Integrins are receptor proteins which are of crucial importance. They are the main way that cells both bind to and respond to the extracellular matrix. To date, 18 alpha and 8 beta subunits have been identified. From these subunits about 24 integrins are formed in human, which implicates that not all possible combinations exist. Interestingly, the alphaV subunit interacts with beta1, beta3, beta5, beta6, and beta8.
a. Please obtain human protein sequences of beta1, beta3, beta5, beta6, and beta8 subunints
b. Please align and obtain their phylogenetic trees of five beta subunints of integrins
c. Please analyzed the domain structures of integrins alphaV and beta 3.
d. Please use mapviewer to find the chromosome positions of integrins beta1, beta3, beta5, beta6, and beta8 subunints.
e. Please compare the differences in integrins beta1, beta3, beta5, beta6, and beta8 subunits.
f. Please comment the result of phylogenetic tree obtained from integrin beta1, beta3, beta5, beta6, and beta8 subunints.
Excise 2. Protein Analysis:
a. Please analyze the conserved domains of integrin alphaVbeta3.
b. Please search for other proteins containing similar domain(s).
c. Please find distant sequence homologs that may not be identified by BLAST.
d. Please obtain the structural neighbors of alphaV subunit.
e. Please show their primary structure analyses including the antigenic site, pI, MW, transmembrane domain, and hydrophobicity.
f. Please identify the possible posttranslational modifications of integrin alphaVbeta3.
g. Please propose the kinases for their phosphorylation sites.
h. Please analyze the secondary structures of integrin alphaVbeta3 .
Excise 3. Protein structure and Modeling:
Integrins are receptor proteins which are of crucial importance. They are the main way that cells both bind to and respond to the extracellular matrix. Until now 18 alpha and 8 beta subunits have been identified. From these subunits about 24 integrins are formed in nature, which implicates that not all possible combinations exist.
a. Please find the PDBids of integrin alphav beta3 and its ligand complex from brookhaven protein data bank.
b. Please use iMoltalk to indentify the residues, which are formed hydrogen bonds between alphav and beta3. Are these residues glycosylated?
c. According to the alignment of beta1, beta3, beta5, beta6, and beta8 subunints, please comment their interactions with integrin alphaV subunit.
d. Please use the structure of integrin alphav beta3 to model the 3D structure of integrin alpha5 beta1 and compare their differences.
e. Please build 3D model structure of alpha5 (N84Q and N182Q mutant) beta1 (N212Q and N269Q mutant).
f. Please identify SNPs of integrin alphav beta3. Are these SNPs involved in the interactions between alphav and beta3 subunits?
Excise 4. Structure display
Please use PyMol to color your structure
a. Please analyze the conserved domains of integrin alphaVbeta3 (pdb1L5G).
b. Please analyze the motifs of integrin alphaVbeta3 (pdb1L5G).
c. Please use different colors to show individual domains of integrin alphaVbeta3 (pdb1L5G).
Excise 5. Protein Modeling, mutation, superimposition, and energy evaluation:
Speb (streptopain) is a cysteine protease found in Streptococcus pyogenes that shows some structural and functional similarity to papain (family C1). The order of the catalytic cysteine/histidine dyad is the same and the surrounding sequences are similar.
a. Please find the PDBids of speb (streptopain )from brookhaven protein data bank (1pvj and 1dki).
b. Please use them to model the 3D structure of mature speb (253 residues starting from QPVV) by using modeling softwares (swissmodel and 3D-JIGSAW). Please compare their differences.
c. Please use the swiss-pdbviewer to superimpose their structures and to obtain their RMSD.
d. Please use the swiss-pdbviewer to compute their energy.
e. Please mutate G384 residue to aspartate and compare its energy with its inital model.
f. Please compare yours results with the reported structure of Speb (2JTC).
Excise 6. Looking for information about ADAM15 with SRS
Find as much information as possible about the humane ADAM protein. Start with a search in the Swiss-Prot protein databank.
*Please use emboss to do the analyses.
a. What is the enzyme code (EC) for the metalloprotease domain of ADAM15? How many proteins belong to this enzyme family? Which reaction do they catalyze?
b. How many introns contains human ADAM15 gene? Which repetitive elements are present in the gene and where? How do they influence the coding sequence?
c. On which chromosome is the gene located? How accurate is this position determined? HINT: GDB is a database with genetic information
d. Are there heriditary diseases related to this gene? HINT: MIM is a database with heriditary information.
e. How many cysteine-bridges are present in ADAM15?
f. search for the secundary structures of this protein?
g. Search for related protein patterns of the ADAM15 protein sequence. Which protein pattern appears to be characteristic for ADAM15 protein family? HINT: PROSITE is a database with protein patterns
h. analyze the Kyte & Doolittle hydropathy profile of ADAM15.
i. analyze the transmembrane doman of ADAM15.
