University of Michigan Invitational - MI — Protein Modeling

A Ramachandran plot is a 2D graph showing allowed backbone angles (phi and psi) for amino acids in proteins. Two of these plots are shown below alongside a diagram of peptide torsion angles.

Match the following interactions with the level of protein structure to which they best correspond.

A. Primary structure
B. Secondary structure
C. Tertiary structure

Fill in the blanks for the following statements which describe the hydrophobic effect on folding proteins.

(A) Increase(s)
(B) No change(s)
(C) Decrease(s)

A classic protein folding experiment is one done by Christian Anfinsen in the 1950s involving the denaturation and renaturation of ribonuclease. Purified ribonuclease can be completely denatured by exposure to a concentrated urea solution in the presence of a reducing agent (in this case, beta-mercaptoethanol). The reducing agent cleaves the four disulfide bonds to yield eight Cys residues, and the urea disrupts the stabilizing hydrophobic interactions, thus freeing the entire polypeptide from its folded conformation. Denaturation of ribonuclease is accompanied by a complete loss of catalytic activity. When the urea and the reducing agent are removed, the randomly coiled, denatured ribonuclease spontaneously refolds into its correct tertiary structure, with full restoration of its catalytic activity. The refolding of ribonuclease is so accurate that the four intrachain disulfide bonds are re-formed in the same positions in the renatured molecule as in the native ribonuclease.

Passage adapted from Lehninger's Principles of Biochemistry, 6th ed.

Protein folding occurs extremely fast– something which appears almost contradictory when considering the number of possible shapes an unfolded peptide can adopt at any step of the process.

You've likely heard of the alpha-helix in your biology classes. However, there are a number of other possible helical conformations found in proteins. The 3₁₀-helix is one such conformation. An image of the alpha-helix and the 3₁₀-helix are shown side-by-side below for reference.

Based on the structures above, which helix would you expect to:

Because of the way peptide bonds and their adjacent groups align in an alpha-helix, the overall helix structure will have a dipole, with a net positive dipole at one terminus and a net negative dipole at the other terminus.

Perming hair uses biochemistry! Making waves and curls involves breaking and reforming bonds found in keratin. Two separate keratin helices will associate to form a left-handed superhelix known as a coiled coil. Hair is first bent to a desired shape, then a reducing agent is added. Once the reducing agent is removed and an oxidizing agent added, hair will retain this new shape.

A number of models are proposed for the folding of a large polypeptide chain. Some of these are shown below. Match the following images and descriptions to the following three models:

(A) Nucleation condensation
(B) Diffusion collision
(C) Hydrophobic collapse

The folding funnel hypotheses of protein folding show a much more complete image of how a peptide chain goes down an energy landscape. A 2D cross-section of this model is shown.

At which of the following labels would one expect to find the following structures? Some labels may be used multiple times, while some may not be used at all.

If not, that's OK. Mostly. Passages from this year's event theme paper (Principles for designing ideal protein structures, doi: 10.1038/nature11600) by Koga et al. (2012) are pasted here for easier reference.

For proteins to fold, the interactions favouring the native state must collectively outweigh the non-native interactions, resulting in funnel-shaped energy landscapes. However, it is not obvious how the ubiquitous non-covalent interactions that stabilize proteins—van der Waals interactions, hydrogen bonding and hydrophobic packing—can selectively favour the biologically relevant unique native structure over the vastly larger number of non-native conformations. Protein design provides an opportunity to investigate this problem: hypotheses about how unique folded structures are encoded in amino-acid sequences can be evaluated by designing proteins de novo and experimentally assessing how well they fold.

We hypothesized that funnel-shaped energy landscapes can be robustly generated by requiring that the local interactions between residues close along the linear sequence, which determine protein secondary structure, and the non-local interactions between residues distant along the chain, which stabilize protein tertiary structure, consistently favour the same folded conformation

Helix-building! Why would the following sequences of amino acids be poor choices for making an alpha-helix at physiological (~7.0) pH?

The fundamental rules describe the junctions between adjacent secondary structure elements (Fig. 1). There are three distinct junction classes in the ab-folds we sought to design—bb, ba and ab—and three corresponding rules. Statement of the rules requires the definition of the chirality (L versus R) of a bb-unit and the orientation (P versus A) of ba- and ab-units.

Figure 1a, bb-rule. L (left-handed) and R (right-handed) bb-units are illustrated (see Fig. 1d for chirality definition). The dependence of chirality on loop length is shown in the histograms.

It is very hard for us to book rooms with computer access for everyone and to beg and plead find enough proctors to make sure no one cheats. Especially for a trial event. So this is the best we've got :) Questions in this section will reference DI-II₁₀ (2LV8), shown below. DI-II₁₀ is a de novo peptide synthesized by Koga et al. (2012) in the previously referenced publication.

We obtained synthetic genes encoding 11 designs for Fold-I, 12 for Fold-II, 14 for Fold-III, 5 for Fold-IV and 12 for Fold-V. None of these proteins is homologous to any known protein (BLAST E-value ,0.02 against the NCBI nr database of nonredundant protein sequences). The proteins were expressed, purified and characterized by circular dichroism spectroscopy, size-exclusion chromatography combined with multi-angle light scattering (SEC-MALS), and NMR spectroscopy

Identify the visualization style used for the images below.

Questions in this section will reference DI-II₁₀ (2LV8), shown below. DI-II₁₀ is a de novo peptide synthesized by Koga et al. (2012) in the previously referenced publication.