12 research outputs found
Nontrivial Behavior of Water in the Vicinity and Inside Lipid Bilayers As Probed by Molecular Dynamics Simulations
The atomic-scale diffusion of water in the presence of several lipid bilayers mimicking biomembranes is characterized <i>via</i> unconstrained molecular dynamics (MD) simulations. Although the overall water dynamics corresponds well to literature data, namely, the efficient braking near polar head groups of lipids, a number of interesting and biologically relevant details observed in this work have not been sufficiently discussed so far; for instance, the fact that waters âsenseâ the membrane unexpectedly early, before water density begins to decrease. In this âtransitional zoneâ the velocity distributions of water and their H-bonding patterns deviate from those in the bulk solution. The boundaries of this zone are well preserved even despite the local (<1 nm size) perturbation of the lipid bilayer, thus indicating a decoupling of the surface and bulk dynamics of water. This is in excellent agreement with recent experimental data. Near the membrane surface, water movement becomes anisotropic, that is, solvent molecules preferentially move outward the bilayer. Deep in the membrane interior, the velocities can even exceed those in the bulk solvent and undergo large-scale fluctuations. The analysis of MD trajectories of individual waters in the middle part of the acyl chain region of lipids reveals a number of interesting rare phenomena, such as the fast (<i>ca.</i> 50 ps) breakthrough across the membrane or long-time (up to 750 ps) âroamingâ between lipid leaflets. The analysis of these events was accomplished to delineate the mechanisms of spontaneous water permeation inside the hydrophobic membrane core. It was shown that such nontrivial dynamics of water in an âalienâ environment is driven by the dynamic heterogeneities of the local bilayer structure and the formation of transient atomic-scale âdefectsâ in it. The picture observed in lipid bilayers is drastically different from that in a primitive membrane mimic, a hydrated cyclohexane slab. The possible biological impact of such phenomena in equilibrated lipid bilayers is discussed
Cardiotoxins: Functional Role of Local Conformational Changes
Cardiotoxins
(CTs) from snake venoms are a family of homologous
highly basic proteins that have extended hydrophobic patterns on their
molecular surfaces. CTs are folded into three β-structured loops
stabilized by four disulfide bridges. Being well-structured in aqueous
solution, most of these proteins are membrane-active, although the
exact molecular mechanisms of CT-induced cell damage are still poorly
understood. To elucidate the structureâfunction relationships
in CTs, a detailed knowledge of their spatial organization and local
conformational dynamics is required. Protein domain motions can be
either derived from a set of experimental structures or generated
via molecular dynamics (MD). At the same time, traditional clustering
algorithms in the Cartesian coordinate space often fail to properly
take into account the local large-scale dihedral angle transitions
that occur in MD simulations. This is because such perturbations are
usually offset by changes in the neighboring dihedrals, thus preserving
the overall protein fold. States with a âlocally perturbedâ
backbone were found in experimental 3D models of some globular proteins
and have been shown to be functionally meaningful. In this work, the
possibility of large-scale dihedral angle transitions in the course
of long-term MD in explicit water was explored for three CTs with
different membrane activities: CT 1, 2 (Naja oxiana) and CT A3 (Naja atra). Analysis
of the MD-derived distributions of backbone torsion angles revealed
several important common and specific features in the structural/dynamic
behavior of these proteins. First, large-amplitude transitions were
detected in some residues located in the functionally important loop
I region. The K5/L6 pair of residues was found to induce a perturbation
of the hydrophobic patterns on the molecular surface of CTsî¸reversible
breaking of a large nonpolar zone (âbottomâ) into two
smaller ones and their subsequent association. Second, the characteristic
sizes of these patterns perfectly coincided with the dimensions of
the nonpolar zones on the surfaces of model two-component (zwitterionic/anionic)
membranes. Taken together with experimental data on the CT-induced
leakage of fluorescent dye from such membranes, these results allowed
us to formulate a two-stage mechanism of CTâmembrane binding.
The principal finding of this study is that even local conformational
dynamics of CTs can seriously affect their functional activity via
a tuning of the membrane binding site â specific âhot
spotsâ (like the K5/L6 pair) in the protein structure
Deciphering Fine Molecular Details of Proteinsâ Structure and Function with a <i>Protein Surface Topography (PST)</i> Method
Molecular
surfaces are the key players in biomolecular recognition
and interactions. Nowadays, it is trivial to visualize a molecular
surface and surface-distributed properties in three-dimensional space.
However, such a representation trends to be biased and ambiguous in
case of thorough analysis. We present a new method to create 2D spherical
projection maps of entire protein surfaces and manipulate with themî¸protein
surface topography (PST). It permits visualization and thoughtful
analysis of surface properties. PST helps to easily portray conformational
transitions, analyze proteinsâ properties and their dynamic
behavior, improve docking performance, and reveal common patterns
and dissimilarities in molecular surfaces of related bioactive peptides.