Excise 1. Create your homepage :
Your homepage must include:
a. Introduction: anything about yourself
b. link to my homepage (http://myweb.ncku.edu.tw/~wjcnmr), to your email address, and to the page of your homework
c. Put a graph in your homepage
d. Link your homepage to google
e. Link your homepage to biosearch
f. Link your homepage to dictionary (http://www.m-w.com/)
g. Link your homepage to biodictionary
h. Link your homepage to any bioinformatics courses
i. Link your homepage to NCBI
j. Link your homepage to expasy
k. Link your homepage to NCKU e-journal
P.S.
1.Put your homepage into your email server.
Excise 2. Databank Search and Protein Sequence Alignment Using Bioedit:
Integrins are receptor proteins which are of crucial importance. They are the main way that cells both bind to and respond to the extracellular matrix. Until now 18 alpha and 8 beta subunits have been identified. From these subunits about 24 integrins are formed in nature, which implicates that not all possible combinations exist.
a. Please ftp and setup the software bioedit.
b. Please obtain integrin protein sequences of 18 alpha and 8 beta subunints
c. Please align and obtain their phylogenetic trees of 18 alpha subunits and 8 beta subunints of integrins
d. Please analyzed the domain structures of integrins alpha2 and alphaV
e. Please use mapviewer to find the integrins
f. Please compare the differences in integrins alpha2 and alphaV
g. Please comment the results of phylogenetic trees obtained from 18 alpha subunits, 8 beta subunints, and their combination.
Excise 3. Gene Analysis:
a. The interacting proteins of ADAMs are integrins. To date, more than 24 human integrins were identified. Please identify these genes and their chromosomal positions.
b. They may be derived form a single gene by alternative splicing. Please describe the possibility.
c. Can you find their mouse homologs and chromosomal positions.
Excise 4. Gene Expression Analyses:
Serial Analysis of Gene Expression (SAGE) is an experimental technique designed to gain a quantitative measure of gene expression. Please go to NCBI's CANCER GENOME ANATOMY PROJECT to do the following analyses.
a. Please idenitfy the SAGE of integrin beta 1 and beta 3
b. Please find the vitural northern of beta 1 and beta 3.
c. Please use the cDNA xProfiler to compare the expression profile of normal and cancer liver. Can you find beta 1 and beta 3 that were differentially expressed in liver cancer cells or tissues.
Excise 5. Protein Analysis:
a. Please analyze the conserved domains of integrins alphaIIBbetaIII and alpha4beta1.
b. Please search for other proteins containing similar domain(s).
c. Please find distant sequence homologs that may not be identified by BLAST.
d. Please obtain the structural neighbors of alphaV subunit.
e. Please show their primary structure analyses including the glycoslation site, MW, and hydrophobicity.
f. Please identify the possible posttranslational modifications of integrins alphaIIBbetaIII and alpha4beta1.
g. Please propose the kinases for their phosphorylation sites.
h. Please analyze the secondary structures of integrins alphaIIBbetaIII and alpha4beta1.
Excise 6. Comparative Microbial Genome Analyis Using Bioinformatics:
a. Please find the genomes of Streptococcus pyogenes strains MGAS315, MGAS8232, MGAS10394, MGASSSI-1, and M1, and determine their phylogentic tree.
b. Please find numbers of genes that they encode and their gene classification based on COG functional categories.
c. Please use Taxplot to compare the genomes of Streptococcus pyogenes strains MGAS315, MGAS8232, MGAS10394, MGASSSI-1, and M1 and to identify their differences in COG.
d. Please use Blast search to identify the proteins that contain the ARGDWN motif in M1 strain.
Excise 7. Protein structure, Modeling, and Display:
Integrins are receptor proteins which are of crucial importance. They are the main way that cells both bind to and respond to the extracellular matrix. Until now 18 alpha and 8 beta subunits have been identified. From these subunits about 24 integrins are formed in nature, which implicates that not all possible combinations exist.
a. Please find the PDBids of integrin alphav beta3 and its ligand complex from brookhaven protein data bank.
b. Please use them to model the 3D structure of integrin alpha5 beta1. Please compare their differences.
c. Please use the dispaly software to print out the model.
