Week 3 lectures continued
... It has been observed that among closely related proteins, some substitutions occurred more readily than others without having a great effect on the protein’s structure or function. ...
... It has been observed that among closely related proteins, some substitutions occurred more readily than others without having a great effect on the protein’s structure or function. ...
Gene Ontology (GO)
... • Many proteins combine functions • Some immunoglobulin structures are thought to have more than 100 different functions (and active/binding sites) • Alternative splicing can generate (partially) alternative structures ...
... • Many proteins combine functions • Some immunoglobulin structures are thought to have more than 100 different functions (and active/binding sites) • Alternative splicing can generate (partially) alternative structures ...
No Slide Title
... (point accepted mutation) means there has been 1 point mutation per 100 residues PAM 1 may be used to generate matrices for greater evolutionary distances by multiplying it repeatedly by itself. PAM250: – 2,5 mutations per residue. – equivalent to 20% matches remaining between two sequences, i.e. 80 ...
... (point accepted mutation) means there has been 1 point mutation per 100 residues PAM 1 may be used to generate matrices for greater evolutionary distances by multiplying it repeatedly by itself. PAM250: – 2,5 mutations per residue. – equivalent to 20% matches remaining between two sequences, i.e. 80 ...
Discussion Problem Set 3 C483 Spring 2014
... 1. What are the two main forces that stabilize an alpha helix? Describe them. How might you test the importance of an n-pi-star interaction? 2. What two things need to be minimized to have a stable alpha helix? 3. Which amino acid regularly adopts a cis peptide bond? Explain why this is possible. 4. ...
... 1. What are the two main forces that stabilize an alpha helix? Describe them. How might you test the importance of an n-pi-star interaction? 2. What two things need to be minimized to have a stable alpha helix? 3. Which amino acid regularly adopts a cis peptide bond? Explain why this is possible. 4. ...
Proteiinianalyysi 5
... • The branchpoints separating subclades of a phylogenetic tree can specify molecular speciation events, and hence evolutionary selection of amino acids • Map trace residues to 3D structures ...
... • The branchpoints separating subclades of a phylogenetic tree can specify molecular speciation events, and hence evolutionary selection of amino acids • Map trace residues to 3D structures ...
Multiple Sequence Alignment
... sequences. There are (n-1)+(n-2)...(nn+1) possibilities. • Calculate the ‘distance’ between each pair of sequences based on these isolated pairwise alignments. • Generate a distance matrix. ...
... sequences. There are (n-1)+(n-2)...(nn+1) possibilities. • Calculate the ‘distance’ between each pair of sequences based on these isolated pairwise alignments. • Generate a distance matrix. ...
Part 4
... • The tertiary structure of a protein involves attractions and repulsions between the R groups of the amino acids in the polypeptide chain. • As interactions occur between different parts of the peptide chain, segments of the chain twist and bend until the protein acquires a specific three-dimension ...
... • The tertiary structure of a protein involves attractions and repulsions between the R groups of the amino acids in the polypeptide chain. • As interactions occur between different parts of the peptide chain, segments of the chain twist and bend until the protein acquires a specific three-dimension ...
Module 5
... (or motifs) common to homologous proteins. These motifs, usually of the order of 10-20 amino acids in length, usually correspond to key functional or structural elements, often domains, and are extremely useful in identifying such features in new uncharacterized proteins. There is a number of such s ...
... (or motifs) common to homologous proteins. These motifs, usually of the order of 10-20 amino acids in length, usually correspond to key functional or structural elements, often domains, and are extremely useful in identifying such features in new uncharacterized proteins. There is a number of such s ...
Slide 1
... Highly insoluble regions represent positions for protein insertion into the membrane. ...
... Highly insoluble regions represent positions for protein insertion into the membrane. ...
Day 6 Carlow Bioinformatics
... (more reliable in MSA than in single seq) MSA improves 2ndary structure (-helix -sheet) prediction by >6%) ...
... (more reliable in MSA than in single seq) MSA improves 2ndary structure (-helix -sheet) prediction by >6%) ...
proteins - Technische Universität München - Physik
... it is folded. This tertiary structure is directly related to its function. ...
... it is folded. This tertiary structure is directly related to its function. ...
ECS 189K - UC Davis
... Briefly, the method works as follows (see illustration below): - The protein chain is defined as a polyline joining the central CA atoms of each residue running from the N-terminal to the C-terminal. Coordinates of the CA atoms are available in the PDB file for the protein of interest - The algorith ...
... Briefly, the method works as follows (see illustration below): - The protein chain is defined as a polyline joining the central CA atoms of each residue running from the N-terminal to the C-terminal. Coordinates of the CA atoms are available in the PDB file for the protein of interest - The algorith ...
Analytical Sciences, Poster AS-101 Kinetics and identification of non
... stimulates the MAP kinase signaling pathway where MAPK8 is activated and in turn phosphorylates a number of transcription factors. The two other proteins are commonly applied as a protein expression tag (MBP) or fluorescent label (GFP). DARPins are a very promising class of nonimmunoglobulin binders ...
