5 research outputs found
Using Kinetic Network Models To Probe Non-Native Salt-Bridge Effects on α‑Helix Folding
Salt–bridge interactions play
an important role in stabilizing
many protein structures, and have been shown to be designable features
for protein design. In this work, we study the effects of non-native
salt bridges on the folding of a soluble alanine-based peptide (Fs
peptide) using extensive all-atom molecular dynamics simulations performed
on the Folding@home distributed computing platform. Using Markov State
Models, we show how non-native salt-bridges affect the folding kinetics
of Fs peptide by perturbing specific conformational states. Furthermore,
we present methods for the automatic detection and analysis of such
states. These results provide insight into helix folding mechanisms
and useful information to guide simulation-based computational protein
design
A Maximum-Caliber Approach to Predicting Perturbed Folding Kinetics Due to Mutations
We
present a maximum-caliber method for inferring transition rates
of a Markov state model (MSM) with perturbed equilibrium populations
given estimates of state populations and rates for an unperturbed
MSM. It is similar in spirit to previous approaches, but given the
inclusion of prior information, it is more robust and simple to implement.
We examine its performance in simple biased diffusion models of kinetics
and then apply the method to predicting changes in folding rates for
several highly nontrivial protein folding systems for which non-native
interactions play a significant role, including (1) tryptophan variants
of the GB1 hairpin, (2) salt-bridge mutations of the Fs peptide helix,
and (3) MSMs built from ultralong folding trajectories of FiP35 and
GTT variants of the WW domain. In all cases, the method correctly
predicts changes in folding rates, suggesting the wide applicability
of maximum-caliber approaches to efficiently predict how mutations
perturb protein conformational dynamics
Surprisal Metrics for Quantifying Perturbed Conformational Dynamics in Markov State Models
Markov state models (MSMs), which
model conformational dynamics
as a network of transitions between metastable states, have been increasingly
used to model the thermodynamics and kinetics of biomolecules. In
considering perturbations to molecular dynamics induced by sequence
mutations, chemical modifications, or changes in external conditions,
it is important to assess how transition rates change, independent
of changes in metastable state definitions. Here, we present a surprisal
metric to quantify the difference in metastable state transitions
for two closely related MSMs, taking into account the statistical
uncertainty in observed transition counts. We show that the surprisal
is a relative entropy metric closely related to the Jensen–Shannon
divergence between two MSMs, which can be used to identify conformational
states most affected by perturbations. As examples, we apply the surprisal
metric to a two-dimensional lattice model of a protein hairpin with
mutations to hydrophobic residues, all-atom simulations of the Fs
peptide α-helix with a salt-bridge mutation, and a comparison
of protein G β-hairpin with its trpzip4 variant. Moreover, we
show that surprisal-based adaptive sampling is an efficient strategy
to reduce the statistical uncertainty in the Jensen–Shannon
divergence, which could be a useful strategy for molecular simulation-based <i>ab initio</i> design
Insights into Peptoid Helix Folding Cooperativity from an Improved Backbone Potential
Peptoids (N-substituted oligoglycines)
are biomimetic polymers
that can fold into a variety of unique structural scaffolds. Peptoid
helices, which result from the incorporation of bulky chiral side
chains, are a key peptoid structural motif whose formation has not
yet been accurately modeled in molecular simulations. Here, we report
that a simple modification of the backbone φ-angle potential
in GAFF is able to produce well-folded <i>cis</i>-amide
helices of (<i>S</i>)-<i>N</i>-(1-phenylÂethyl)Âglycine
(Nspe), consistent with experiment. We validate our results against
both QM calculations and NMR experiments. For this latter task, we
make quantitative comparisons to sparse NOE data using the Bayesian
Inference of Conformational Populations (BICePs) algorithm, a method
we have recently developed for this purpose. We then performed extensive
REMD simulations of Nspe oligomers as a function of chain length and
temperature to probe the molecular forces driving cooperative helix
formation. Analysis of simulation data by Lifson–Roig helix–coil
theory show that the modified potential predicts much more cooperative
folding for Nspe helices. Unlike peptides, per-residue entropy changes
for helix nucleation and extension are mostly positive, suggesting
that steric bulk provides the main driving force for folding. We expect
these results to inform future work aimed at predicting and designing
peptoid peptidomimetics and tertiary assemblies of peptoid helices
Diverted Total Synthesis of Carolacton-Inspired Analogs Yields Three Distinct Phenotypes in <i>Streptococcus mutans</i> Biofilms
The
oral microbiome is a dynamic environment inhabited by both commensals
and pathogens. Among these is Streptococcus mutans, the causative agent of dental caries, the most prevalent childhood
disease. Carolacton has remarkably specific activity against S. mutans, causing acid-mediated cell death during
biofilm formation; however, its complex structure limits its utility.
Herein, we report the diverted total synthesis and biological evaluation
of a rationally designed library of simplified analogs that unveiled
three unique biofilm phenotypes further validating the role of natural
product synthesis in the discovery of new biological phenomena