The goal of protein structure prediction by threading is to find a best
... commonly used by macromolecular modeling software. Instead, most threading objective functions are determined empirically by statistical analysis of the 3D data deposited in the Protein Data Bank (PDB). Thus they are often referred to as empirical potentials or knowledge-based potentials. In the cas ...
... commonly used by macromolecular modeling software. Instead, most threading objective functions are determined empirically by statistical analysis of the 3D data deposited in the Protein Data Bank (PDB). Thus they are often referred to as empirical potentials or knowledge-based potentials. In the cas ...
Supplementary Information
... superimpositions and figures were prepared with the program MOLMOL (2). 3D structures for p53 are available for several p53 stretches and domains. However, a structure of the region between amino acids 61 and 93 is missing, probably due to higher residual dynamics. Since the results presented in thi ...
... superimpositions and figures were prepared with the program MOLMOL (2). 3D structures for p53 are available for several p53 stretches and domains. However, a structure of the region between amino acids 61 and 93 is missing, probably due to higher residual dynamics. Since the results presented in thi ...
themes and objectives
... Discuss various illnesses caused by specific types of bacteria. Thoroughly discuss the role of antibiotics in fighting bacterial infections and how bacteria counter this through resistance. ...
... Discuss various illnesses caused by specific types of bacteria. Thoroughly discuss the role of antibiotics in fighting bacterial infections and how bacteria counter this through resistance. ...
Prediction of Anti-parallel and Parallel Beta
... amino acids, and length distribution [Baldi et al, 2000]. These statistics are then fed into a bi-directional recurrent neural networks(BRNN). Their experiments on 836 protein sequences shows an accuracy of 84%. Although the numbers are very encouraging, the data sets they used are very unbalanced s ...
... amino acids, and length distribution [Baldi et al, 2000]. These statistics are then fed into a bi-directional recurrent neural networks(BRNN). Their experiments on 836 protein sequences shows an accuracy of 84%. Although the numbers are very encouraging, the data sets they used are very unbalanced s ...
Structural investigation of single biomolecules
... worm-like chain (WLC) model is a continuous filament with chain bending stiffness built in, and is a better model for molecules such as double-stranded DNA. In the WLC model, the persistence length represents the length over which the initial orientation is randomised. Both models can be extended to ...
... worm-like chain (WLC) model is a continuous filament with chain bending stiffness built in, and is a better model for molecules such as double-stranded DNA. In the WLC model, the persistence length represents the length over which the initial orientation is randomised. Both models can be extended to ...
Question 1 - University of Missouri
... Conformations New NMR techniques can gather local conformations and long-range interactions even under strongly denaturing conditions to obtain plausible all-atom models of the unfolded state at increasing accuracy. ...
... Conformations New NMR techniques can gather local conformations and long-range interactions even under strongly denaturing conditions to obtain plausible all-atom models of the unfolded state at increasing accuracy. ...
COMBINING MOLECULAR DOCKING WITH RECEPTOR DOMAIN
... Results: To study the effect of receptor flexibility we used the ATP – Ca-ATPase complex. In experimental structures of the complex ATP-analogues simultaneously interact with two active sites which are situated in different protein domains. In the apoform the distance between these sites is too larg ...
... Results: To study the effect of receptor flexibility we used the ATP – Ca-ATPase complex. In experimental structures of the complex ATP-analogues simultaneously interact with two active sites which are situated in different protein domains. In the apoform the distance between these sites is too larg ...
Structure analysis of FAAP24 reveals single-stranded DNA
... information, Table S1. The backbone chemical shift assignment (CO, Cα, Cβ, amide H and N) of the full-length (FL) protein was also achieved successfully. However, the TALOS+ result indicates that a 22-residue linker connecting these two domains is exceedingly flexible in solution. The N-terminal tai ...
... information, Table S1. The backbone chemical shift assignment (CO, Cα, Cβ, amide H and N) of the full-length (FL) protein was also achieved successfully. However, the TALOS+ result indicates that a 22-residue linker connecting these two domains is exceedingly flexible in solution. The N-terminal tai ...
Notes for website #1..
... transcription of the proteins involved, we can describe how oncogenes fit into the picture of chemical carcinogenesis using the activity of mutant Ras as an example. Oncogenes were initially discovered in transforming retroviral genomes and identified as mutated cellular genes or pieces of cellular ...
... transcription of the proteins involved, we can describe how oncogenes fit into the picture of chemical carcinogenesis using the activity of mutant Ras as an example. Oncogenes were initially discovered in transforming retroviral genomes and identified as mutated cellular genes or pieces of cellular ...
