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Protein Folding Dynamics

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Protein Folding Dynamics

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Protein Folding Dynamics

  • The molecular dynamics of protein folding: proteins use a cooperative folding method to go from their unfolded state to their native or folded state; thermodynamics plays a role in achieving a folded protein.

KEY FEATURES OF PROTEIN FOLDING

  • Protein folding begins co-translationally.
  • Alpha helices and beta sheets are amphipathic
    – One face is hydrophobic and one is hydrophilic.
  • The interior of a protein has exclusively hydrophobic side chains.
    – Exception: transmembrane proteins that transport polar substances across cell membranes have a hydrophobic exterior and a hydrophilic interior.
  • Changes in free energy dictate this directionality: from unfolded → folded.
  • The unfolded state: helix formation and hydrophobic collapse begins.
  • The total entropy associated with the protein decreases as it approaches its folded state: a wide range of unfolded states, only a single native, folded state for the protein exists.
    – 2nd law of Thermodynamics: the protein is being made within the system of the entire cell; having a small compact protein allows for more molecular interactions in the cell around it → more entropy in the entire cell.

CHANGES IN ENERGY FROM THE UNFOLDED TO FOLDED STATE

  • Native state of a protein is more energetically favorable than its unfolded state.
  • The number of residues in the native state increases as the protein folds.
  • Proteins go sharply from being completely folded to unfolded (folding intermediates are unstable).
  • Protein folding is "all or none": proteins fold via cooperative transition → loss of stability in one part of the structure disrupts the bonds, and the entire structure collapses.
  • Molten globule form: protein lacks the stabilizing interactions to hold it together.

LEVINTHAL'S PARADOX

  • Proteins take as little as a microsecond to completely fold, despite the astronomical possible conformations for each polypeptide sequence.
  • In a protein with just 100 amino acids, there are 3100 possible conformations: even if each conformation took one billionth of a second, an entire protein would still take hours to fold completely.

CUMULATIVE SELECTION

  • Richard Dawkins proposed that partially correct intermediates are retained in the process and decrease the time necessary for the protein to fold.
  • Energy difference between folded and unfolded states is fairly small: for any individual amino acid, it's miniscule.

NUCLEATION CONDENSATION MODEL

Addresses how we get from unfolded to folded: local regions adopt their specific structural preferences and then interact with each other to stabilize the folding protein.

Full-Length Text

  • Here we will learn about the molecular dynamics of protein folding.
    • Proteins use a cooperative folding method to go from their unfolded state to their native or folded state. In this tutorial we will specifically discuss the role that thermodynamics plays in achieving a folded protein.
  • Start a table, so we can list some key features of protein folding.
  • Denote that protein folding begins co-translationally, meaning that as the N-terminal is synthesized and leaves the ribosome, it immediately begins to fold itself.
  • Denote that alpha helices and beta sheets are amphipathic, which means that that they have one face that's entirely hydrophobic and one that's hydrophilic.
  • Denote that the interior of a protein has exclusively hydrophobic side chains; thus, they localize along the inside of the protein to avoid the hydrophilic environment of the cell.
    • The exception is transmembrane proteins that transport polar substances across cell membranes: they have a hydrophobic exterior and a hydrophilic interior.
    • The reason is that the interior of cell membranes is hydrophobic, thus the exterior of the transmembrane protein needs to be hydrophobic as well.

With that information as a background, now let's use an energy diagram to learn more about the thermodynamics of protein folding.

  • First, lightly outline a funnel.
    • This shape represents energy changes in the polypeptide chain during the protein folding process.
  • Label the top of the funnel "unfolded state" and the bottom point of the funnel "native or folded state."
    • We will see that changes in free energy dictate this directionality: from unfolded to folded.
      Indicate that the unfolded state is where helix formation and hydrophobic collapse begins.
  • Draw a horizontal double-headed arrow at the top of the funnel and label it entropy, which is the degree of disorder in an environment.
  • Show that the total entropy associated with the protein decreases as it approaches its folded state (the width of the funnel decreases) because although there is a wide range of unfolded states, only a single native, folded state for the protein exists.
    • Although this may seem to contradict the 2nd law of Thermodynamics, which states that systems act to increase disorder, if we consider that the protein is being made within the system of the entire cell, then having a small compact protein allows for more molecular interactions in the cell around it, and therefore more entropy in the entire cell.

