Onur Sercinoglu

Onur Sercinoglu
Gebze Technical University | GYTE · Department of Bioengineering

PhD in Bioengineering

About

30
Publications
7,903
Reads
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116
Citations
Introduction
Researcher in the fields of computational biophysics, bioengineering, immunoinformatics, bioinformatics and structural biology.
Additional affiliations
October 2020 - January 2021
Gebze Technical University
Position
  • Professor (Assistant)
Description
  • I am currently an Assistant Professor of Bioengineering at Gebze Technical University. As a member of Bioengineering Department, I am involved in teaching as well as research activities. I also handle regular minor administrative tasks.
March 2019 - October 2020
Recep Tayyip Erdoğan Üniversitesi
Position
  • Professor (Assistant)
Description
  • I worked at RTEU, Rize, to start a new department (Bioengineering) under Faculty of Engineering. Besides research activities, I've designed a curriculum for the Bioengineering Undergraduate Program, and taught undergrads Programming Basics using Python, and acted as the Vice Head of Bioengineering Department.
Education
September 2012 - October 2018
Marmara University
Field of study
  • Bioengineering
September 2008 - July 2011
Technische Universität Hamburg
Field of study
  • Biotechnology
September 2003 - July 2008
Ege University
Field of study
  • Bioengineering

Publications

Publications (30)
Article
Full-text available
The discovery of novel chemotherapeutics that act through different mechanisms is critical for dealing with tumor heterogeneity and therapeutic resistance. We previously reported a saponin analog (AG-08) that induces non-canonical necrotic cell death and is auspicious for cancer therapy. Here, we describe that the key element in triggering this uni...
Preprint
Full-text available
Induction of distinct cell death pathways is critical to deal with tumor heterogeneity and therapeutic resistance. In our previous study, we reported a promising saponin analog (AG-08) for cancer therapy inducing non-canonical necrotic cell death. Here, we describe that AG-08 forms unique supramolecular structures responsible for its biological act...
Article
Antigen presentation by major histocompatibility complex (MHC) proteins to T-cell receptors (TCRs) plays a crucial role in triggering the adaptive immune response. Most of our knowledge on TCR-peptide-loaded major histocompatibility complex (pMHC) interaction stemmed from experiments yielding static structures, yet the dynamic aspects of this molec...
Article
Full-text available
There is a growing concern for male reproductive health as studies suggest that there is a sharp increase in prostate cancer and other fertility related problems. Apart from lifestyle, pollutants are also known to negatively affect the reproductive system. In addition to many other compounds that have been shown to alter androgen signaling, several...
Article
The resistance of microbes to commonly used antibiotics has become a worldwide health problem. A major underlying mechanism of microbial antibiotic resistance is the export of drugs from bacterial cells. Drug efflux is mediated through the action of multidrug resistance efflux pumps located in the bacterial cell membranes. The critical role of bact...
Article
Full-text available
Class I Major Histocompatibility Complex (MHC) binds short antigenic peptides with the help of Peptide Loading Complex (PLC), and presents them to T-cell Receptors (TCRs) of cytotoxic T-cells and Killer-cell Immunglobulin-like Receptors (KIRs) of Natural Killer (NK) cells. With more than 10000 alleles, human MHC (Human Leukocyte Antigen, HLA) is th...
Conference Paper
Background: Endocrine-disrupting effects of industrial chemicals, including pesticides, have become a worldwide concern. These chemicals bind to androgen receptors (AR) and regulate their activity1. AR antagonists may induce a conformational change in helix 12 (H12) upon binding to the ligand binding pocket (LBP) located within the ligand binding d...
Preprint
Full-text available
Class I Major Histocompatibility Complex (MHC) binds short antigenic peptides with the help of Peptide Loading Complex (PLC), and presents them to T-cell Receptors (TCRs) of cytotoxic T-cells and Killer-cell Immunglobulin-like Receptors (KIRs) of Natural Killer (NK) cells. With more than 10000 alleles, the Human Leukocyte Antigen (HLA) chain of MHC...
Article
Major Histocompatibility Complex (MHC) is a cell surface glycoprotein that binds to foreign antigens and presents them to T lymphocyte cells on the surface of Antigen Presenting Cells (APCs) for appropriate immune recognition. Recently, studies focusing on peptide-based vaccine design have allowed a better understanding of peptide immunogenicity me...
Article
Full-text available
ProSNEx (Protein Structure Network Explorer) is a web service for construction and analysis of Protein Structure Networks (PSNs) alongside amino acid flexibility, sequence conservation and annotation features. ProSNEx constructs a PSN by adding nodes to represent residues and edges between these nodes using user-specified interaction distance cutof...