This paper describes basic usage of PST with an example of small G-proteins
conformational transitions, mapping of caspase-1 intersubunit interface,
and intrinsic âcomplementarityâ in the conotoxinâacetylcholine
binding protein complex. We suggest that PST is a beneficial approach
for structureâfunction studies of bioactive peptides and small
proteins
Multistate Organization of Transmembrane Helical Protein Dimers Governed by the Host Membrane
Association of transmembrane (TM) helices taking place
in the cell
membrane has an important contribution to the biological function
of bitopic proteins, among which receptor tyrosine kinases represent
a typical example and a potent target for medical applications. Since
this process depends on a complex interplay of different factors (primary
structures of TM domains and juxtamembrane regions, composition and
phase of the local membrane environment, etc.), it is still far from
being fully understood. Here, we present a computational modeling
framework, which we have applied to systematically analyze dimerization
of 18 TM helical homo- and heterodimers of different bitopic proteins,
including the family of epidermal growth factor receptors (ErbBs).
For this purpose, we have developed a novel surface-based modeling
approach, which not only is able to predict particular conformations
of TM dimers in good agreement with experiment but also provides screening
of their conformational heterogeneity. Using all-atom molecular dynamics
simulations of several of the predicted dimers in different model
membranes, we have elucidated a putative role of the environment in
selection of particular conformations. Simulation results clearly
show that each particular bilayer preferentially stabilizes one of
possible dimer conformations, and that the energy gain depends on
the interplay between structural properties of the protein and the
membrane. Moreover, the character of protein-driven perturbations
of the bilayer is reflected in the contribution of a particular membrane
to the free energy gain. We have found that the approximated dimerization
strength for ErbBs family can be related to their oncogenic ability
Adaptable Lipid Matrix Promotes ProteinâProtein Association in Membranes
The cell membrane is âstuffedâ
with proteins, whose
transmembrane (TM) helical domains spontaneously associate to form
functionally active complexes. For a number of membrane receptors,
a modulation of TM domainsâ oligomerization has been shown
to contribute to the development of severe pathological states, thus
calling for detailed studies of the atomistic aspects of the process.
Despite considerable progress achieved so far, several crucial questions
still remain: How do the helices recognize each other in the membrane?
What is the driving force of their association? Here, we assess the
dimerization free energy of TM helices along with a careful consideration
of the interplay between the structure and dynamics of protein and
lipids using atomistic molecular dynamics simulations in the hydrated
lipid bilayer for three different model systems â TM fragments
of glycophorin A, polyalanine and polyleucine peptides. We observe
that the membrane driven association of TM helices exhibits a prominent
entropic character, which depends on the peptide sequence. Thus, a
single TM peptide of a given composition induces strong and characteristic
perturbations in the hydrophobic core of the bilayer, which may facilitate
the initial âcommunicationâ between TM helices even
at the distances of 20â30 Ă
. Upon tight helixâhelix
association, the immobilized lipids accommodate near the peripheral
surfaces of the dimer, thus disturbing the packing of the surrounding.
The dimerization free energy of the modeled peptides corresponds to
the strength of their interactions with lipids inside the membrane
being the lowest for glycophorin A and similarly higher for both homopolymers.
We propose that the ability to accommodate lipid tails determines
the dimerization strength of TM peptides and that the lipid matrix
directly governs their association
Kalium database
<p>Complete
copy of Kalium 2.0 database in the CSV format, six .csv files:<br></p>
<p>Activity.csv</p>
<p>Organism.csv</p>
<p>OrganismClass.csv</p>
<p>TargetCannel.csv</p>
<p>Toxin.csv</p>
<p>ToxinFamily.csv</p>
<p> </p>
<p>export_all_tc.csv
contains data in the format of concatenated Ligand cards presented in an
expanded manner. This looks similar to the export file, which can be downloaded
from Kalium by users, but contains additional information for each entry.</p>
<p> </p>
<p>In export_all_act.csv
each string describes the activity of every Kalium entry against a particular
target (potassium channel isoform).</p
Role of Dimerization Efficiency of Transmembrane Domains in Activation of Fibroblast Growth Factor Receptor 3
Mutations
in transmembrane (TM) domains of receptor tyrosine kinases
are shown to cause a number of inherited diseases and cancer development.
Here, we use a combined molecular modeling approach to understand
molecular mechanism of effect of G380R and A391E mutations on dimerization
of TM domains of human fibroblast growth factor receptor 3 (FGFR3).
