The Experts below are selected from a list of 5151 Experts worldwide ranked by ideXlab platform
Wolfhard Janke - One of the best experts on this subject based on the ideXlab platform.
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Conformational transitions in random heteropolymer models
The Journal of chemical physics, 2014Co-Authors: Viktoria Blavatska, Wolfhard JankeAbstract:We study the conformational properties of Heteropolymers containing two types of monomers A and B, modeled as self-avoiding random walks on a regular lattice. Such a model can describe in particular the sequences of hydrophobic and hydrophilic residues in proteins (K.F. Lau and K.A. Dill, Macromolecules {\bf 22}, 3986 (1989)) and polyampholytes with oppositely charged groups (Y. Kantor and M. Kardar, Europhys. Lett.{\bf 28}, 169 (1994)). Treating the sequences of the two types of monomers as quenched random variables, we provide a systematic analysis of possible generalizations of this model. To this end we apply the pruned-enriched Rosenbluth chain-growth algorithm (PERM), which allows us to obtain the phase diagrams of extended and compact states coexistence as function of both the temperature and fraction of A and B monomers along the heteropolymer chain.
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Different Kinds of Protein Folding Identified with a Coarse-Grained Heteropolymer Model
arXiv: Soft Condensed Matter, 2009Co-Authors: Stefan Schnabel, Michael Bachmann, Wolfhard JankeAbstract:Applying multicanonical simulations we investigated folding properties of off-lattice Heteropolymers employing a mesoscopic hydrophobic-polar model. We study for various sequences folding channels in the free-energy landscape by comparing the equilibrium conformations with the folded state in terms of an angular overlap parameter. Although all investigated heteropolymer sequences contain the same content of hydrophobic and polar monomers, our analysis of the folding channels reveals a variety of characteristic folding behaviors known from realistic peptides.
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Thermodynamics and kinetics of a Gō proteinlike heteropolymer model with two-state folding characteristics
The Journal of chemical physics, 2008Co-Authors: Anna Kallias, Michael Bachmann, Wolfhard JankeAbstract:We present results of Monte Carlo computer simulations of a coarse-grained hydrophobic-polar Gō-like heteropolymer model and discuss thermodynamic properties and kinetics of an exemplified heteropolymer, exhibiting two-state folding behavior. It turns out that general, characteristic folding features of realistic proteins with a single free-energy barrier can also be observed in this simplified model, where the folding transition is primarily driven by the hydrophobic force.
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Thermodynamics and Kinetics of a Go Proteinlike Heteropolymer Model with Two-State Folding Characteristics
The Journal of chemical physics, 2008Co-Authors: Anna Kallias, Michael Bachmann, Wolfhard JankeAbstract:We present results of Monte Carlo computer simulations of a coarse-grained hydrophobic-polar Go-like heteropolymer model and discuss thermodynamic properties and kinetics of an exemplified heteropolymer, exhibiting two-state folding behavior. It turns out that general, characteristic folding features of realistic proteins with a single free-energy barrier can also be observed in this simplified model, where the folding transition is primarily driven by the hydrophobic force.
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Multicanonical study of coarse-grained off-lattice models for folding Heteropolymers.
Physical review. E Statistical nonlinear and soft matter physics, 2005Co-Authors: Michael Bachmann, Handan Arkin, Wolfhard JankeAbstract:We have performed multicanonical simulations of hydrophobic-hydrophilic Heteropolymers with two simple effective, coarse-grained off-lattice models to study the influence of specific interactions in the models on conformational transitions of selected sequences with 20 monomers. Another aspect of the investigation was the comparison with the purely hydrophobic homopolymer and the study of general conformational properties induced by the "disorder" in the sequence of a heteropolymer. Furthermore, we applied an optimization algorithm to sequences with up to 55 monomers and compared the global-energy minimum found with lowest-energy states identified within the multicanonical simulation. This was used to find out how reliable the multicanonical method samples the free-energy landscape, in particular for low temperatures.
Michelle Momany - One of the best experts on this subject based on the ideXlab platform.
