Controls exerted by the Aib residue: Helix formation and helix reversal This article is a US Government work and, as such, is in the public domain in the United States of America.

Abstract

Background Digital time‐lapse microscopy using Nomarski‐DIC requires that an autofocusing system adapt to changes in cell shape, size, and position while contending with drift, noise, and hysteresis in the microscope and imager. We have designed and implemented an autofocusing system that tracks subjects under dynamic conditions and maintains focus within a threshold of discriminability. Methods With the use of proven and novel algorithms for autofocusing in Nomarski, we performed “virtual” experiments on recorded image stacks to simulate drift and sudden displacements and test the search algorithm response. Results We found that combining a simple [1, −1] contrast function with an adaptive “warmer–colder” focusing algorithm yields a reasonable compromise between focusing precision and noise tolerance. This method was implemented to record growth kinetics of yeast cells in single and multiple fields of view over several hours. Conclusions We have implemented a robust digital autofocus that maintains focus on optically complex samples imaged at high resolution. The tolerance of this system of drift and vibration suggests that it is a practical system for time‐lapse imaging in many biological applications. Cytometry 49:159–169, 2002. © 2002 Wiley‐Liss, Inc.

The R.E.D. tools: advances in RESP and ESP charge derivation and force field library building

“…Similar conclusions were obtained for alpha-aminoisobutyric acid in the R.E.D. Tools tutorial 64, 92, 93…”

“…The R.E.D. Tools tutorial describes charge derivation and force field library building for the molecular fragments of alpha-aminoisobutyric acid 64, 92, 93. This second example is also available in R.E.DD.B.…”

Simulated Evolution of Emergent Chiral Structures in Polyalanine

“…The nature of helix reversals involving a change in chirality has been studied in model peptides. 78,79 A small number of examples of helix-reversals are found in natural proteins by searching the Protein Data Bank for contiguous R L stretches of residues using WHATIF. 80 The structure of alanine racemase 81 contains a mirror-Schellman C-capping interaction which then leads into a right-handed R-helix ( Figure 11).…”

Crystal structure of a hydrophobic 19-residue peptide helix containing three centrally located d amino acids

“…For the crystal with a formula containing (4,22), for example, where positive and values for ␣-helices consisting of L residues are ''partially allowed'' and, by inference, negative and values for D residues in ␣-helices. Experimental observations of the incorporation of single D residues in righthanded helical peptides or, conversely, L residues into lefthanded helical segments are available (23,24). A double D residue segment in a 13-residue right-handed helix has been reported in crystals (25).…”