According to results of Monte Carlo conformational search in the implicit
membrane and further molecular dynamics simulations, TM dimer of this
receptor is able to form a number of various conformations, which
differ significantly by the free energy of association in a full-atom
model bilayer. The aforementioned mutations affect dimerization efficiency
of TM segments and lead to repopulation of conformational ensemble
for the dimer. Particularly, both mutations do not change the dimerization
free energy of the predominant (putative ânon-activeâ)
symmetric conformation of TM dimer, while affect dimerization efficiency
of its asymmetric (âintermediateâ) and alternative symmetric
(putative âactiveâ) models. Results of our simulations
provide novel atomistic prospective of the role of G380 and A391E
mutations in dimerization of TM domains of FGFR3 and their consecutive
contributions to the activation pathway of the receptor
Dissecting structural basis of the unique substrate selectivity of human enteropeptidase catalytic subunit
<div><p>Enteropeptidase is a key enzyme in the digestion system of higher animals. It initiates enzymatic cascade cleaving trypsinogen activation peptide after a unique sequence DDDDK. Recently, we have found specific activity of human enteropeptidase catalytic subunit (L-HEP) being significantly higher than that of its bovine ortholog (L-BEP). Moreover, we have discovered that L-HEP hydrolyzed several nonspecific peptidic substrates. In this work, we aimed to further characterize species-specific enteropeptidase activities and to reveal their structural basis. First, we compared hydrolysis of peptides and proteins lacking DDDDK sequence by L-HEP and L-BEP. In each case human enzyme was more efficient, with the highest hydrolysis rate observed for substrates with a large hydrophobic residue in P2-position. Computer modeling suggested enzyme exosite residues 96 (Arg in L-HEP, Lys in L-BEP) and 219 (Lys in L-HEP, Gln in L-BEP) to be responsible for these differences in enteropeptidase catalytic activity. Indeed, human-to-bovine mutations Arg96Lys, Lys219Gln shifted catalytic properties of L-HEP toward those of L-BEP. This effect was amplified in case of the double mutation Arg96Lys/Lys219Gln, but still did not cover the full difference in catalytic activities of human and bovine enzymes. To find a missing link, we studied monopeptide benzyl-arginine-β-naphthylamide hydrolysis. L-HEP catalyzed it with an order lower <i>K</i><sub>m</sub> than L-BEP, suggesting the monopeptide-binding S1 site input into catalytic distinction between two enteropeptidase species. Together, our findings suggest structural basis of the unique catalytic properties of human enteropeptidase and instigate further studies of its tentative physiological and pathological roles.</p>
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Antimicrobial Peptides Induce Growth of Phosphatidylglycerol Domains in a Model Bacterial Membrane
We performed microsecond long coarse-grained molecular dynamics simulations to elucidate the lateral structure and domain dynamics of a phosphatidylethanolamine (PE)/phosphatidylglycerol (PG) mixed bilayer (7/3), mimicking the inner membrane of gram-negative bacteria. Specifically, we address the effect of surface bound antimicrobial peptides (AMPs) on the lateral organization of the membrane. We find that, in the absence of the peptides, the minor PG fraction only forms small clusters, but that these clusters grow in size upon binding of the cationic AMPs. The presence of AMPs systematically affects the dynamics and induces long-range order in the structure of PG domains, stabilizing the separation between the two lipid fractions. Our results help in understanding the initial stages of destabilization of cytoplasmic bacterial membranes below the critical peptide concentration necessary for disruption, and provide a possible explanation for the multimodal character of AMP activity
Impact of membrane partitioning on the spatial structure of an S-type cobra cytotoxin
<p>Cobra cytotoxins (CTs) belong to the three-fingered protein family. They are classified into S- and P-types, the latter exhibiting higher membrane-perturbing capacity. In this work, we investigated the interaction of CTs with phospholipid bilayers, using coarse-grained (CG) and full-atom (FA) molecular dynamics (MD). The object of this work is a CT of an S-type, cytotoxin I (CT1) from <i>N.oxiana</i> venom. Its spatial structure in aqueous solution and in the micelles of dodecylphosphocholine (DPC) were determined by <sup>1</sup>H-NMR spectroscopy. Then, via CG- and FA MD-computations, we evaluated partitioning of CT1 molecule into palmitoyloleoylphosphatidylcholine (POPC) membrane, using the toxin spatial models, obtained either in aqueous solution, or detergent micelle. The latter model exhibits minimal structural changes upon partitioning into the membrane, while the former deviates from the starting conformation, loosing the tightly bound water molecule in the loop-2. These data show that the structural changes elicited by CT1 molecule upon incorporation into DPC micelle take place likely in the lipid membrane, although the mode of the interaction of this toxin with DPC micelle (with the tips of the all three loops) is different from its mode in POPC membrane (primarily with the tip of the loop-1 and both the tips of the loop-1 and loop-2).</p