Gene Section ENC1 (ectodermal-neural cortex (with BTB-like domain)) Atlas of Genetics and Cytogenetics
... 589AA and 66130 Da. NRP/B/ENC1 is a member of a growing family of proteins that contains two major structural elements: A BTB/POZ domain in the Nterminus and kelch motif in the C-terminus [See above]. The BTB/POZ domain, consisting of approximately 115 amino acids is found in several members of the ...
... 589AA and 66130 Da. NRP/B/ENC1 is a member of a growing family of proteins that contains two major structural elements: A BTB/POZ domain in the Nterminus and kelch motif in the C-terminus [See above]. The BTB/POZ domain, consisting of approximately 115 amino acids is found in several members of the ...
Different subcellular localisations of TRIM22 suggest species
... immunoblotting with the anti-V5 antibody detected human V5-tagged TRIM22 (Fig. 3b). These results showed that hTRIM22 and rhTRIM22 indeed interact, most likely via their coiled-coil domains, and therefore co-localise upon co-expression. Differences in subcellular localisation are due to polymorphism ...
... immunoblotting with the anti-V5 antibody detected human V5-tagged TRIM22 (Fig. 3b). These results showed that hTRIM22 and rhTRIM22 indeed interact, most likely via their coiled-coil domains, and therefore co-localise upon co-expression. Differences in subcellular localisation are due to polymorphism ...
Troponin-I Mouse Skeletal Muscle
... with cTnI detectable in the blood for up to 5 days and cTnT for 7-10 days following MI. This allows an MI to be detected if the patient presents late. Troponin T and I are very sensitive. There is always a low level release of CK and CK-MB from skeletal muscle at a low level all the time so there is ...
... with cTnI detectable in the blood for up to 5 days and cTnT for 7-10 days following MI. This allows an MI to be detected if the patient presents late. Troponin T and I are very sensitive. There is always a low level release of CK and CK-MB from skeletal muscle at a low level all the time so there is ...
Chapter 1: Biological Introduction: RING domain proteins
... the ubiquitination of the substrate. At least three different classes of E3 ligases have been found that mediate substrate ubiquitination. These E3 enzymes differ in the domain that recognizes the E2 enzymes, which can be a RING, a PHD (plant homeodomain) or a HECT (Homologous to E6AP COOH terminus) ...
... the ubiquitination of the substrate. At least three different classes of E3 ligases have been found that mediate substrate ubiquitination. These E3 enzymes differ in the domain that recognizes the E2 enzymes, which can be a RING, a PHD (plant homeodomain) or a HECT (Homologous to E6AP COOH terminus) ...
workshops
... pepplot makes parallel plot of protein 2ry structure and hydrophobicity. peptidestructure predicts 2ry structure for a peptide, used by 'plotstructure'. plotstructure plot output of 'peptidestructure'. moment makes contour plot of helical hydrophobic moment of a peptide sequence. helicalwheel plots ...
... pepplot makes parallel plot of protein 2ry structure and hydrophobicity. peptidestructure predicts 2ry structure for a peptide, used by 'plotstructure'. plotstructure plot output of 'peptidestructure'. moment makes contour plot of helical hydrophobic moment of a peptide sequence. helicalwheel plots ...
Intrinsically Disordered Linker and Plasma Membrane
... may function as a linker to span the distance between the PM and the cER membrane. For a simple linker function, the biophysical parameters such as flexibility and Stokes radius are expected to be relevant but not the exact amino acid sequence. We constructed a gene in which the region encoding for ...
... may function as a linker to span the distance between the PM and the cER membrane. For a simple linker function, the biophysical parameters such as flexibility and Stokes radius are expected to be relevant but not the exact amino acid sequence. We constructed a gene in which the region encoding for ...
Protein domain
A protein domain is a conserved part of a given protein sequence and (tertiary) structure that can evolve, function, and exist independently of the rest of the protein chain. Each domain forms a compact three-dimensional structure and often can be independently stable and folded. Many proteins consist of several structural domains. One domain may appear in a variety of different proteins. Molecular evolution uses domains as building blocks and these may be recombined in different arrangements to create proteins with different functions. Domains vary in length from between about 25 amino acids up to 500 amino acids in length. The shortest domains such as zinc fingers are stabilized by metal ions or disulfide bridges. Domains often form functional units, such as the calcium-binding EF hand domain of calmodulin. Because they are independently stable, domains can be ""swapped"" by genetic engineering between one protein and another to make chimeric proteins.