CSC334 Lab10

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Finding the Secondary Structure of a Protein

The page on Secondary Structures in Wikipedia defines it well:

In biochemistry and structural biology, secondary structure is the general three-dimensional form of local segments of biopolymers such as proteins and nucleic acids (DNA/RNA). It does not, however, describe specific atomic positions in three-dimensional space, which are considered to be tertiary structure.

Secondary structure is formally defined by the hydrogen bonds of the biopolymer, as observed in an atomic-resolution structure. In proteins, the secondary structure is defined by patterns of hydrogen bonds between backbone amide and carboxyl groups (sidechain-mainchain and sidechain-sidechain hydrogen bonds are irrelevant), where the DSSP definition of a hydrogen bond is used. In nucleic acids, the secondary structure is defined by the hydrogen bonding between the nitrogenous bases.

Goal

In this lab we use the PSIPRED system to get the secondary structure of a protein.

Steps

• Connect to the Psipred system at bioinf.cs.ucl.ac.uk/psipred/
• Click on CLICK HERE TO ENTER THE SERVER
• Copy/Paste a protein sequence in FASTA format (without the first text line). Here we are using a sequence we obtained in Lab #9 for the E. Coli sequence reference AAF33488:

MESTVDTELLKTFLEVSRTRHFGRAAEALYLTQSAVSFRIRQLENQLGVNLFTRHRNNIRLTTAGEKLLP
YAETLMNTWQAARKEVAHTSRHNEFSIGASASLWECMLNAWLGRLYQLQEPQSGLQFEARIAQRQSLVKQ
LHERQLDLLITTEAPKMDEFSSQLLGHFTLALYCSSPARKKSELNYLRLEWGPDFQQHETGLIAADEVPV
LTTSSAELARQQLSALNGCSWLPVNWANEKGGLHTVADSATLSRPLYAIWLQNSDKYSLICDLLKTDVLD
EQ

• Accept the defaults, enter your email address, then click on Predict

• Wait a while
• Wait some more
• Depending on the number of job requests at Psipred, you may have to wait quite a while. If this is too long and you want to continue with one of the sequences I was able to get processed ahead of time and get back via email, follow this link:
  • CSC334 E-coli AAF33488

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