Excise 8. Looking for information about ADAM15 with SRS
Find as much information as possible about the humane ADAM protein. Start with a search in the Swiss-Prot protein databank.
*Please use emboss to do the analyses.
a. What is the enzyme code (EC) for the metalloprotease domain of ADAM15? How many proteins belong to this enzyme family? Which reaction do they catalyze?
b. How many introns contains human ADAM15 gene? Which repetitive elements are present in the gene and where? How do they influence the coding sequence?
c. On which chromosome is the gene located? How accurate is this position determined? HINT: GDB is a database with genetic information
d. Are there heriditary diseases related to this gene? HINT: MIM is a database with heriditary information.
e. How many cysteine-bridges are present in ADAM15?
f. search for the secundary structures of this protein?
g. Search for related protein patterns of the ADAM15 protein sequence. Which protein pattern appears to be characteristic for ADAM15 protein family? HINT: PROSITE is a database with protein patterns
h. analyze the Kyte & Doolittle hydropathy profile of ADAM15.
i. analyze the transmembrane doman of ADAM15.
Excise 9. Protein Modeling, mutation, superimposition, and energy evaluation:
Speb (streptopain) is a cysteine protease found in Streptococcus pyogenes that shows some structural and functional similarity to papain (family C1). The order of the catalytic cysteine/histidine dyad is the same and the surrounding sequences are similar.
a. Please find the PDBids of speb (streptopain )from brookhaven protein data bank (1pvj and 1dki).
b. Please use them to model the 3D structure of mature speb (253 residues starting from QPVV) by using modeling softwares (swissmodel and 3D-JIGSAW). Please compare their differences.
c. Please use the swiss-pdbviewer to superimpose their structures and to obtain their RMSD.
c. Please use the swiss-pdbviewer to compute their energy.
d. Please mutate G384 residue to aspartate and compare its energy with its inital model.
Excise 1. Create your homepage :
Your homepage must include:
a. Introduction: anything about yourself
b. link to my homepage (http://sparc22.cc.ncku.edu.tw/~wjcnmr), to your email address, and to the page of your homework
c. Put a graph in your homepage
d. Link your homepage to google
e. Link your homepage to biosearch
f. Link your homepage to dictionary (http://www.m-w.com/)
g. Link your homepage to biodictionary
h. Link your homepage to any bioinformatics courses
i. Link your homepage to NCBI
j. Link your homepage to expasy
k. Link your homepage to NCKU e-journal
P.S.
1.Put your homepage into your email server.
Excise 2. Databank Search and Protein Sequence Alignment Using Bioedit:
a. Please ftp and setup the software bioedit.
b. Please obtain 100 protein sequences of the snake venom proteins.
c. Please analyzed the domain structures of rhodosotmin.
d. Please align and obtain their phylogenetic tree of the disintegrin domain.
e. Please use mapviewer to find ADAM.
f. Please compare the differences of the disintegrin domains between ADAM and the snake venom proteins.
Excise 3. Gene Analysis:
a. The interacting proteins of ADAMs are integrins. To date, more than 24 human integrins were identified. Please identify them and their chromosomal positions.
b. They may be derived form a single gene by alternative splicing. Please describe the possibility.
c. Can you find their mouse homologs and chromosomal positions.
Excise 4. Protein Analysis:
a. Please analyze possible functional domains of integrins alphaIIBbetaIII and alpha4beta1.
b. Please show their primary structure analyses including the glycoslation site, MW, and hydrophobicity.
c. Please identify the possible posttranslational modifications of integrins alphaIIBbetaIII and alpha4beta1.
d. Please propose the kinases for their phosphorylation sites.
e. Please analyze the secondary structures of iintegrins alphaIIBbetaIII and alpha4beta1.
f. Please provide phylogentic relationships for human integrins.
Excise 5. Protein structure, Modeling, and Display:
Integrins are receptor proteins which are of crucial importance. They are the main way that cells both bind to and respond to the extracellular matrix. Until now 18 alpha and 8 beta subunits have been identified. From these subunits about 25 integrins are formed in nature, which implicates that not all possible combinations exist.
a. Please find the PDBids of integrin alphav beta3 and its ligand complex from brookhaven protein data bank.
b. Please use them to model the 3D structure of integrin alphaIIb beta3. Please compare their differences.
c. Please use the dispaly software to print out the model.
