniques to study the full-length pr ...
... adopted. A protein with high levels of disorder (most of the length) would likely prove to be difficult to crystallise even with major sequence edits. In that case, solution based methods, such as CD, NMR or small angle X-ray scattering (SAXS) would be sensible techniques to study the full-length pr ...
Task - Illustrative Mathematics
... more open-ended modeling task. It poses the question by showing a photo of the box, but the students have to formulate a plan to answer it. It is worth spending some time discussing reasonable levels of numerical precision. While the percentage of quinoa which is protein is given to three digits of ...
... more open-ended modeling task. It poses the question by showing a photo of the box, but the students have to formulate a plan to answer it. It is worth spending some time discussing reasonable levels of numerical precision. While the percentage of quinoa which is protein is given to three digits of ...
7 Putting genetics into optogenetics: knocking out proteins with light
... The RING finger E3 ligase family has been used to destabilize specific proteins [8]. These proteasome-dependent degrons differ in their method for inducing interactions between the E3 ubiquitin ligase complex and the target protein. The protein can be destabilized by: amino acids at the N-terminus o ...
... The RING finger E3 ligase family has been used to destabilize specific proteins [8]. These proteasome-dependent degrons differ in their method for inducing interactions between the E3 ubiquitin ligase complex and the target protein. The protein can be destabilized by: amino acids at the N-terminus o ...
Elastin
... They can be stretched to several times their normal length, but recoil to their original shape when the stretching force is relaxed. ...
... They can be stretched to several times their normal length, but recoil to their original shape when the stretching force is relaxed. ...
Evolution of Function in Protein Superfamilies, from a Structural
... The recent growth in protein databases has revealed the functional diversity of many protein superfamilies. We have assessed the functional variation of homologous enzyme superfamilies containing two or more enzymes, as de®ned by the CATH protein structure classi®cation, by way of the Enzyme Commiss ...
... The recent growth in protein databases has revealed the functional diversity of many protein superfamilies. We have assessed the functional variation of homologous enzyme superfamilies containing two or more enzymes, as de®ned by the CATH protein structure classi®cation, by way of the Enzyme Commiss ...
AMIN domains have a predicted role in localization of diverse
... A similar situation can be expected in Pseudomonas aeruginosa, whose PilQ protein also contains AMIN domains: even though PilQ itself has not been localized, several other proteins involved in the biogenesis of type IV pilus have been shown to be polar in this species (Chiang et al., 2005); and (iv) ...
... A similar situation can be expected in Pseudomonas aeruginosa, whose PilQ protein also contains AMIN domains: even though PilQ itself has not been localized, several other proteins involved in the biogenesis of type IV pilus have been shown to be polar in this species (Chiang et al., 2005); and (iv) ...
Sequence±structure±function studies of tRNA
... SPOUT superfamily includes only a few characterized RNAspeci®c enzymes with 2¢-O-ribose or guanosine-N1 modi®cation speci®city that will not be discussed further in this article. The Rossmann-fold superfamily (hereafter referred to as `MTases') groups together enzymes acting on RNA, DNA, proteins, l ...
... SPOUT superfamily includes only a few characterized RNAspeci®c enzymes with 2¢-O-ribose or guanosine-N1 modi®cation speci®city that will not be discussed further in this article. The Rossmann-fold superfamily (hereafter referred to as `MTases') groups together enzymes acting on RNA, DNA, proteins, l ...
Structural And Functional Studies Of Nicotinamide Adenine
... Figure 3.11 SpNadD structural homolog active site comparisons .....................................75 Figure 3.12 SpNadD putative substrate binding pocket ....................................................76 Figure 4.1 Schematic of general spNadE reaction .......................................... ...
... Figure 3.11 SpNadD structural homolog active site comparisons .....................................75 Figure 3.12 SpNadD putative substrate binding pocket ....................................................76 Figure 4.1 Schematic of general spNadE reaction .......................................... ...
Cis-trans isomerization of omega dihedrals in Proteins
... Evolution.Due to their structural and functional importance,cis peptide bonds in proteins are expected to be conserved during evolution. The first conservation study was made on a set of nonhomologous and high resolution structures (sequence identity <25% and resolution ≤2.0Å) (Lorenzen et al. 2005) ...
... Evolution.Due to their structural and functional importance,cis peptide bonds in proteins are expected to be conserved during evolution. The first conservation study was made on a set of nonhomologous and high resolution structures (sequence identity <25% and resolution ≤2.0Å) (Lorenzen et al. 2005) ...
Ben-Hur1 pdf
... classification methods such as Support Vector Machines (SVMs). 31.3.1 The discrete motif composition kernel In this chapter we use discrete sequence motifs extracted using the eMOTIF method (Nevill-Manning et al., 1998, Huang and Brutlag, 2001), which is described here briefly. A motif is a simple r ...
