Researcher:
Erman, Burak

Profile Picture
ORCID

Job Title

Faculty Member

First Name

Burak

Last Name

Erman

Name

Name Variants

Erman, Burak

Email Address

Birth Date

Filters

Advanced Search

Filter by

Settings

Researcher Of Publications: search.filters.isAuthorOfPublication.e2ab677b-4cd4-49c1-8435-b884b34d6094

Search Results

Now showing 1 - 10 of 122
  • Placeholder
    PublicationMetadata only
    Effects of ligand binding upon flexibility of proteins
    (Wiley-Blackwell, 2015) Department of Chemical and Biological Engineering; Erman, Burak; Faculty Member; Department of Chemical and Biological Engineering; College of Engineering; 179997
    Binding of a ligand on a protein changes the flexibility of certain parts of the protein, which directly affects its function. These changes are not the same at each point, some parts become more flexible and some others become stiffer. Here, an equation is derived that gives the stiffness map for proteins. The model is based on correlations of fluctuations of pairs of points in proteins, which may be evaluated at different levels of refinement, ranging from all atom molecular dynamics to general elastic network models, including the simplest case of isotropic Gaussian Network Model. The latter is used, as an example, to evaluate the changes of stiffness upon dimerization of ACK1. Proteins 2015; 83:805-808. (c) 2015 Wiley Periodicals, Inc.
  • Placeholder
    PublicationMetadata only
    Quasi-harmonic fluctuations of two bound peptides
    (Wiley-Blackwell, 2012) N/A; Department of Chemical and Biological Engineering; Gür, Mert; Erman, Burak; PhD Student; Faculty Member; Department of Chemical and Biological Engineering; Graduate School of Sciences and Engineering; College of Engineering; 216930; 179997
    Binding of two short peptides of sequences ASN-ASP-MET-PHE-ARG-LEU and LEU-LEU-PHE-MET-GLN-HIS and their bound complex structures is studied. Molecular dynamic simulations of the three structures around their respective minimum energy conformations are performed and a quasi-harmonic analysis is performed over the trajectories generated. The fluctuation correlation matrix is constructed for all C-alpha-atoms of the peptides for the full trajectory. The spring constant matrix between peptide C-alpha-atoms is obtained from the correlation matrix. Statistical thermodynamics of fluctuations, the energies, entropies, and the free energies of binding are discussed in terms of the quasi-harmonic model. Sites contributing to the stability of the system and presenting high affinity for binding are determined. Contribution of hydrophobic forces to binding is discussed. Quasi-harmonic approximation identifies the essential subspace of motions, the important interactions, and binding sites, gives the energetic contribution of each individual interaction, and filters out noise observed in molecular dynamics owing to uncorrelated motions. Comparison of the molecular dynamics results with those of the quasi-harmonic model shows the importance of entropy change, resulting from water molecules being liberated from the surfaces of the two peptides upon binding.
  • Placeholder
    PublicationMetadata only
    Control of optical anisotropy at large deformations in PMMA/chlorinated-PHB (PHB-Cl) blends: mechano-optical behavior
    (Elsevier Sci Ltd, 2006) Yalçın, Barış; Çakmak, Mükerrem; Arkın, Ali Hakan; Hazer, Baki; Department of Chemical and Biological Engineering; Erman, Burak; Faculty Member; Department of Chemical and Biological Engineering; College of Engineering; 179997
    There is a continuing need to produce polymer films with high optical clarity with ability to dial in the optical properties including refractive indices and optical anisotropies. In this research, we investigated the mechano-optical behavior of PMMA/PHB-Cl blend films during uniaxial deformation and mapped out the composition-birefringence-processing relationships. The results indicate the presence of a broad glass transition for the composition range investigated that indicates the development of micro-heterogeneities particularly at the higher concentration of PHB-Cl. However, this did not detrimentally influence the optical transparency of the solvent cast films as the size of these micro-heterogeneities remains well below the size range to affect the transparency. Optical retardation behavior of the films can be altered from negative to positive by increasing the PHB-Cl concentration from 0 to 20 wt%. The films with 18 wt% PHB-Cl are predicted to exhibit zero birefringence even when they are stretched to large deformations. This dialability of optical properties makes these materials suitable for optical device applications such as CD and DVDs as well as optical retarder films for liquid-crystal display applications. (c) 2006 Elsevier Ltd. All rights reserved.
  • Placeholder
    PublicationMetadata only
    The introduction of hydrogen bond and hydrophobicity effects into the rotational isomeric states model for conformational analysis of unfolded peptides
    (Iop Publishing Ltd, 2009) N/A; Department of Mechanical Engineering; Department of Chemical and Biological Engineering; Engin, Özge; Sayar, Mehmet; Erman, Burak; Master Student; Faculty Member; Faculty Member; Department of Mechanical Engineering; Department of Chemical and Biological Engineering; Graduate School of Sciences and Engineering, College of Engineering; College of Engineering; N/A; 109820; 179997