Excise 6. Comparative Microbial Genome Analyis Using Bioinformatics:
a. Please find the genomes of Streptococcus pyogenes strains MGAS315, MGAS8232, and M1 and determine their phylogentic tree.
b. Please find numbers of genes that they encode and their gene classification based on COG functional categories.
c. Please use Taxplot to compare the genomes of Streptococcus pyogenes strains MGAS315, MGAS8232, and M1 and to identify their differences in COG.
Excise 7. Gene Expression Analyses:
Serial Analysis of Gene Expression (SAGE) is an experimental technique designed to gain a quantitative measure of gene expression. Please identify the SAGE of interleukin enhancer binding factors. Please go to NCBI's CANCER GENOME ANATOMY PROJECT to do the following analyses.
a. Please find the vitural northern of interleukin enhancer binding factors.
b. Please use the cDNA xProfiler to compare the expression profile of normal and cancer liver. Please indentify the genes that were only expressed in cancer cells.
Excise 1. Create your homepage :
Your homepage must include:
a. Introduction: anything about yourself
b. link to my homepage (http://sparc22.cc.ncku.edu.tw/~wjcnmr), to your email address, and to the page of your homework
c. Put a graph in your homepage
d. Link your homepage to general search
e. Link your homepage to biosearch
f. Link your homepage to biodictionary
g. Link your homepage to any bioinformatics course
h. Link your homepage to NCBI
i. Link your homepage to expasy
j. Link your homepage to NCKU e-journal
P.S.
1.Put your homepage into your email server.
2.You have to submit your homework to your homepage. From now on I will go to your homepage and give the grade.
Excise 2. Genbank Search and Protein Sequence Alignments:
a. Please find the protein sequences of interleukin enhancer binding factors (ILF-1, ILF-2, and ILF-3), and myocyte nuclear factors (MNF-a and MNF-b).
b. Please align them and provide possible reasons for their functional differences.
c. Serial Analysis of Gene Expression, or SAGE, is an experimental technique designed to gain a quantitative measure of gene expression. Please go to NCBI's CANCER GENOME ANATOMY PROJECT to do the following analyses.Please identify the SAGE of interleukin enhancer binding factors.
Excise 3. Gene Analysis:
a. Interleukin enhancer binding factors and myocyte nuclear factors are human and mouse proteins, respectively. Please identify their chromosomal positions.
b. They may be derived form a single gene by alternative splicing. Please describe the possibility.
c. Can you find their homologs for the other species.
Excise 4. Protein Analysis:
a. Please analyze possible functional domains of ILF-1 and MNF-a
b. Please show their primary structure analyses including the glycoslation site, MW, and hydrophobicity.
c. Please identify the possible posttranslational modifications of ILF-1 and MNF-a.
d. Please propose the kinases for their phosphorylation sites.
e. Please analyze the secondary structures of interleukin enhancer binding factors (ILF-1, ILF-2, and ILF-3) and myocyte nuclear factors (MNF-a and MNF-b).
f. Please provide phylogentic relationships for ILF-1, ILF-2, MNF-a and MNF-b.
Excise 5. Protein structure, Modeling, and Display: MNF-a contains a DNA-binding domain (289-389) and is homologous to that of genesis protein which has a winged helix-turn-helix structure.
a. Please find the PDBids of genesis and genesis/DNA complex from brookhaven protein data bank.
b. Please use 3D structures of genesis genesis/DNA complex as the templates to model the 3D structure of DNA-binding domain of MNF-a. However, you may get two different structures. Please provide the reasons for their differences.
c. Please use the dispaly software to print out the model for the DNA-binding domain of MNF-a.
Excise 1. Create your homepage :
a. Introduce yourself
b. link to my homepage (http://sparc22.cc.ncku.edu.tw/~wjcnmr); link to your email address; link to the page of your homework; Put a graph in your homepage
c. Put your homepage into your email server
d. Link your homepage to general search
e. Link your homepage to biosearch
f. Link your homepage to biodictionary
g. Link your homepage to course of bioinformatics
h. Link your homepage to biological databases
i. Link your homepage to pubmed
j. Link your homepage to e-journal
P.S. You have to submit your homework to your homepage. From now on I will go to your homepage and give the grade.
