Proteins and Sequence Alignment Tools in Molecular Microbiology
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Proteins and Sequence Alignment Tools in Molecular Microbiology

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Questions and Answers

Which program is described as a free program for multiple sequence alignment editing, visualization, and analysis?

  • Jalview (correct)
  • InterPro
  • UniProt
  • NCBI Protein

    • Which tool is used for sequence/alignment editing and has a file conversion feature for -fasta and -Nexus formats?

  • Pfam
  • MUSCLE
  • Jalview (correct)
  • MAFFT

    • Which protein database is not mentioned in the text?

  • PDB
  • KEGG (correct)
  • UniProt
  • GenBank

    • Which publication discusses Java bioinformatics analysis web services for multiple sequence alignment?

    <p>Procter JB et al. (2011)</p> Signup and view all the answers

    What tool can be used to identify membrane-spanning proteins based on hydrophobicity?

    <p>ExPASY server (ProtScale)</p> Signup and view all the answers

    What are protein motifs usually associated with?

    <p>Specific function</p> Signup and view all the answers

    Where can information on protein families be found?

    <p>Pfam database</p> Signup and view all the answers

    What reflects the evolution of complex proteins in many mammalian proteins?

    <p>'Mosaic proteins' due to domain shuffling</p> Signup and view all the answers

    Which tool can be used for protein secondary structure predictions?

    <p>SWISS MODEL WORKSPACE</p> Signup and view all the answers

    What does the Protein Data Bank (PDB) contain?

    <p>Three-dimensional structural data for proteins</p> Signup and view all the answers

    What is the formula for Gibbs free energy?

    <p>G = H - TS</p> Signup and view all the answers

    What physiochemical property do nonpolar amino acid side chains exhibit?

    <p>Hydrophobicity</p> Signup and view all the answers

    What method involves finding related proteins with known 3D structures to use as templates for modeling a protein's structure?

    <p>Homology modeling</p> Signup and view all the answers

    Which atoms must buried polar atoms be bonded to, according to the considerations for protein folding?

    <p>Other buried polar atoms</p> Signup and view all the answers

    What is the main purpose of excluding water molecules from the interior of a protein?

    <p>To pack the interior densely</p> Signup and view all the answers

    Which method involves scanning a protein sequence for amino acid patterns associated with particular folds?

    <p>Fold recognition</p> Signup and view all the answers

    What resource can be used for searching the SWISS-MODEL template library for suitable template structures?

    <p>SWISS-MODEL WORKSPACE Tools</p> Signup and view all the answers

    What physiochemical property allows polar R groups to hydrogen bond with other polar groups or with polar solvents?

    <p>Polarity</p> Signup and view all the answers

    What method locates potential helical regions and beta strands in a protein sequence?

    <p>Attempts to predict secondary structures</p> Signup and view all the answers

    What is the main limitation of de novo prediction method for protein structure prediction?

    <p>Difficulty in finding suitable templates for modeling</p> Signup and view all the answers

    Which database can be used to scan a protein sequence for amino acid patterns known from previous work associated with a particular fold?

    <p>SWISS-MODEL</p> Signup and view all the answers

    Which program is described as a free program for multiple sequence alignment editing, visualization, and analysis?

    <p>Jalview</p> Signup and view all the answers

    What is the formula for Gibbs free energy?

    <p>$ riangle G = riangle H - T riangle S$</p> Signup and view all the answers

    Which publication discusses Java bioinformatics analysis web services for multiple sequence alignment?

    <p>Bioinformatics 27: 20012002</p> Signup and view all the answers

    Where can information on protein families be found?

    <p>Pfam</p> Signup and view all the answers

    What is the main purpose of excluding water molecules from the interior of a protein?

    <p>To densely pack the interior and stabilize the protein structure</p> Signup and view all the answers

    What physiochemical property allows polar R groups to hydrogen bond with other polar groups or with polar solvents?

    <p>Polarity</p> Signup and view all the answers

    Which method involves finding related proteins with known 3D structures to use as templates for modeling a protein's structure?

    <p>Homology modeling</p> Signup and view all the answers

    What reflects the evolution of complex proteins in many mammalian proteins?