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Diversity of opisthokont septin proteins reveals structural constraints and conserved motifs
BMC Evolutionary Biology, 2019Co-Authors: Benjamin Auxier, Mary L Berbee, Michelle MomanyAbstract:Background Septins are cytoskeletal proteins important in cell division and in establishing and maintaining cell polarity. Although septins are found in various eukaryotes, septin genes had the richest history of duplication and diversification in the animals, fungi and protists that comprise opisthokonts. Opisthokont septin paralogs encode modular proteins that assemble into heteropolymeric higher order structures. The Heteropolymers can create physical barriers to diffusion or serve as scaffolds organizing other morphogenetic proteins. How the paralogous septin modules interact to form Heteropolymers is still unclear. Through comparative analyses, we hoped to clarify the evolutionary origin of septin diversity and to suggest which amino acid residues were responsible for subunit binding specificity. Results Here we take advantage of newly sequenced genomes to reconcile septin gene trees with a species phylogeny from 22 animals, fungi and protists. Our phylogenetic analysis divided 120 septins representing the 22 taxa into seven clades (Groups) of paralogs. Suggesting that septin genes duplicated early in opisthokont evolution, animal and fungal lineages share septin Groups 1A, 4 and possibly also 1B and 2. Group 5 septins were present in fungi but not in animals and whether they were present in the opisthokont ancestor was unclear. Protein homology folding showed that previously identified conserved septin motifs were all located near interface regions between the adjacent septin monomers. We found specific interface residues associated with each septin Group that are candidates for providing subunit binding specificity. Conclusions This work reveals that duplication of septin genes began in an ancestral opisthokont more than a billion years ago and continued through the diversification of animals and fungi. Evidence for evolutionary conservation of ~ 49 interface residues will inform mutagenesis experiments and lead to improved understanding of the rules guiding septin heteropolymer formation and from there, to improved understanding of development of form in animals and fungi.
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distinct septin Heteropolymers co exist during multicellular development in the filamentous fungus aspergillus nidulans
PLOS ONE, 2014Co-Authors: Yainitza Hernandezrodriguez, Shunsuke Masuo, Darryl Johnson, Ron Orlando, Amy Smith, Mara Coutorodriguez, Michelle MomanyAbstract:Septins are important components of the cytoskeleton that are highly conserved in eukaryotes and play major roles in cytokinesis, patterning, and many developmental processes. Septins form Heteropolymers which assemble into higher-order structures including rings, filaments, and gauzes. In contrast to actin filaments and microtubules, the molecular mechanism by which septins assemble is not well-understood. Here, we report that in the filamentous fungus Aspergillus nidulans, four core septins form heteropolymeric complexes. AspE, a fifth septin lacking in unicellular yeasts, interacts with only one of the core septins, and only during multicellular growth. AspE is required for proper localization of three of the core septins, and requires this same subset of core septins for its own unique cortical localization. The ΔaspE mutant lacks developmentally-specific septin higher-order structures and shows reduced spore production and slow growth with low temperatures and osmotic stress. Our results show that at least two distinct septin heteropolymer populations co-exist in A. nidulans, and that while AspE is not a subunit of either heteropolymer, it is required for assembly of septin higher-order structures found in multicellular development.
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Posttranslational modifications and assembly of septin Heteropolymers and higher-order structures.
Current opinion in microbiology, 2012Co-Authors: Yainitza Hernández-rodríguez, Michelle MomanyAbstract:Septins are cytoskeletal elements that contain a highly conserved canonical G domain flanked by more divergent N- and C-termini. Septin monomers form Heteropolymers that in turn associate into a variety of higher-order structures. SUMOylation, acetylation and phosphorylation of septins have all been reported; however, there are no examples of residues that are universally modified suggesting that posttranslational modifications of septins evolved relatively recently. Within the conserved G domain, posttranslational modifications cluster in regions near the G interface, consistent with roles in modulating heteropolymer assembly. Within the highly diverged N- and C-termini, posttranslational modifications are scattered randomly, consistent with roles in modulating assembly of higher-order structures that are unique to individual organisms.