Excise 2. ftp and install freewares :
a. acrobat for pdf documents
b. weblab viewer for macromolecule display
c. pDRAW for plasmid drawing
P.S. If you hard time to download the files from orignal sites, please try my ftp server (140.116.93.26). Files are under the directory /disk2/temp.
Username:guest
Password:nmr
Excise 3. Protein/DNA analysis :
a. Please find DNA and protein sequences of human integrin aIIB (GPIIB) subunit.
b. Please analyze the primary structure information of integrin aIIb subunit.
c. Please analyze the secondary structure information of integrin aIIb subunit.
d. Please analyze the tertiary structure information of integrin aIIb subunit.
e. Please analyze the interaction sites between integrin aIIb and b3 subunits.
e. Please align the protein sequences of integrin aIIb and b3 subunits from human, pig, and rat.
Excise 4. Protein Modeling:
a.Please find the protein and cDNA (gi:4758599) sequences of ILF-1.
b.Please find the PDBid of genesis from brookhaven protein data bank.
c. Please use 3D structure of genesis as the template to model the 3D structure of DNA-binding domain of ILF-1.
d. Please use the Weblab Viewer to print the model for the DNA-binding domain of ILF-1.
Excise 1. Create your homepage (at least 3 pages):
a. Introduce yourself
b. link to my homepage (http://sparc22.cc.ncku.edu.tw/~wjcnmr); link to your email address; link to the page of your homework; Put a graph in your homepage
c. Put your homepage into your email server
P.S. You have to submit your homework to your homepage. From now on I will go to your homepage and give the grade.
Excise 2. Links
a. Link your homepage to general search
b. Link your homepage to biosearch
c. Link your homepage to biodictionary
d. Link your homepage to course of bioinformatics
e. Link your homepage to biological databases
f. Link your homepage to pubmed
g. Link your homepage to e-journal
h. ftp acrobat
Excise 3. Genbank Search and protein sequence alignments
a. Use Genbank website to search the protein sequences of the disintegrin domain of human MDC15 , kistrin, flavoridin, and bitistatin.
b. Use Align website to align the protein sequences of disintegrin domain of human MDC15 to that of kistrin, flavoridin, and bitistatin.
c. Use Dialign website to align the protein sequences of disintegrin domain of human MDC15 to that of kistrin, flavoridin, and bitistatin.
d. Use Blast website to find the homologous proteins of the disintegrin domain of human MDC15.
Excise 4. Display the 3D structure of proteins
a. Please go to Rasmol website to ftp the Rasmol software and install it.
b. Please go to the Protein Databank website to ftp the coordinates of kistrin (3D structure).
c. Use the Rasmol to display 3D protein structure of kistrin and print it out.
Excise 5. Molecular Modeling
a. Use Genbank (pdb databank) website to search the protein sequence of murine ets-1 transcription factor.
b. Build a K364L mutant and use SWISS-MODEL website to build the molecular model of this mutant. Please use pdb1etc as template.
Excise 6. Protein analysis
a. Pick one of protein analysis software from ExPASy or CMSMBR Protein Characterization tools websites and show your work step by step in Chinese.
a. Please find the information about HHR23A (human), HHR23B (human), and RAD23 (S. cerevisiae) homolog A protein, such as location of chromosome, function and structure.
b. Please find the protein and cDNA sequences of HHR23A, HHR23B, and RAD23.
c. Please use the software Bioedit to align the protein sequences of HHR23A, HHR23B, and RAD23.
Excise 2. Cloning
a. Use primer (http://alces.med.umn.edu/rawprimer.html) to design the sense and antisense primers with HindIII and EcoRI recognition, respectively.
b. Please use the software Bioedit to construct the cDNA of HHR23A into pET-21a.
c. Show your final plasmid map.
Excise 3. Protein structure, Modeling, and Display
Based on sequence homology, HHR23A has two ubiquitin-associated domains (UBA1 and UBA2) which are residues 160-205 and 319-363, respectively.
a. Please align UBA1 and UBA2.
b. Please find the PDBid of UBA2 from brookhaven protein data bank.
c. Please use UBA2 as the template to model the 3D structure of UBA1.
d. Please use Weblab viewer to display the model for the UBA1 of HHR23A.
Excise 1.
Please use chinese search engine to find any information regarding 基因轉殖, 生物晶片, 生物資訊.
Excise 2. Please use search engine to find any information regarding bioinformatics, biochip, and transgenic plants.