VL 8

Question 1

Protein folding an Levinthals paradox?

Answer 1

DNA translated RNA tranlsated Protein structure.
A Protein needs a certain structure for folding.

Levinthal’s paradox is the observation that the time required for a protein to explore all possible conformations is astronomically large, leading to the question of how proteins fold so quickly in cells. It highlights the complexity of protein folding and the need for guided folding pathways driven by specific interactions.

Question 2

What Databases are for what?

Answer 2

UniProt –> Sequence database (ca 500 000 sequences)
!) SwissProt and TrEMBL one of the major components of the UNiProt Knowledge
TrEMBL

SwissProt is manually annotated and reviewed (human annotated) ca 500 000 entires

TrEMBL is automatically annotated and not reviewed
(computer annotated) ca 87 200 000 entries

PDB –> Structure database (ca. 90 000 structures)

Sequence space is much larger than structure space

Question 3

What is a Chameleon Sequence?

Answer 3

This problem involves a significant structural change in a few amino acids or even a single one if they alter their position within a specific shape. e.g unfold

chameleons are in all-helix conformation in one structure and in all-sheet conformation in another

Propensity (Neigung) value (cham/aa) > 1 –> tendency to appear more often in chameleon sequences

Question 4

What would you use to plot PDB data?

Answer 4

A contact map.
A contact map shows how close are atoms to each other.
Like a Hydrogen Bound plot

(close to Ramachandran plot)

Question 5

What does DSSP mean?

Answer 5

DSSP means Dictionary Secondary Structures of Proteins

Its like a shortcut for structures (SPICKER)

• H = α-helix
• G = 3-helix (3/10 helix)
• I = 5-helix (π-helix)
• B = residue in isolated β-bridge
• E = extended strand, participates in β-ladder * C=coil
• T = hydrogen bonded turn
• S=bend
  –> Simplification: H=(H,G,I),E=(E,B),C=(C,T,S)

Question 6

What if we have no structure data yet, only sequence data?
Predicting secondary structures.

Answer 6

The Chou-Fasman method is a protein secondary structure prediction algorithm developed in the late 1970s. It assigns probabilities for three main secondary structure elements (alpha-helix, beta-sheet, and random coil) based on empirical parameters derived from known protein structures. While it was an early attempt at prediction, more advanced methods are used today.

–> this is still a popular algorithm and a lot of webpages allow you to perform it.

Question 7

What is structural Alignment? (3d)

Answer 7

Structural alignment is a method used to compare and align the 3D structures of proteins or biomolecules. It helps identify similarities, functional motifs, and evolutionary relationships between molecules.

• 3D matching
  2 Structures match if
  1. correspondence
  2. Alignment (low RMSD)
• RMSD Value (Root Mean Square Deviation)

Question 8

Basic Operation of structural Alignment? (3D)

Answer 8

1. Translation
   move structure together, so the mass center is laying over each other
2. Rotation
   try to minimise RMSD value
   * mostly only backbone C’s are used
   * RMSD value indicate the divergence of two
   structures
   * alignment can be complicated
   * changes in relative orientation of domains
   –> inflation of RMSD value
   * also a sequence alignment is produced
   –> percent sequence identity is also retrieved
3. Multiple partial matches

–> Problem: sometimes you have a bad RMSD value and a higher number of match residues (and the opposite)

Question 9

CE Algorithm?

Answer 9

The CE (Combinatorial Extension) algorithm is a widely used method for comparing and aligning protein structures based on their 3D coordinates. It uses dynamic programming to find the best alignment that maximizes the structural similarity score. The algorithm is computationally efficient and effective for detecting similarities between proteins with different sizes and folds.

Protein structure alignment by incremental Combinatorial Extension (CE) of the optimal path.
Define Alignment Fragment Pair (AFP) as a continuous segment of protein A (submatrix) aligned against a continuous segment of protein B (submatrix) - without gaps.

Goal:
Find a “good” local alignment for structures of proteins A and B

basic idea:
1. select some initial AFP
2. build an alignment path by incrementally adding AFPs in a way that satisfies the conditions on the previous slide
3. repeat step (2) until the length of each protein is traversed, or until no “good” AFPs remain

Question 10

What is Homstrad Alignment (2D)?

Answer 10

Homstrad (Homologous Structure Alignment Database) is a database that provides curated structural alignments of homologous protein families. It focuses on proteins with similar structures but varying sequences, known as homologs.

Sequence is written down and you compare the two sequences.