Michael Bachmann - One of the best experts on this subject based on the ideXlab platform.
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Different Kinds of Protein Folding Identified with a Coarse-Grained Heteropolymer Model
arXiv: Soft Condensed Matter, 2009Co-Authors: Stefan Schnabel, Michael Bachmann, Wolfhard JankeAbstract:Applying multicanonical simulations we investigated folding properties of off-lattice Heteropolymers employing a mesoscopic hydrophobic-polar model. We study for various sequences folding channels in the free-energy landscape by comparing the equilibrium conformations with the folded state in terms of an angular overlap parameter. Although all investigated heteropolymer sequences contain the same content of hydrophobic and polar monomers, our analysis of the folding channels reveals a variety of characteristic folding behaviors known from realistic peptides.
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Thermodynamics and kinetics of a Gō proteinlike heteropolymer model with two-state folding characteristics
The Journal of chemical physics, 2008Co-Authors: Anna Kallias, Michael Bachmann, Wolfhard JankeAbstract:We present results of Monte Carlo computer simulations of a coarse-grained hydrophobic-polar Gō-like heteropolymer model and discuss thermodynamic properties and kinetics of an exemplified heteropolymer, exhibiting two-state folding behavior. It turns out that general, characteristic folding features of realistic proteins with a single free-energy barrier can also be observed in this simplified model, where the folding transition is primarily driven by the hydrophobic force.
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Thermodynamics and Kinetics of a Go Proteinlike Heteropolymer Model with Two-State Folding Characteristics
The Journal of chemical physics, 2008Co-Authors: Anna Kallias, Michael Bachmann, Wolfhard JankeAbstract:We present results of Monte Carlo computer simulations of a coarse-grained hydrophobic-polar Go-like heteropolymer model and discuss thermodynamic properties and kinetics of an exemplified heteropolymer, exhibiting two-state folding behavior. It turns out that general, characteristic folding features of realistic proteins with a single free-energy barrier can also be observed in this simplified model, where the folding transition is primarily driven by the hydrophobic force.
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Multicanonical study of coarse-grained off-lattice models for folding Heteropolymers.
Physical review. E Statistical nonlinear and soft matter physics, 2005Co-Authors: Michael Bachmann, Handan Arkin, Wolfhard JankeAbstract:We have performed multicanonical simulations of hydrophobic-hydrophilic Heteropolymers with two simple effective, coarse-grained off-lattice models to study the influence of specific interactions in the models on conformational transitions of selected sequences with 20 monomers. Another aspect of the investigation was the comparison with the purely hydrophobic homopolymer and the study of general conformational properties induced by the "disorder" in the sequence of a heteropolymer. Furthermore, we applied an optimization algorithm to sequences with up to 55 monomers and compared the global-energy minimum found with lowest-energy states identified within the multicanonical simulation. This was used to find out how reliable the multicanonical method samples the free-energy landscape, in particular for low temperatures.
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Conformational transitions of Heteropolymers
Computer Physics Communications, 2005Co-Authors: Michael Bachmann, Wolfhard JankeAbstract:We study conformational transitions of simple coarse-grained models for protein-like Heteropolymers on the simple cubic lattice and off-lattice, respectively, by means of multicanonical sampling algorithms. The effective hydrophobic/polar models do not require the knowledge of the native topology for a given sequence of residues as input. Therefore these models are eligible to investigate general properties of the tertiary folding behavior of such protein-like Heteropolymers.
Shekhar Garde - One of the best experts on this subject based on the ideXlab platform.
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Structure and dynamics of single hydrophobic/ionic Heteropolymers at the vapor-liquid interface of water.
