Peptide calculations

No. Tryptic peptides Calculated mass Determined mass Sequence... 

The electrophoretic mobility of a peptide, determined relative to the EOF or to a standard, can be used for identification. Because at pH 2.5 the EOF is virtually suppressed and difficult to determine experimentally, (26) the relative electrophoretic mobilities of the nine peptides were determined using an internal standard, Dynorphin A fragment 1-13. The apparent mobility (p pp) of the reference peptide Dynorphin was found to be 3.05 x 10" ( Dyn== L x L/1 x V Ld=40 cm, Lt=47 cm, t=274.26 sec, V= 22500 Volts). For each peptide the apparent electrophoretic mobility was then determined experimentally and an electrophoretic mobility relative to the reference peptide calculated ( Tt = l app Poyn ) These values are given in Table 1. 

Hermans, J., Yun, R. H., Anderson, A. G. Precision of free-energies calculated by molecular dynamics simulations of peptides in solution. J. Comp. Chem. 13 (1992) 429-442... 

Conformational free energy simulations are being widely used in modeling of complex molecular systems [1]. Recent examples of applications include study of torsions in n-butane [2] and peptide sidechains [3, 4], as well as aggregation of methane [5] and a helix bundle protein in water [6]. Calculating free energy differences between molecular states is valuable because they are observable thermodynamic quantities, related to equilibrium constants and... 

The second application of the CFTI approach described here involves calculations of the free energy differences between conformers of the linear form of the opioid pentapeptide DPDPE in aqueous solution [9, 10]. DPDPE (Tyr-D-Pen-Gly-Phe-D-Pen, where D-Pen is the D isomer of /3,/3-dimethylcysteine) and other opioids are an interesting class of biologically active peptides which exhibit a strong correlation between conformation and affinity and selectivity for different receptors. The cyclic form of DPDPE contains a disulfide bond constraint, and is a highly specific S opioid [llj. Our simulations provide information on the cost of pre-organizing the linear peptide from its stable solution structure to a cyclic-like precursor for disulfide bond formation. Such... 

N is the number of point charges within the molecule and Sq is the dielectric permittivity of the vacuum. This form is used especially in force fields like AMBER and CHARMM for proteins. As already mentioned, Coulombic 1,4-non-bonded interactions interfere with 1,4-torsional potentials and are therefore scaled (e.g., by 1 1.2 in AMBER). Please be aware that Coulombic interactions, unlike the bonded contributions to the PEF presented above, are not limited to a single molecule. If the system under consideration contains more than one molecule (like a peptide in a box of water), non-bonded interactions have to be calculated between the molecules, too. This principle also holds for the non-bonded van der Waals interactions, which are discussed in Section 7.2.3.6. 

In general, the first step in virtual screening is the filtering by the application of Lipinski s Rule of Five [20]. Lipinski s work was based on the results of profiling the calculated physical property data in a set of 2245 compounds chosen from the World Drug Index. Polymers, peptides, quaternary ammonium, and phosphates were removed from this data set. Statistical analysis of this data set showed that approximately 90% of the remaining compounds had ... 

Hagler A T and S Lifson 1974. Energy Functions for Peptides and Proteins. II. The Amide Hydrogen Bond and Calculation of Amide Crystal Properties. Journal of the American Chemical Society 96 5327-5335. 

An example is shown in Figure 7 for the case of the coil-to-helix transition. The endpoints of the calculation are an unstructured coil Tr and helix rp. Intermediate peptide structures correspond to transition intermediates defining the pathway l(r). 

R Abagyan, M Totrov. Biased probability Monte Carlo conformational searches and electrostatic calculations for peptides and proteins. I Mol Biol 235 983-1002, 1994. 

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