19 research outputs found
Evolved Minimal Frustration in Multifunctional Biomolecules
Protein folding is
often viewed in terms of a funneled potential
or free energy landscape. A variety of experiments now indicate the
existence of multifunnel landscapes, associated with multifunctional
biomolecules. Here, we present evidence that these systems have evolved
to exhibit the minimal number of funnels required to fulfill their
cellular functions, suggesting an extension to the principle of minimum
frustration. We find that minimal disruptive mutations result in additional
funnels, and the associated structural ensembles become more diverse.
The same trends are observed in an atomic cluster. These observations
suggest guidelines for rational design of engineered multifunctional
biomolecules
Energy Landscapes for the Aggregation of Aβ<sub>17–42</sub>
The aggregation of the Aβ peptide
(Aβ<sub>1–42</sub>) to form fibrils is a key feature
of Alzheimer’s disease.
The mechanism is thought to be a nucleation stage followed by an elongation
process. The elongation stage involves the consecutive addition of
monomers to one end of the growing fibril. The aggregation process
proceeds in a stop-and-go fashion and may involve off-pathway aggregates,
complicating experimental and computational studies. Here we present
exploration of a well-defined region in the free and potential energy
landscapes for the Aβ<sub>17–42</sub> pentamer. We find
that the ideal aggregation process agrees with the previously reported
dock-lock mechanism. We also analyze a large number of additional
stable structures located on the multifunnel energy landscape, which
constitute kinetic traps. The key contributors to the formation of
such traps are misaligned strong interactions, for example the stacking
of F19 and F20, as well as entropic contributions. Our results suggest
that folding templates for aggregation are a necessity and that aggregation
studies could employ such species to obtain a more detailed description
of the process
Kinetics of Molecular Diffusion and Self-Assembly: Glycine on Cu{110}
Nanofabrication and
the growth of self-assembled monolayers (SAM) of organic molecules
are increasingly important in various industries, including microelectronics
and health care. Glycine adsorbed on Cu{110} provides a good model
with a rich phenomenological space to explore and understand the self-assembly
of more complex amino acids. Our focus is on (a) the dynamics exhibited
by glycine molecules already adsorbed on Cu{110} when diffusing on
the metal surface and (b) the chemical kinetics of how these molecules
form clusters, networks, and islands. The stochastic discrete event
algorithm we employ can be viewed as a multiscale approach, based
on density functional energies and transition barriers. The method
extends from the femtosecond time-scale of molecular rotations to
the nano- and microsecond range of molecular self-assembly. Hydrogen-bonds
and van der Waals forces play a crucial role in pattern formation.
Investigations of chemical kinetics show that enantiopure, homochiral
islands are an intermediate step during the formation process of larger
stable racemic, heterochiral islands, especially when two islands
merge. At lower temperature, defects stabilize mainly homochiral clusters
and prevent the molecules from synchronizing their footprint orientation,
in contrast to higher temperature. On the way, we solve the long-standing
puzzle of how the pseudocentered (3 × 2) enantiopure clusters
can have glide plane symmetry. We end with a comparison to similar
amino acids, such as alanine and proline. The results provide insight
into mechanisms for fine-tuning the self-organization of organic molecules
on metal surfaces
Evolution of the Potential Energy Landscape with Static Pulling Force for Two Model Proteins
The energy landscape is analyzed for off-lattice bead
models of protein L and protein G as a function of a static pulling
force. Two different pairs of attachment points (pulling directions)
are compared in each case, namely, residues 1/56 and 10/32. For the
terminal residue pulling direction 1/56, the distinct global minimum
structures are all extended, aside from the compact geometry that
correlates with zero force. The helical turns finally disappear at
the highest pulling forces considered. For the 10/32 pulling direction,
the changes are more complicated, with a variety of competing arrangements
for beads outside the region where the force is directly applied.
These alternatives produce frustrated energy landscapes, with low-lying
minima separated by high barriers. The calculated folding pathways
in the absence of force are in good agreement with previous work.
The N-terminal hairpin folds first for protein L and the C-terminal
hairpin for protein G, which exhibits an intermediate. However, for
a relatively low static force, where the global minimum retains its
structure, the folding mechanisms change, sometimes dramatically,
depending on the protein and the attachment points. The scaling relations
predicted by catastrophe theory are found to hold in the limit of
short path lengths
Clusters of Coarse-Grained Water Molecules
Global optimization for molecular
clusters can be significantly
more difficult than for atomic clusters because of the coupling between
orientational and translational degrees of freedom. A coarse-grained
representation of the potential can reduce the complexity of this
problem, while retaining the essential features of the intermolecular
interactions. In this study, we use a basin-hopping algorithm to locate
putative global minima for clusters of coarse-grained water molecules
modeled using a monatomic water potential for cluster sizes 3 ≤ <i>N</i> ≤ 55. We characterize
these structures and identify structural trends using ideas from graph
theory. The agreement with atomistic results and experiment is rather
patchy, which we attribute to the tetrahedral bias in the three-body
potential that results in too few nearest neighbor contacts and premature
emergence of bulk-like structure. In spite of this issue, the results
offer further useful insight into the relationship between the structure
of clusters and bulk phases, and the mathematical form of a widely
used model potential
Conformational Energy Landscape of the Ritonavir Molecule
Conformational polymorphism of ritonavir,
a well-known pharmaceutical
drug, is intricately linked to its efficacy in the treatment of acquired
immunodeficiency syndrome (AIDS). Polymorphic transition from the
crystalline form I to form II leads to the loss of bioactivity. The
constituent ritonavir molecules adopt a trans configuration about
the carbamate torsion angle in the form I crystal, and a cis configuration
in the form II crystal. Investigating the energetics and mechanistic
features of conformational transitions at the single molecule level
is a key step toward decoding the complex features of the solid state
polymorphism. In this work, we employ the energy landscape framework
to investigate the conformational transitions of an isolated ritonavir
molecule. The landscape is explored using discrete path sampling (DPS)
and visualized in terms of disconnectivity graphs. We identify two
distinct funnels corresponding to the two molecular forms that are
identified by crystallography. The two regions can be reliably distinguished
using the carbamate torsion angle, and the corresponding interconversion
rates are predicted to follow Arrhenius behavior. The results provide
mechanistic insight into pathways for cis ↔ trans interconversion
at the molecular level and may also help in elucidating the polymorphic
transitions in the crystal state
Energy Landscapes, Folding Mechanisms, and Kinetics of RNA Tetraloop Hairpins
RNA
hairpins play a pivotal role in a diverse range of cellular
functions, and are integral components of ribozymes, mRNA, and riboswitches.
