Researcher:
Dalgıçdır, Cahit

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PhD Student

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Cahit

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Dalgıçdır

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Dalgıçdır, Cahit

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Now showing 1 - 8 of 8
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    Publication
    From macroscopic to molecular interfaces: how do they alter protein conformation?
    (Cell Press, 2015) Department of Mechanical Engineering; N/A; Sayar, Mehmet; Dalgıçdır, Cahit; Faculty Member; PhD Student; Department of Mechanical Engineering; College of Engineering; Graduate School of Sciences and Engineering; 109820; N/A
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    Publication
    Improvement in gas permeability of biaxially stretched PET films blended with high barrier polymers: the role of chemistry and processing conditions
    (Elsevier, 2010) Özen, İlhan; Bozoklu, Guelay; Yücel, Orçun; Ünsal, Emre; Çakmak, Muekerrem; Menceloğlu, Yusuf Ziya; N/A; Dalgıçdır, Cahit; PhD Student; Graduate School of Sciences and Engineering; N/A
    Improvement in oxygen gas barrier properties of polyester/polyamide blends used in packaging industry is the main objective of the present study. For this purpose poly(ethylene terephthalate) (PET)/poly(m-xylene adipamide) (nylon-MXD6) (95/5 w/w) and poly(ethylene terephthalate-co-isophthalate) copolymer (PETI)/MXD6 (95/5 w/w) blends have been prepared with a PET copolymer which consists of 5 wt.% sodium sulfonated isophthalate (PET-co-5SIPA) as compatibilizer and a carboxyl-terminated polybutadiene (CTPB) as filler by using a co-rotating intermeshing twin screw extruder. The effects of chemical architecture and morphology on oxygen gas permeability and processability were analyzed by using a range of characterization techniques including differential scanning calorimetry (DSC) scanning electron microscopy (SEM), oxygen gas permeability analyzer, and a special computer controlled uniaxial stretching system that provides real-time measurement of true stress, true strain and birefringence. The morphological analysis revealed that PETco-5SIPA was an effective compatibilizer for both PET/MXD6 and PETI/MXD6 blends. DSC analysis and spectral-birefringence technique were used to understand the thermal and stress-induced crystallization behavior of the blends. Morphological analysis of the films after biaxial stretching indicated that the spherical nylon phase was converted to 75 nm thick disks during stretching (aspect ratio L/W = 6) that creates a tortuous pathway for oxygen ingress. Stretching enhanced the barrier properties of PET/MXD6 and PETI/MXD6 blends. (C) 2009 Elsevier Ltd. All rights reserved.
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    Publication
    Multiscale simulations of partially disordered systems
    (2017) Globisch, C.; Peter, C.; N/A; Department of Mechanical Engineering; Dalgıçdır, Cahit; Sayar, Mehmet; PhD Student; Faculty Member; Department of Mechanical Engineering; Graduate School of Sciences and Engineering; College of Engineering; N/A; 109820
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    Publication
    Conformation and aggregation of LKα14 peptide in bulk water and at the air/water ınterface
    (Amer Chemical Soc, 2015) N/A; Department of Mechanical Engineering; Dalgıçdır, Cahit; Sayar, Mehmet; PhD Student; Faculty Member; Department of Mechanical Engineering; Graduate School of Sciences and Engineering; College of Engineering; N/A; 109820
    Historically, the protein folding problem has mainly been associated with understanding the relationship between amino acid sequence and structure. However, it is known that both the conformation of individual molecules and their aggregation strongly depend on the environmental conditions. Here, we study the aggregation behavior of the model peptide LK alpha 14 (with amino acid sequence LKKLLKLLKKLLKL) in bulk water and at the air/water interface. We start by a quantitative analysis of the conformational space of a single LK alpha 14 in bulk water. Next, in order to analyze the aggregation tendency of LK alpha 14, by using the umbrella sampling technique we calculate the potential of mean force for pulling a single peptide from an n-molecule aggregate. In agreement with the experimental results, our calculations yield the optimal aggregate size as four. This equilibrium state is achieved by two opposing forces: Coulomb repulsion between the lysine side chains and the reduction of solvent accessible hydrophobic surface area upon aggregation. At the vacuum/water interface, however, even dimers of LK alpha 14 become marginally stable, and any larger aggregate falls apart instantaneously. Our results indicate that even though the interface is highly influential in stabilizing the a-helix conformation for a single molecule, it significantly reduces the attraction between two LK alpha 14 peptides, along with their aggregation tendency.
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    Publication
    Correction to “conformation and aggregation of LKα14 peptide in bulk water and at the air/water interface”
    (Amer Chemical Soc, 2019) N/A; N/A; N/A; Department of Mechanical Engineering; Özgür, Beytullah; Dalgıçdır, Cahit; Sayar, Mehmet; PhD Student; PhD Student; Faculty Member; Department of Mechanical Engineering; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; College of Engineering; N/A; N/A; 109820
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    PublicationOpen Access
    A transferable coarse-grained model for diphenylalanine: how to represent an environment driven conformational transition
    (American Institute of Physics (AIP) Publishing, 2013) Peter, Christine; N/A; Department of Mechanical Engineering; Dalgıçdır, Cahit; Şensoy, Özge; Sayar, Mehmet; PhD Student; Faculty Member; Department of Mechanical Engineering; Graduate School of Sciences and Engineering; N/A; N/A; 109820