... stimulates the MAP kinase signaling pathway where MAPK8 is activated and in turn phosphorylates a number of transcription factors. The two other proteins are commonly applied as a protein expression tag (MBP) or fluorescent label (GFP). DARPins are a very promising class of nonimmunoglobulin binders ...
Proteins are biopolymers construced from similar building blocks
... qualitatively different. High pressure (typically 5-10 kbar) will change the three dimensional structure of the protein drastically, resulting in a loss of biological function. The molecule undergoes nonelastic structural alteration under high pressure. This phase transition is called pressure unfol ...
... qualitatively different. High pressure (typically 5-10 kbar) will change the three dimensional structure of the protein drastically, resulting in a loss of biological function. The molecule undergoes nonelastic structural alteration under high pressure. This phase transition is called pressure unfol ...
Word copy
... alignments of protein sequences. This program (>20,000 lines of source code) was written in Pascal on Vax computers over several years. It has many features, some of which are: Construction of databases, including annotation options; Use of arbitrary motif weight, amino acid property and amino a ...
... alignments of protein sequences. This program (>20,000 lines of source code) was written in Pascal on Vax computers over several years. It has many features, some of which are: Construction of databases, including annotation options; Use of arbitrary motif weight, amino acid property and amino a ...
Protein Structure
... What are the monomers/building blocks for proteins? • Amino Acids! There are 20 different types. They are connected by Peptide Bonds to form Proteins Proteins are also called Polypeptides ...
... What are the monomers/building blocks for proteins? • Amino Acids! There are 20 different types. They are connected by Peptide Bonds to form Proteins Proteins are also called Polypeptides ...
Homology modeling with SWISS
... protein when only its amino acid sequence and the complete atomic structure of at least one other reference protein is known • The reference protein must be structurally homologous to the model protein being build. Structural segments, which are thought to be conserved within the family of homologou ...
... protein when only its amino acid sequence and the complete atomic structure of at least one other reference protein is known • The reference protein must be structurally homologous to the model protein being build. Structural segments, which are thought to be conserved within the family of homologou ...
Ligand Binding - Stroud -Lecture 1
... • Thermodynamics of Protein Assembly • Structural Change on complexation • Empirical fitting of Atomic Interactions with Free Energy of Association • Estimate of free energy of H bonds and charge interactions in protein complexes and role of hydrophobic effect _______________________________________ ...
... • Thermodynamics of Protein Assembly • Structural Change on complexation • Empirical fitting of Atomic Interactions with Free Energy of Association • Estimate of free energy of H bonds and charge interactions in protein complexes and role of hydrophobic effect _______________________________________ ...
Tertiary Structure to X-Ray Crystallography
... While structures in data depositories like the Protein Data Bank seem very authoritative and inspire confidence, interpreting X-ray crystallographic data is not easy. The diffraction data is converted to an electron density map, which shows the location of different atoms within the protein. The cla ...
... While structures in data depositories like the Protein Data Bank seem very authoritative and inspire confidence, interpreting X-ray crystallographic data is not easy. The diffraction data is converted to an electron density map, which shows the location of different atoms within the protein. The cla ...
Deep architectures for protein contact map prediction
... Protein residue-residue contact prediction is the problem of predicting whether any two residues in a protein sequence are spatially close to each other in the folded 3D structure. For a protein of N amino acids, the contact map is an NxN matrix C whose elements are by: ...
... Protein residue-residue contact prediction is the problem of predicting whether any two residues in a protein sequence are spatially close to each other in the folded 3D structure. For a protein of N amino acids, the contact map is an NxN matrix C whose elements are by: ...
Protein Structure Prediction not a trivial matter
... stability is not fully understood The primary sequence may not fully specify the tertiary structure (chaperones have the ability to induce proteins to fold in ...
... stability is not fully understood The primary sequence may not fully specify the tertiary structure (chaperones have the ability to induce proteins to fold in ...
Document
... “if two peptides stretches exhibit sufficient similarity at the sequence level, then they are likely to be biologically related” ...
... “if two peptides stretches exhibit sufficient similarity at the sequence level, then they are likely to be biologically related” ...
Klauda-NCTU-Oct31
... for timescales that are not reachable with traditional computational approaches. One aspect of our research is understanding the mechanism of lipid exchange between cell organelles. This involves proteins that aid in lipid transport by forming membrane contact sites. One example is the oxysterol bin ...
... for timescales that are not reachable with traditional computational approaches. One aspect of our research is understanding the mechanism of lipid exchange between cell organelles. This involves proteins that aid in lipid transport by forming membrane contact sites. One example is the oxysterol bin ...
Supplementary Material
... The secondary structure definitions of amino acids were generated with DSSP [1] considering only three groups: helical (H), extended (E) and coil (C). Based on this 7 types of protein interfaces can be defined taking into consideration the amount of each of the three basic secondary structural eleme ...
... The secondary structure definitions of amino acids were generated with DSSP [1] considering only three groups: helical (H), extended (E) and coil (C). Based on this 7 types of protein interfaces can be defined taking into consideration the amount of each of the three basic secondary structural eleme ...
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.