Langmuir : the ACS journal of surfaces and colloids, 2014Co-Authors: Srivathsan Vembanur, Vasudevan Venkateshwaran, Shekhar GardeAbstract:We focus on the conformational stability, structure, and dynamics of hydrophobic/charged homopolymers and Heteropolymers at the vapor–liquid interface of water using extensive molecular dynamics simulations. Hydrophobic polymers collapse into globular structures in bulk water but unfold and sample a broad range of conformations at the vapor–liquid interface of water. We show that adding a pair of charges to a hydrophobic polymer at the interface can dramatically change its conformations, stabilizing hairpinlike structures, with molecular details depending on the location of the charged pair in the sequence. The translational dynamics of homopolymers and Heteropolymers are also different, whereas the homopolymers skate on the interface with low drag, the tendency of charged groups to remain hydrated pulls the Heteropolymers toward the liquid side of the interface, thus pinning them, increasing drag, and slowing the translational dynamics. The conformational dynamics of Heteropolymers are also slower than t...
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structure and dynamics of single hydrophobic ionic Heteropolymers at the vapor liquid interface of water
Langmuir, 2014Co-Authors: Srivathsan Vembanur, Vasudevan Venkateshwaran, Shekhar GardeAbstract:We focus on the conformational stability, structure, and dynamics of hydrophobic/charged homopolymers and Heteropolymers at the vapor–liquid interface of water using extensive molecular dynamics simulations. Hydrophobic polymers collapse into globular structures in bulk water but unfold and sample a broad range of conformations at the vapor–liquid interface of water. We show that adding a pair of charges to a hydrophobic polymer at the interface can dramatically change its conformations, stabilizing hairpinlike structures, with molecular details depending on the location of the charged pair in the sequence. The translational dynamics of homopolymers and Heteropolymers are also different, whereas the homopolymers skate on the interface with low drag, the tendency of charged groups to remain hydrated pulls the Heteropolymers toward the liquid side of the interface, thus pinning them, increasing drag, and slowing the translational dynamics. The conformational dynamics of Heteropolymers are also slower than t...
Srivathsan Vembanur - One of the best experts on this subject based on the ideXlab platform.
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Structure and dynamics of single hydrophobic/ionic Heteropolymers at the vapor-liquid interface of water.
Langmuir : the ACS journal of surfaces and colloids, 2014Co-Authors: Srivathsan Vembanur, Vasudevan Venkateshwaran, Shekhar GardeAbstract:We focus on the conformational stability, structure, and dynamics of hydrophobic/charged homopolymers and Heteropolymers at the vapor–liquid interface of water using extensive molecular dynamics simulations. Hydrophobic polymers collapse into globular structures in bulk water but unfold and sample a broad range of conformations at the vapor–liquid interface of water. We show that adding a pair of charges to a hydrophobic polymer at the interface can dramatically change its conformations, stabilizing hairpinlike structures, with molecular details depending on the location of the charged pair in the sequence. The translational dynamics of homopolymers and Heteropolymers are also different, whereas the homopolymers skate on the interface with low drag, the tendency of charged groups to remain hydrated pulls the Heteropolymers toward the liquid side of the interface, thus pinning them, increasing drag, and slowing the translational dynamics. The conformational dynamics of Heteropolymers are also slower than t...
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structure and dynamics of single hydrophobic ionic Heteropolymers at the vapor liquid interface of water
Langmuir, 2014Co-Authors: Srivathsan Vembanur, Vasudevan Venkateshwaran, Shekhar GardeAbstract:We focus on the conformational stability, structure, and dynamics of hydrophobic/charged homopolymers and Heteropolymers at the vapor–liquid interface of water using extensive molecular dynamics simulations. Hydrophobic polymers collapse into globular structures in bulk water but unfold and sample a broad range of conformations at the vapor–liquid interface of water. We show that adding a pair of charges to a hydrophobic polymer at the interface can dramatically change its conformations, stabilizing hairpinlike structures, with molecular details depending on the location of the charged pair in the sequence. The translational dynamics of homopolymers and Heteropolymers are also different, whereas the homopolymers skate on the interface with low drag, the tendency of charged groups to remain hydrated pulls the Heteropolymers toward the liquid side of the interface, thus pinning them, increasing drag, and slowing the translational dynamics. The conformational dynamics of Heteropolymers are also slower than t...