    One of the major challenges in the development of coarse grained (CG) simulation models that aim at biomolecular structure formation processes is the correct representation of an environment-driven conformational change, for example, a folding/unfolding event upon interaction with an interface or upon aggregation. In the present study, we investigate this transferability challenge for a CG model using the example of diphenylalanine. This dipeptide displays a transition from a trans-like to a cis-like conformation upon aggregation as well as upon transfer from bulk water to the cyclohexane/water interface. Here, we show that one can construct a single CG model that can reproduce both the bulk and interface conformational behavior and the segregation between hydrophobic/hydrophilic medium. While the general strategy to obtain nonbonded interactions in the present CG model is to reproduce solvation free energies of small molecules representing the CG beads in the respective solvents, the success of the model strongly depends on nontrivial decisions one has to make to capture the delicate balance between the bonded and nonbonded interactions. In particular, we found that the peptide's conformational behavior is qualitatively affected by the cyclohexane/water interaction potential, an interaction that does not directly involve the peptide at all but merely influences the properties of the hydrophobic/hydrophilic interface. Furthermore, we show that a small modification to improve the structural/conformational properties of the CG model could dramatically alter the thermodynamic properties. (C) 2013 AIP Publishing LLC.
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    PublicationOpen Access
    A multi-state coarse grained modeling approach for an intrinsically disordered peptide
    (American Institute of Physics (AIP) Publishing, 2017) Department of Chemical and Biological Engineering; N/A; Sayar, Mehmet; Dalgıçdır, Cahit; Ramezanghorbani, Farhad; Faculty Member; PhD Student; Department of Chemical and Biological Engineering; College of Engineering; Graduate School of Sciences and Engineering; 109820; N/A; N/A
    Many proteins display a marginally stable tertiary structure, which can be altered via external stimuli. Since a majority of coarse grained (CG) models are aimed at structure prediction, their success for an intrinsically disordered peptide's conformational space with marginal stability and sensitivity to external stimuli cannot be taken for granted. In this study, by using the LK alpha 14 peptide as a test system, we demonstrate a bottom-up approach for constructing a multi-state CG model, which can capture the conformational behavior of this peptide in three distinct environments with a unique set of interaction parameters. LK alpha 14 is disordered in dilute solutions; however, it strictly adopts the alpha-helix conformation upon aggregation or when in contact with a hydrophobic/hydrophilic interface. Our bottom-up approach combines a generic base model, that is unbiased for any particular secondary structure, with nonbonded interactions which represent hydrogen bonds, electrostatics, and hydrophobic forces. We demonstrate that by using carefully designed all atom potential of mean force calculations from all three states of interest, one can get a balanced representation of the nonbonded interactions. Our CG model behaves intrinsically disordered in bulk water, folds into an alpha-helix in the presence of an interface or a neighboring peptide, and is stable as a tetrameric unit, successfully reproducing the all atom molecular dynamics simulations and experimental results.
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    PublicationOpen Access
    Tipping the scale from disorder to alpha-helix: folding of amphiphilic peptides in the presence of macroscopic and molecular interfaces
    (Public Library of Science, 2015) Globisch, Christoph; Peter, Christine; N/A; Department of Mechanical Engineering; Dalgıçdır, Cahit; Sayar, Mehmet; PhD Student; Faculty Member; Department of Mechanical Engineering; Graduate School of Sciences and Engineering; College of Engineering; N/A; 109820
    Secondary amphiphilicity is inherent to the secondary structural elements of proteins. By forming energetically favorable contacts with each other these amphiphilic building blocks give rise to the formation of a tertiary structure. Small proteins and peptides, on the other hand, are usually too short to form multiple structural elements and cannot stabilize them internally. Therefore, these molecules are often found to be structurally ambiguous up to the point of a large degree of intrinsic disorder in solution. Consequently, their conformational preference is particularly susceptible to environmental conditions such as pH, salts, or presence of interfaces. In this study we use molecular dynamics simulations to analyze the conformational behavior of two synthetic peptides, LKKLLKLLKKLLKL (LK) and EAA LAEALAEALAE (EALA), with built-in secondary amphiphilicity upon forming an alpha-helix. We use these model peptides to systematically study their aggregation and the influence of macroscopic and molecular interfaces on their conformational preferences. We show that the peptides are neither random coils in bulk water nor fully formed alpha helices, but adopt multiple conformations and secondary structure elements with short lifetimes. These provide a basis for conformation-selection and population-shift upon environmental changes. Differences in these peptides' response to macroscopic and molecular interfaces (presented by an aggregation partner) can be linked to their inherent alpha-helical tendencies in bulk water. We find that the peptides' aggregation behavior is also strongly affected by presence or absence of an interface, and rather subtly depends on their surface charge and hydrophobicity.