    Relative contributions of local and non-local interactions to the unfolded conformations of peptides are examined by using the rotational isomeric states model which is a Markov model based on pairwise interactions of torsion angles. the isomeric states of a residue are well described by the Ramachandran map of backbone torsion angles. the statistical weight matrices for the states are determined by molecular dynamics simulations applied to monopeptides and dipeptides. Conformational properties of tripeptides formed from combinations of alanine, valine, tyrosine and tryptophan are investigated based on the Markov model. Comparison with molecular dynamics simulation results on these tripeptides identifies the sequence-distant long-range interactions that are missing in the Markov model. these are essentially the hydrogen bond and hydrophobic interactions that are obtained between the first and the third residue of a tripeptide. a systematic correction is proposed for incorporating these long-range interactions into the rotational isomeric states model. Preliminary results suggest that the Markov assumption can be improved significantly by renormalizing the statistical weight matrices to include the effects of the long-range correlations.
  • Placeholder
    PublicationMetadata only
    Elastomers and rubberlike elasticity
    (Oxford University Press (OUP), 2017) Mark, James E.; Department of Chemical and Biological Engineering; Erman, Burak; Faculty Member; Department of Chemical and Biological Engineering; College of Engineering; 179997
    This article focuses on the rubberlike elasticity of elastomers, with particular emphasis on rubberlike materials that exhibit high deformability and recoverability. It begins with a discussion of the variety of practical ways to form and characterize a rubber-elastic network, including random chemical crosslinking, highly specific chemical end-linking, polymerizations with multi-functional monomers, physical aggregation, and crosslinking in solution and in the deformed state. It then considers the effects of network structure on elastomeric properties, along with the results of elasticity experiments regarding the mechanical properties of elastomeric materials. It also examines the evolution of theories of rubber elasticity describes the specific properties of swollen polymer gels where the possibility of solvent exchange leads to some dramatic transformations in the system. Finally, it evaluates new emerging classes of rubber-elastic materials, such as liquid crystalline elastomers, where the internal microstructure added to the random network leads to some unique mechanical properties.
  • Placeholder
    PublicationMetadata only
    Palladium nanoparticles by electrospinning from Poly(acrylonitrile- co -acrylic acid)-PdCl 2 solutions. relations between preparation conditions, particle size, and catalytic activity
    (American Chemical Society (ACS), 2004) Demir, MM; Gülgün, MA; Menceloğlu, YZ; Abramchuk, SS; Makhaeva, EE; Khokhlov, AR; Matveeva, VG; Sulman, MG; Department of Chemical and Biological Engineering; Erman, Burak; Faculty Member; Department of Chemical and Biological Engineering; College of Engineering; 179997
    Catalytic palladium (Pd) nanoparticles on electrospun copolymers of acrylonitrile and acrylic acid (PAN-AA) mats were produced via reduction of PdCl2 with hydrazine. Fiber mats were electrospun from homogeneous solutions of PAN-AA and PdCl2 in dimethylformamide (DMF). Pd cations were reduced to Pd metals when fiber mats were treated in an aqueous hydrazine solution at room temperature. Pd atoms nucleate and form small crystallites whose sizes were estimated from the peak broadening of X-ray diffraction peaks. Two to four crystallites adhere together and form agglomerates. Agglomerate sizes and fiber diameters were determined by scanning and transmission electron microscopy. Spherical Pd nanoparticles were dispersed homogeneously on the electrospun nanofibers. The effects of copolymer composition and amount of PdCl2 on particle size were investigated. Pd particle size mainly depends on the amount of acrylic acid functional groups and PdCl2 concentration in the spinning solution. Increasing acrylic acid concentration on polymer chains leads to larger Pd nanoparticles. In addition, Pd particle size becomes larger with increasing PdCl2 concentration in the spinning solution. Hence, it is possible to tune the number density and the size of metal nanoparticles. The catalytic activity of the Pd nanoparticles in electrospun mats was determined by selective hydrogenation of dehydrolinalool (3,7-dimethyloct-6-ene-1-yne-3-ol, DHL) in toluene at 90 degreesC. Electrospun fibers with Pd particles have 4.5 times higher catalytic activity than the current Pd/Al2O3 catalyst.
  • Placeholder
    PublicationMetadata only
    Structural cooperativity in histone H3 tail modifications
    (Wiley, 2011) N/A; Department of Chemical and Biological Engineering; Department of Computer Engineering; Department of Chemical and Biological Engineering; Şanlı, Deniz; Keskin, Özlem; Gürsoy, Attila; Erman, Burak; Researcher; Faculty Member; Faculty Member; Faculty Member; Department of Computer Engineering; Department of Chemical and Biological Engineering; Graduate School of Sciences and Engineering; College of Engineering; College of Engineering; College of Engineering; N/A; 26605; 8745; 179997
