Reading Mode Understanding why and how proteins fold continues to be a grand challenge in science. Left handed. Right handed. Left handed zwitterion. Right handed zwitterion. Right helix. NCI surface. Share this: Skype Print More Email. Ferrocene « Henry Rzepa says:.
April 17, at pm. Confirming the Fischer convention as a structurally correct representation of absolute configuration. March 13, at pm. The conformational preference of s-cis amides. If you were to mesure, the rise of a full turn is 5.
Alpha helices are nearly all right-handed. To see that this one is righthanded, hold your right hand with the thumb pointing up and the fingers loosely curled; trying to match the spiral of the helix, move slowly along the direction your thumb points and curl along the line of your fingers, as though tightening a screw. When that motion matches the backbone spiral if done with the right hand, then the helix is righthanded.
For a righthanded alpha-helix, it should be in the range of to degrees. Click on the next N and you will get the psi angle, which should be between and degrees. Continue down the helix backbone, getting omega near degrees , phi, psi, etc.
These helical phi,psi values are in the well-populated area in the lower left of the Ramachandran plot shown on the right. All Rights Reserved. The Alpha Helix An alpha helix is an element of secondary structure in which the amino acid chain is arranged in a spiral. In summary, the ideal alpha helix has the following properties: It completes one turn every 3. All residues participating in an alpha-helix have similar phi,psi angles. The understanding of the inaccessible and accessible Ramachandran regions is crucial for the understanding of the distribution of the empirically determined backbone conformations.
Oxygen atoms are red, nitrogen atoms are blue, and carbon atoms are cyan. In this study we distinguish between naturally occurring AA pairs which we name as transitions. By naming pairs as transitions we actually emphasize the importance of directionality when dealing with polypeptides. By observing Fig. The difference between the different transitions is in the mean value of the specific distribution. An interesting result presented in Fig. The fluctuations of the measured values are the result of measurement, thermal, and other sources of noise.
The symmetrical fluctuation pattern allows drawing the following conclusion: by focusing on some circular contour on Fig. The implication of this observation will be further discussed within the Heterogeneous transitions section.
The samples for c and d are marked according to the filtering level: green circles for Level 0, blue diamonds for Level 1, black asterisks for Level 2, and red stars for Level 3. The mean value of each of the naturally occurring transitions is displayed in Fig. The inset of Fig. Figure 2d presents the same transitions as in Fig. A clear migration towards regions of high alignment score is observed with increasing filtering level.
In Fig. Having the distributions of the naturally occurring transitions, we divide the analysis into two parts: 20 homogeneous same AAs and heterogeneous different AAs transitions analysis. The optimal conformation in this case is determined by van der Waals steric interactions. Single letter amino acid AA codes are placed on the mean calculated conformation.
Letters are colored according to the AA group: green for uncharged polar, red for acidic, blue for basic, black for hydrophobic, magenta for special.
The four filtering levels are of increasing levels of order, where Level 0 filtering is the less ordered and might even include non-helical conformations. Level 2 filtering includes a subset of conformations that must satisfy hydrogen bond HB alignment criterion with a weak threshold. Level 3 filtering is the most ordered filtering criterion with a strong HB alignment threshold. MALEK are the AAs with the highest helix propensity and are closely spread around the center of each filtering level, especially in filtering Level 0 and Level 1.
G and P are known for their low helix propensity and show a clear tendency to stay away from the overall mean helical behavior. The basic AA HIS, demonstrates the highest amount of residues per turn among all the basic AAs and the propensity to stay above the overall mean amount of residues per turn in all the filtering levels. To assert this premise we performed Conceptual Simulations 1 and 2 as described in the Methods section and depicted in Fig.
The results of the inflated virtual residue in Fig. Illustration of the four conceptual simulations and the resulting effects on the helical conformation. The bond length d was set to 1. As may be observed in Fig. The exceptions of THR in the lower filters might be explained by its polar nature. The results for Conceptual Simulation 2 that focus on the effect of increasing distance of the virtual residue, presented in Fig. On the atomic scale, charged particles may induce local effects similar to those applied by an electric field 26 , 27 , Thus, we tested the effect of an applied electric field as illustrated in Fig.
In the last simulation shown in Fig. To perform the comparison between a measured conformation to some predicted conformation we calculate the energetic cost of the predicted conformation relative to the measured conformation. The rationale behind such averaging is to give more weight to the more aligned helical structures higher filtering levels.
Table 1 presents the energy difference between the measured conformations to the predicted conformations for the heterogeneous transitions for filtering Level 1 tables for other levels may be found in Supporting Information. The conformations were predicted by calculating the arithmetic mean of the homogeneous conformations. The energy differences were calculated using Equation 2 , by defining the measured conformation as the minimum energy conformation. The asymmetry issue is enough to conclude that in most cases predicted conformations will differ from the real conformations.
Nevertheless, if energy differences are tolerable, the prediction of heterogeneous conformations may sometimes be useful especially when excluding PRO. If IPH was absolutely correct than we would expect that all the values presented in Table 1 would equal to 0. A possible explanation to the observed deviation between heterogeneous transitions to their homogeneous average is the interaction between residues — residues that do not interact chemically, sterically, or in any other way are expected to demonstrate stochastic conformational behavior, i.
Thus, we can conclude that the higher the energy difference between the heterogeneous conformation to the average homogeneous, the higher the interaction between the residues with the exception of PRO that may result in high deviations because of its limited degrees of freedom. The transformation was validated by comparing our observations with those found in the literature. In the 2 nd part we explain how we organized the PDB data from less ordered helical structures to more ordered helical structures and how the PDB redundancy issue was treated.
In the 3 rd part we adjust the base simulation model to conceptually demonstrate how the shape of the residue affects the helical conformation, and how the environment affects the helical shape by applying external electric field, and external mechanical forces. The base model consists of 30 AA-long polypeptide backbone without residues and was used as the basis for the calculations carried out in this study.
All the geometrical values for the base model were sampled directly from PDB. The values confirmed the proper function of the custom software designed for the sampling and analysis used in this study. No hydrogen atoms were included in the base model. Another example secondary structure proteins is the beta pleated sheet. The side chains point out o apart [2]. Jump to: navigation , search.
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