... classification methods such as Support Vector Machines (SVMs). 31.3.1 The discrete motif composition kernel In this chapter we use discrete sequence motifs extracted using the eMOTIF method (Nevill-Manning et al., 1998, Huang and Brutlag, 2001), which is described here briefly. A motif is a simple r ...
Chemical Shift Restraints Tools and Methods
... Can be measured with great accuracy Contain a lot of structural informations (CSI, TALOS,...) In some cases they are the “only” available data ...
... Can be measured with great accuracy Contain a lot of structural informations (CSI, TALOS,...) In some cases they are the “only” available data ...
A bioinformatics study concerning the structural and functional
... The structural and functional characteristics of caveolin proteins have not yet been well defined, but some useful information can be obtained through sequence based predictions using structural bioinformatics tools. In the present study, a bioinformatics investigation was performed in which, to the ...
... The structural and functional characteristics of caveolin proteins have not yet been well defined, but some useful information can be obtained through sequence based predictions using structural bioinformatics tools. In the present study, a bioinformatics investigation was performed in which, to the ...
294_2005_38_MOESM43_ESM - Springer Static Content Server
... different organisms only align well within the kinase domain. In contrast, size is rather well conserved, with a coefficient of variation of 4.7 and 3.6%, respectively. The orthologue from A. nidulans appears to be missanotated, as the sequence contains both the MAPKKK domain and a fungal transporte ...
... different organisms only align well within the kinase domain. In contrast, size is rather well conserved, with a coefficient of variation of 4.7 and 3.6%, respectively. The orthologue from A. nidulans appears to be missanotated, as the sequence contains both the MAPKKK domain and a fungal transporte ...
X-ray structure of functional full-length dynein motor domain - SPring-8
... associated cellular components. Among them, the heavy chain (molecular mass ≥500 kDa), belonging to the AAA+ superfamily of mechanochemical enzymes, is solely responsible for dynein’s fundamental motor activities, such as ATP-hydrolysis, ATP-sensitive microtubule-binding and microtubule-based motile ...
... associated cellular components. Among them, the heavy chain (molecular mass ≥500 kDa), belonging to the AAA+ superfamily of mechanochemical enzymes, is solely responsible for dynein’s fundamental motor activities, such as ATP-hydrolysis, ATP-sensitive microtubule-binding and microtubule-based motile ...
Disallowed Ramachandran Conformations of Amino Acid Residues
... Bulky hydrophobic residues which are found predominantly in well packed interiors of proteins like Leu, Ile, Val and Phe do not generally adopt disallowed conformations. The bulky charged residues Glu, Lys and Arg also have a relatively low propensity for backbone distortions. An unusually high prop ...
... Bulky hydrophobic residues which are found predominantly in well packed interiors of proteins like Leu, Ile, Val and Phe do not generally adopt disallowed conformations. The bulky charged residues Glu, Lys and Arg also have a relatively low propensity for backbone distortions. An unusually high prop ...
here - Dr. Alan Dombkowski
... The output text box displays one line per potential disulfide. Each line shows a pair of residues that have the appropriate geometry to form a disulfide bond if the residues were mutated to cysteines. The analysis is based on the assumption that the mutations would not significantly perturb the prot ...
... The output text box displays one line per potential disulfide. Each line shows a pair of residues that have the appropriate geometry to form a disulfide bond if the residues were mutated to cysteines. The analysis is based on the assumption that the mutations would not significantly perturb the prot ...
Orthologs, paralogs and homology inference Where are we now?
... – Infer only from annotations with experimental evidence – Use explicit evolutionary model: inheritance (maybe with modification) from a common ancestor! • Homology inference is actually two inferences – 1. the common ancestor has the same annotation as its descendant that has been characterized – 2 ...
... – Infer only from annotations with experimental evidence – Use explicit evolutionary model: inheritance (maybe with modification) from a common ancestor! • Homology inference is actually two inferences – 1. the common ancestor has the same annotation as its descendant that has been characterized – 2 ...
A Positive Selection Function for miRNA
... The combinations are then translated For example, miRNA let-7 (6) in the 5′ to 3′ has one open reading frame and three open reading frames in its antiparallel complement in the 5′ to 3′ direction. The antiparallel complement would correspond to coding sequences which would appear in mRNA which are ...
... The combinations are then translated For example, miRNA let-7 (6) in the 5′ to 3′ has one open reading frame and three open reading frames in its antiparallel complement in the 5′ to 3′ direction. The antiparallel complement would correspond to coding sequences which would appear in mRNA which are ...
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.