Now let's consider changes in energy from the unfolded to folded state.

  • On the left of our funnel draw a vertical up arrow for energy because the native state of a protein is more energetically favorable than its unfolded state.
  • Now on the right of our funnel, draw a vertical down arrow going from 0% to 100% and label it "Residues in native conformations": the number of residues in the native state increases as the protein folds.
    • Although our diagram implies a protein folding gradient, in actuality, proteins go sharply from being completely folded to unfolded (folding intermediates are unstable).
  • So now, write that protein folding is "all or none" because proteins fold via cooperative transition, which means that all of the smaller interactions of a protein give it its folded shape.
    • Much like a house of cards, loss of stability in one part of the structure, disrupts the bonds and the entire structure collapses.

Now let's show these transitions and intermediates.

  • Redraw our funnel so that it looks like it's melting: each peak represents an intermediary structure.
  • Towards the middle of our funnel, demarcate the molten globule state and use arrows to show energy flow towards the neck of the funnel.
  • In the molten globule form, the protein appears molten because it lacks the stabilizing interactions to hold it together.
  • Now label the transition region and discrete folding intermediates to show that there are multiple steps in the process.

But during folding, do proteins go through all possible combinations? The short answer is that would be impossible!

  • Write that according to Levinthal's paradox, proteins take as little as a microsecond to completely fold, despite the astronomical possible conformations for each polypeptide sequence.
    • In a protein with just 100 amino acids, there are 3100 possible conformations. Even if each conformation took one billionth of a second, an entire protein would still take hours to fold completely.
    • In contrast, Richard Dawkins proposed cumulative selection, which says that partially correct intermediates are retained in the process and decrease the time necessary for the protein to fold.
    • However, the energy difference between folded and unfolded states is fairly small, which means for any amino acid, it's miniscule.
  • So given the issues identified with Levinthal's paradox and cumulative selection, how do we explain protein folding? The nucleation condensation model is one wide-accepted explanation.
  • Near the top of our funnel, draw a squiggle to represent an unfolded protein, which is completely disordered.
  • At the bottom of the funnel, draw a folded protein as follows: three antiparallel beta sheets, then an alpha helix then another beta sheet then another alpha helix. A model of our fully functional protein.
    • The nucleation condensation model addresses how we get from unfolded to folded: it proposes that local regions adopt their specific structural preferences and then interact with each other to stabilize the folding protein.
  • So, now let's add some intermediates to show how localized areas have strong preferences, which influence conglomerate folding of the protein.
  • First, below our unfolded protein, draw a partially folded protein with a long strand, then a beta strand, then an alpha helix, another beta strand and another alpha helix, so we can see that the shape of the whole protein begins to change once we establish some secondary structure.
  • Now, draw a second intermediate: three antiparallel beta strands, alpha helix, beta strand, alpha helix structure, but not quite folded. This second intermediate is more complete but not quite in the native state.

We can use an analogy that allows us to personify protein folding.

  • Draw a small group of friends: label them A through E.
    • The friends represent localized regions of our protein.
  • Draw a small group of stores: number them 1 through 5.
    • The stores represent folding states.
  • Indicate that friend A NEEDS to go to Store 1 whereas friend B NEEDS to go to Store 2.
  • So now encircle stores 1 through 4 and label them as part of Mall I.
  • Encircle stores 2 through 5 and label them as part of Mall II.

What Mall must the friends go to make everyone happy?

  • Show that they go to Mall I.
  • Then, within Mall I, friends C and E choose to go to store 3 and friend D chooses to go to store 4 because they didn't have strong preferences for which stores they would visit.
    • However, since friends A and B have already provided the framework for the shopping trip, they will choose stores based on whichever mall they are in.