    <p>Amino acid side chain physiochemical versatility</p> Signup and view all the answers

    Which tool is used for protein secondary structure predictions?

    <p>$\text{Sequence Feature Scan}$</p> Signup and view all the answers

    What method locates potential helical regions and beta strands in a protein sequence?

    <p>Attempts to predict secondary structures</p> Signup and view all the answers

    What are protein motifs usually associated with?

    <p>Specific functions or activities</p> Signup and view all the answers

    Which database can be used to scan a protein sequence for amino acid patterns known from previous work associated with a particular fold?

    <p>SWISS-MODEL Workspace</p> Signup and view all the answers

    What is the main limitation of de novo prediction method for protein structure prediction?

    <p>It cannot predict novel folds.</p> Signup and view all the answers

    Which program is described as a free program for multiple sequence alignment editing, visualization, and analysis?

    <p>Expert Protein Analysis System (ExPASy)</p> Signup and view all the answers

    Where can information on protein families be found?

    <p>NCBI resources</p> Signup and view all the answers

    What tool can be used to identify membrane-spanning proteins based on hydrophobicity?

    <p>Sequence Feature Scan</p> Signup and view all the answers

    What tool can be used to predict the secondary structure of proteins?

    <p>SWISS MODEL WORKSPACE</p> Signup and view all the answers

    Where can information on protein domains be found?

    <p>Pfam database</p> Signup and view all the answers

    What is the main purpose of the Protparam tool?

    <p>Obtaining basic information about a protein</p> Signup and view all the answers

    Which database contains three-dimensional structural data for proteins?

    <p>Protein Data Bank (PDB)</p> Signup and view all the answers

    What reflects the evolution of complex proteins in many mammalian proteins?

    <p>Mosaic proteins due to domain shuffling</p> Signup and view all the answers

    Which tool can be used to identify membrane-spanning proteins based on hydrophobicity?

    <p>ProtScale</p> Signup and view all the answers

    What physiochemical property do nonpolar amino acid side chains exhibit?

    <p>Low solubility in water</p> Signup and view all the answers

    What does the PDB ID identify?

    <p>Three-dimensional structural data of proteins</p> Signup and view all the answers

    Which method involves scanning a protein sequence for amino acid patterns associated with particular folds?

    <p>Protein motifs identification using PROSITE library</p> Signup and view all the answers

    What physiochemical property allows polar R groups to hydrogen bond with other polar groups or with polar solvents?

    <p>Tendency to form hydrogen bonds with polar groups</p> Signup and view all the answers

    What reflects the evolution of complex proteins in many mammalian proteins?

    <p>Mosaic proteins due to domain shuffling</p> Signup and view all the answers

    Where can information on protein motifs be found?

    <p>PROSITE library</p> Signup and view all the answers

    Which tool can be used to study coevolution in protein families?

    <p>MISTIC2</p> Signup and view all the answers

    What is the purpose of Mutual Information Circos (MI Circo)?

    <p>To represent MSA position conservation and information content</p> Signup and view all the answers

    What is the strategy involving Phyre2 and MISTIC?

    <p>Use Phyre2 to find nearest neighbors and use MISTIC to get preliminary secondary and 3D structure</p> Signup and view all the answers

    What does the Colored square boxes of the second circle in Mutual Information Circos (MI Circo) indicate?

    <p>MSA position conservation</p> Signup and view all the answers

    Which program is used for inter-protein contact prediction using deep learning?

    <p>ComplexContact</p> Signup and view all the answers

    What is the main purpose of the ConSurf server?

    <p>Estimating the evolutionary conservation of amino/nucleic acid positions</p> Signup and view all the answers

    Which tool is used for protein dynamics and sequence analysis?

    <p>ProDy</p> Signup and view all the answers

    Where can information on the effect of mutations on protein structure be found?

    <p>foldxsuite.crg.eu</p> Signup and view all the answers

    What is the resource used for searching the SWISS-MODEL template library for suitable template structures?

    <p>swissmodel.expasy.org/repository/</p> Signup and view all the answers

    What method does MEGA6 use for phylogenetic analysis?

