Thermodynamics of semiconductor-binding peptides in solution

Since we are interested in rather specific problems, a mesoscopic coarse-grained model of the type we employed successfully in the past chapters is not sufficient in the present context, because secondary stmctures are of relevance here. For this purpose, a simplified efficient all-atom modeP [223,271,272] was used to obtain the results to be discussed in the following [343]. 

As before, thermodynamic quantities are obtained by canonical statistics of the simulation data. Each conformation X is uniquely defined by the set of degrees of freedom, i.e., the set of dihedral backbone and side-chain angles of each amino acid j=, . M  

Temperature dependence of the specific heat C i in units of the gas constant / for the sequences S1-S4. Also shown are typicai iow-energy conformations of the peptides. Note the changed iocation of proiine (P) in sequence S3, if compared to the other sequences, and the different type of its secondary structure. After [343], 

In order to quantify the tendencies of these peptides to form secondary stmctures, it is useful to investigate the average a-helical and -strand content as a function of temperature. We define a residue as or-helical if its Ramachandran angles p and satisfy (f) e (—90°,—30°) and e (—77°,—17°), and (n ) denotes the fraction of the 10 iimer residues that are a-helical. Similarly, np) is the average )3-strand content and it is defined as the fraction of the 10 inner residues with Ramachandran angles satisfying 4 6 (-150°, -90°) and 6 (90°, 150°). 

A closer inspection of the low-energy stmctures shown in Fig. 14.4 reveals that in the hehcal stmctures the a-helix does not span the entire chain, but rather the region between residues 3 to 12. The N-terminal section of the sequence is not or-helical, as there is a 

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