Article
Caspases are members of a highly regulated aspartate-cysteine protease family which have important roles in apoptosis. Pharmaceutical studies focused on these molecules since they are involved in diseases such as cancer and neurodegenerative disorders. A small molecule which binds to the dimeric interface away from the binding site induces a confor...
Article
Full-text available
Atomistic molecular dynamics (MD) simulations generate a wealth of information related to the dynamics of proteins. If properly analyzed, this information can lead to new insights regarding protein function and assist wet-lab experiments. Aiming to identify interactions between individual amino acid residues and the role played by each in the conte...
Article
Full-text available
Biyolojik sistemler, birbirleri ile sürekli bilgi alışverişinde bulunan ağyapılar, biyolojik moleküller de bu yapının temel noktaları olarak tanımlanabilirler. Yaşamsal süreklilik açısından sistemin herhangi bir noktasında oluşacak bir sinyalin, hücreler arasında, hücre içinde veya hücre dışından hücre içine iletilmesi büyük önem taşımaktadır. Bu ç...
Poster
We report a tool for efficient computation and characterization of pairwise amino acid residue interaction energies from MD simulations
Article
Human Major Histocompatibility Complex class I (MHC I) –or Human Leukocyte Antigen (HLA)- proteins present intracellularly processed peptides to cytotoxic T lymphocytes in the adaptive immune response to pathogens. A high level of polymorphism in human MHC I proteins defines the peptide-binding specificity of thousands of different MHC alleles. How...
Poster
Highly polymorphic Major Histocompatibility Complex (MHC, also termed Human Leukocyte Antigens, or HLA in humans) proteins bind peptide fragments generated as a result of the action of the proteasome machinery in Antigen Presenting Cells and present them on the cell surface to T-cell Receptor molecules. The flexibility profile of the molecular surf...
Article
Full-text available
A single amino acid difference (Asp116His), having a key role in a pathogenesis pathway, distinguishes HLA-B*27:05 and HLA-B*27:09 sub-types as associated and non-associated with ankylosing spondylitis, respectively. In this study, molecular docking simulations were carried out with the aim of comprehending the differences in the binding behavior o...
Conference Paper
Understanding the characteristic dynamics of different Human Leukocyte Antigen (HLA) alleles of the peptide-loaded Major Histocompatibility Complex (pMHC) may help explain mechanism of initial steps in T-cell activa- tion. Molecular Dynamics (MD), as a fully atomistic simulation method, is commonly used to explain the functional effect of polymorph...
Conference Paper
Peptide-loaded Major Histocompatibility Complex‭ (‬pMHC‭) ‬proteins play a key role in the transmission of molecular signals through the immune system via their interaction with T-cell receptors.‭ ‬Many alleles and sub-types of these proteins are found to be associated with autoimmune diseases‭; ‬hence the importance of understanding the mechanism...
Conference Paper
The dynamic behavior of peptide-loaded Major Histocompatibility Complex‭ (‬pMHC‭) ‬plays a role in defining the immunogenicity of the pMHC-T-cell Receptor interaction.‭ ‬However,‭ ‬due to the highly polymorphic nature of the antigen chain of the complex‭ (‬Human Leukocyte Antigens,‭ ‬HLA‭) ‬and the limitation of experimental and computational metho...

Questions

Question (1)
Question
Dear all,
I would like to calculate pairwise non-bonded interaction energies between amino acid residues in a protein over the length of MD simulation trajectories produced by the NAMD 2.9 software using the CHARMM 27 force-field.
Currently I use the namdenergy.tcl script for this purpose. I apply a minimum distance cutoff between alpha carbon positions to reduce the number of combinations as well as a stride for frames to be read. I have also written a Python program which divides the list of combinations into chunks (to take advantage of the multiple processors) and calls vmd (and subsequently the namdenergy) using an another external tcl script in parallel processes via the python multiprocessing module.
I want to include as many frames as possible in my calculation to avoid missing possibly interesting changes in the interaction energies since I also calculate the correlations between them in a later analysis step. However, when I reduce the stride value, the time required to finish the computation increases rather exponentially. 
Namdenergy creates a temporary DCD file prior to each calculation. Also, if I move the files to a solid-state drive and run the calculation there, it speeds up by a factor of two, leading me to think that the computation is I/O bound.
So is there a more efficient/faster way to do this kind of computation (e.g. another computational tool) or is this just a speed limit that I have to live with?

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Projects

Projects (3)
Project
The aim of the thesis is the screening of new EPIs for the most common multidrug resistance efflux pumps of ABC and MFS classes.