    <p>Maximum Likelihood (ML) method and Neighbor Joining (NJ) method plus bootstrap analysis</p> Signup and view all the answers

    Where can information on predicting the secondary structure of proteins be found?

    <p>raptorx.uchicago.edu/ComplexContact/</p> Signup and view all the answers

    What does the ConSurf server estimate based on phylogenetic relations between homologous sequences?

    <p>Evolutionary conservation of amino/nucleic acid positions in a protein/DNA/RNA molecule</p> Signup and view all the answers

    Which tool can be used to predict the effect of mutations on protein structure?

    <p>foldxsuite.crg.eu</p> Signup and view all the answers

    Where can information on estimating the evolutionary conservation of amino/nucleic acid positions be found?

    <p><a href="https://consurf.tau.ac.il/overview.php">https://consurf.tau.ac.il/overview.php</a></p> Signup and view all the answers

    Study Notes

    Protein Structure and Function Overview

    • Hydrophobicity can identify membrane-spanning proteins such as transporters or signal transducers, and ExPASY server (ProtScale) can be used for this purpose.
    • ProtScale computes and represents the profile produced by any amino acid scale on a selected protein, based on different chemical and physical properties of the amino acids.
    • Rps3 (ribosomal protein SSU #3) has hydrophobicity scores between 4.6 and -4.6, with a score of 4.6 being the most hydrophobic and a score of -4.6 being the most hydrophilic.
    • A good start to get basic information about a protein, including hydrophobicity and other physiochemical properties, is the Protparam tool.
    • Protein motifs are usually short conserved amino acid sequences associated with a specific function and can be found in the PROSITE library.
    • Protein domains are regions of a protein that fold into semi-autonomous structures, and the Pfam database contains information on protein families.
    • Many mammalian proteins are "Mosaic proteins" due to domain shuffling, which reflects the evolution of complex proteins.
    • Protein secondary structure predictions can be made for helix, beta strands, coils, order/disorder using tools like SWISS MODEL WORKSPACE or PRALINE.
    • The Protein Data Bank (PDB) is a database containing three-dimensional structural data for proteins.
    • Protein stability and folding aim for the native state, which should be the thermodynamically most favorable state according to the second law of thermodynamics at constant temperature.
    • The PDB ID is an accession number used to identify three-dimensional structural data of proteins.
    • The Protein Secondary Structure Prediction Server can be used to predict the secondary structure of proteins.

    Protein Structure and Function Overview

    • Hydrophobicity can identify membrane-spanning proteins such as transporters or signal transducers, and ExPASY server (ProtScale) can be used for this purpose.
    • ProtScale computes and represents the profile produced by any amino acid scale on a selected protein, based on different chemical and physical properties of the amino acids.
    • Rps3 (ribosomal protein SSU #3) has hydrophobicity scores between 4.6 and -4.6, with a score of 4.6 being the most hydrophobic and a score of -4.6 being the most hydrophilic.
    • A good start to get basic information about a protein, including hydrophobicity and other physiochemical properties, is the Protparam tool.
    • Protein motifs are usually short conserved amino acid sequences associated with a specific function and can be found in the PROSITE library.
    • Protein domains are regions of a protein that fold into semi-autonomous structures, and the Pfam database contains information on protein families.
    • Many mammalian proteins are "Mosaic proteins" due to domain shuffling, which reflects the evolution of complex proteins.
    • Protein secondary structure predictions can be made for helix, beta strands, coils, order/disorder using tools like SWISS MODEL WORKSPACE or PRALINE.
    • The Protein Data Bank (PDB) is a database containing three-dimensional structural data for proteins.
    • Protein stability and folding aim for the native state, which should be the thermodynamically most favorable state according to the second law of thermodynamics at constant temperature.
    • The PDB ID is an accession number used to identify three-dimensional structural data of proteins.
    • The Protein Secondary Structure Prediction Server can be used to predict the secondary structure of proteins.

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    Description

    This quiz covers topics related to proteins, protein databases such as UniProt and NCBI Protein, as well as sequence alignment tools like MAFFT and MUSCLE. It also includes information about the multiple sequence alignment editor Jalview.

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