However, the mechanistic and kinetic details of RNA hairpin folding,
which are key determinants of most of its biological functions, are
poorly understood. In this work, we use the discrete path sampling
(DPS) approach to explore the energy landscapes of two RNA tetraloop
hairpins, and provide insights into their folding mechanisms and kinetics
in atomistic detail. Our results show that the potential energy landscapes
have a distinct funnel-like bias toward the folded hairpin state,
consistent with efficient structure-seeking properties. Mechanistic
and kinetic information is analyzed in terms of kinetic transition
networks. We find microsecond folding times, consistent with temperature
jump experiments, for hairpin folding initiated from relatively compact
unfolded states. This process is essentially driven by an initial
collapse, followed by rapid zippering of the helix stem in the final
phase. Much lower folding rates are predicted when the folding is
initiated from extended chains, which undergo longer excursions on
the energy landscape before nucleation events can occur. Our work
therefore explains recent experiments and coarse-grained simulations,
where the folding kinetics exhibit precisely this dependency on the
initial conditions
A Local Rigid Body Framework for Global Optimization of Biomolecules
We present a local rigid body framework for simulations
of biomolecules.
In this framework, arbritrary sets of atoms may be treated as rigid
bodies. Such groupings reduce the number of degrees of freedom, which
can result in a significant reduction of computational time. As benchmarks,
we consider global optimization for the tryptophan zipper (trpzip
1, 1LE0; using the CHARMM force field) and chignolin (1UAO; using
the AMBER force field). We use a basin-hopping algorithm to find the
global minima and compute the mean first encounter time from random
starting configurations with and without the local rigid body framework.
Minimal groupings are used, where only peptide bonds, termini, and
side chain rings are considered rigid. Finding the global minimum
is 4.2 and 2.5 times faster, respectively, for trpzip 1 and chignolin,
within the local rigid body framework. We further compare <i>O</i>(10<sup>5</sup>) low-lying local minima to the fully relaxed
unconstrained representation for trpzip 1 at different levels of rigidification.
The resulting Pearson correlation coefficients, and thus the apparent
intrinsic rigidity of the various groups, appear in the following
order: side chain rings > termini > trigonal planar centers
≥
peptide bonds ≫ side chains. This approach is likely to be
even more beneficial for structure prediction in larger biomolecules
What Makes Telomeres Unique?
Telomeres
are repetitive nucleotide sequences, which are essential
for protecting the termini of chromosomes. Thousands of such repetitions
are necessary to maintain the stability of the whole chromosome. Several
similar repeated telomeric sequences have been found in different
species, but why has nature chosen them? What features do telomeres
have in common? In this article, we study the physical properties
of human-like (TTAGGG), plant (TTTAGG), insect (TTAGG), and Candida guilermondi (GGTGTAC) telomeres in comparison
with seven control, nontelomeric sequences. We used steered molecular
dynamics with the nucleic acid united residue (NARES) coarse-grained
force field, which we compared with the all-atom AMBER14 force field
and experimental data. Our results reveal important features in all
of the telomeric sequences, including their exceptionally high mechanical
resistance and stability to untangling and stretching, compared to
those of nontelomeric sequences. We find that the additional stability
of the telomeres comes from their ability to form triplex structures
and wrap around loose chains of linear DNA by regrabbing the chain.
We find that, with slower pulling speed, regrabbing and triplex formation
is more frequent. We also found that some of the sequences can form
triplexes experimentally, such as TTTTTCCCC, and can mimic telomeric
properties
A Local Rigid Body Framework for Global Optimization of Biomolecules
We present a local rigid body framework for simulations
of biomolecules.
In this framework, arbritrary sets of atoms may be treated as rigid
bodies. Such groupings reduce the number of degrees of freedom, which
can result in a significant reduction of computational time. As benchmarks,
we consider global optimization for the tryptophan zipper (trpzip
1, 1LE0; using the CHARMM force field) and chignolin (1UAO; using
the AMBER force field). We use a basin-hopping algorithm to find the
global minima and compute the mean first encounter time from random
starting configurations with and without the local rigid body framework.
Minimal groupings are used, where only peptide bonds, termini, and
side chain rings are considered rigid. Finding the global minimum
is 4.2 and 2.5 times faster, respectively, for trpzip 1 and chignolin,
within the local rigid body framework. We further compare <i>O</i>(10<sup>5</sup>) low-lying local minima to the fully relaxed
unconstrained representation for trpzip 1 at different levels of rigidification.
The resulting Pearson correlation coefficients, and thus the apparent
intrinsic rigidity of the various groups, appear in the following
order: side chain rings > termini > trigonal planar centers
≥
peptide bonds ≫ side chains. This approach is likely to be
even more beneficial for structure prediction in larger biomolecules