An official website of the United States government
Deep learning research, from ResNet to AlphaFold2, convincingly shows that deep learning can predict the native conformation of a given protein sequence with high accu- racy. Accounting for the plasticity of protein molecules remains challenging, and powerful algorithms are needed to sample the conformation space of a given amino-acid sequence. In the complex and high-dimensional energy surface that accompanies this space, it is critical to explore a broad range of areas. In this paper, we present a novel evolutionary algorithm that guides its optimization process with a memory of the explored conformation space, so that it can avoid searching already explored regions and search in the unexplored regions. The algorithm periodically consults an evolving map that stores already sampled non- redundant conformations to enhance exploration during selection. Evaluation on diverse datasets shows superior performance of the algorithm over the state-of-the-art algorithms.
more »
« less
Single-Conformation Spectroscopy of Capped Aminoisobutyric Acid Dipeptides: The Effect of C-Terminal Cap Chromophores on Conformation
- Award ID(s):
- 1764148
- PAR ID:
- 10099395
- Date Published:
- Journal Name:
- The Journal of Physical Chemistry A
- Volume:
- 123
- Issue:
- 19
- ISSN:
- 1089-5639
- Page Range / eLocation ID:
- 4178 to 4187
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
More Like this
-
-
Small angle neutron scattering was used to measure single chain radii of gyration of end-linked polymer gels before and after cross-linking to calculate the prestrain, which is the ratio of the average chain size in a cross-linked network to that of a free chain in solution. The prestrain increased from 1.06 ± 0.01 to 1.16 ± 0.02 as gel synthesis concentration decreased near the overlap concentration, indicating that the chains are slightly more stretched in the network than in solution. Dilute gels with higher loop fractions were found to be spatially homogeneous. Form factor and volumetric scaling analyses independently confirmed that elastic strands stretch by 2–23% from Gaussian conformations to create a space-spanning network, with increased stretching as network synthesis concentration decreases. Prestrain measurements reported here serve as a point of reference for network theories that rely on this parameter for the calculation of mechanical properties.more » « less
-
The 26S proteasome is the macromolecular machine responsible for the bulk of protein degradation in eukaryotic cells. As it degrades a ubiquitinated protein, the proteasome transitions from a substrate-accepting conformation (s1) to a set of substrate-processing conformations (s3 like), each stabilized by different intramolecular contacts. Tools to study these conformational changes remain limited, and although several interactions have been proposed to be important for stabilizing the proteasome’s various conformations, it has been difficult to test these directly under equilibrium conditions. Here, we describe a conformationally sensitive Förster resonance energy transfer assay, in which fluorescent proteins are fused to Sem1 and Rpn6, which are nearer each other in substrate-processing conformations than in the substrate-accepting conformation. Using this assay, we find that two sets of interactions, one involving Rpn5 and another involving Rpn2, are both important for stabilizing substrate-processing conformations. Mutations that disrupt these interactions both destabilize substrate-processing conformations relative to the substrate-accepting conformation and diminish the proteasome’s ability to successfully unfold and degrade hard-to-unfold substrates, providing a link between the proteasome’s conformational state and its unfolding ability.more » « less
- Free Publicly Accessible Full Text
-
Accepted Manuscript1.0
- Journal Article:
- https://doi.org/10.1021/acs.jpca.9b01698