    Post-translational modifications of histone H3 tails have crucial roles in regulation of cellular processes. There is cross-regulation between the modifications of K4, K9, and K14 residues. The modifications on these residues drastically promote or inhibit each other. In this work, we studied the structural changes of the histone H3 tail originating from the three most important modifications; tri-methylation of K4 and K9, and acetylation of K14. We performed extensive molecular dynamics simulations of four types of H3 tails: (i) the unmodified H3 tail having no chemical modification on the residues, (ii) the tri-methylated lysine 4 and lysine 9 H3 tail (K4me3K9me3), (iii) the tri-methylated lysine 4 and acetylated lysine 14 H3 tail (K4me3K14ace), and (iv) tri-methylated lysine 9 and acetylated lysine 14 H3 tail (K9me3K14ace). Here, we report the effects of K4, K9, and K14 modifications on the backbone torsion angles and relate these changes to the recognition and binding of histone modifying enzymes. According to the Ramachandran plot analysis; (i) the dihedral angles of K4 residue are significantly affected by the addition of three methyl groups on this residue regardless of the second modification, (ii) the dihedral angle values of K9 residue are similarly altered majorly by the tri-methylation of K4 residue, (iii) different combinations of modifications (tri-methylation of K4 and K9, and acetylation of K14) have different influences on phi and psi values of K14 residue. Finally, we discuss the consequences of these results on the binding modes and specificity of the histone modifying enzymes such as DIM-5, GCN5, and JMJD2A.
  • Placeholder
    PublicationMetadata only
    Quasi-harmonic analysis of mode coupling in fluctuating native proteins
    (Iop Publishing Ltd, 2010) N/A; Department of Chemical and Biological Engineering; Gür, Mert; Erman, Burak; PhD Student; Faculty Member; Department of Chemical and Biological Engineering; Graduate School of Sciences and Engineering; College of Engineering; 216930; 179997
    Mode coupling and anharmonicity in a native fluctuating protein are investigated in modal space by projecting the motion along the eigenvectors of the fluctuation correlation matrix. The probability distribution of mode fluctuations is expressed in terms of tensorial Hermite polynomials. Molecular dynamics trajectories of Crambin are generated and used to evaluate the terms of the polynomials and to obtain the modal energies. The energies of a few modes exhibit large deviations from the harmonic energy of kT/2 per mode, resulting from coupling to the surroundings, or to another specific mode or to several other modes. Slowest modes have energies that are below that of the harmonic, and a few fast modes have energies significantly larger than the harmonic. Detailed analysis of the coupling of these modes to others is presented in terms of the lowest order two-mode coupling terms. Finally, the effects of mode coupling on conformational properties of the protein are investigated.
  • Placeholder
    PublicationMetadata only
    Rubberlike elasticity a molecular primer second edition preface to the second edition
    (Cambridge Univ Press, 2007) Mark, James E; Department of Chemical and Biological Engineering; Erman, Burak; Faculty Member; Department of Chemical and Biological Engineering; College of Engineering; 179997
    N/A
  • Placeholder
    PublicationMetadata only
    Molecular dynamics simulations provide molecular insights into the role of HLA-B51 in Behcet's disease pathogenesis
    (2020) Gür, Mert; Gölcük, Mert; Gül, Ahmet; Department of Chemical and Biological Engineering; Erman, Burak; Faculty Member; Department of Chemical and Biological Engineering; College of Engineering; 179997
    Behcet's disease is an inflammatory disorder of unknown etiology. Genetic tendency has an important role in its pathogenesis, and HLA-B51, a class I MHC antigen, has been recognized as the strongest susceptibility factor for Behcet's disease. Despite the confirmation of the association of HLA-B51 with Behcet's disease in different populations, its pathogenic mechanisms remain elusive. HLA-B51 differs in only two amino acids from HLA-B52, other split antigen of HLA-B5, which is not associated with Behcet's disease. These two amino acids are located in the B pocket of the antigen-binding groove, which occupies the second amino acids of the bound peptides. To understand the nature of the HLA-peptide interactions, differences in structure and dynamics of two HLA alleles were investigated by molecular dynamics simulations using YAYDGKDYI, LPRSTVINI, and IPYQDLPHL peptides. For HLA-B51, all bound peptides fluctuated to larger extent than HLA-B52. Free energy profiles of unbinding process for YAYDGKDYI by steered molecular dynamics simulations showed that unbinding from HLA-B52 results in greater free energy differences than HLA-B51. These results suggest the possibility of an instability of HLA-B51 associated with the repertoire of peptides, and this finding may provide significant insight to its pathogenic role in Behcet's disease.