From Protein Structure to Function with Bioinformatics.pdf

9 Protein Dynamics: From Structure to Function 237while the AMPbd, comprising helices α 2and α 3, assumes a half-open conformation.In doing so, α 2bends towards helix α 4of the CORE by 15 degrees withrespect to α 3. This opening of the AMP binding cleft could facilitate an efficientrelease of the formed product. For the second phase, a partially correlated openingof the LID domain together with the AMPbd is observed. Compared to coarsegrainedapproaches, all-atom TEE-REX simulations allow detailed analyses ofinter-residue interactions. For ADK, a highly stable salt bridge between residuesAsp118 and Lys136 forms during phase one, connecting the LID and COREdomains. Estimating the total non-bonded interaction between LID and CORE, itwas found that this salt-bridge contributes substantially to the interaction of thetwo domains. Breaking this salt bridge via mutation, e.g. Asp118Ala, should thusdecrease the stability of the open state. From a comparison of fourteen ProteinData Bank (PDB) structures from yeast, maize, human and bacterial ADK, elevenstructures feature such a salt-bridge motif at the LID-CORE interface.Alternative transition pathways seem possible, however an analysis of all TEE-REXsimulations suggests a high free energy barrier obstructing the full opening of theAMPbd after the LID has opened. Together with the observed larger fluctuations in secondarystructure elements, indicating high internal strain energies, the enthalpic penaltyalong this route possibly renders it unfavourable as a transition pathway of ADK.9.4 Methods for Functional Mode PredictionAs discussed in the previous section, functional modes in proteins are usually thosewith the lowest frequencies. Apart from molecular dynamics based techniques,there are several alternative methods that focus on the prediction of these essentialdegrees of freedom based on a single input structure.9.4.1 Normal Mode AnalysisNormal mode analysis (NMA) is one of the major simulation techniques used toprobe the large-scale, shape-changing motions in biological molecules (Gō et al.1983; Brooks and Karplus 1983; Levitt et al. 1983). These motions are often coupledto function and a consequence of binding other molecules like substrates,drugs or other proteins. In NMA studies it is implicitly assumed that the normalmodes with the largest fluctuation (lowest frequency modes) are the ones that arefunctionally relevant, because, like function they exist by evolutionary “design”rather than by chance.Normal mode analysis is a harmonic analysis. The underlying assumption is thatthe conformational energy surface can be approximated by a parabola, despite thefact that functional modes at physiological temperatures are highly anharmonic