Theses supervised by Prof. Dr. Burak Erman
13 theses · Koç University
Melanopsin ve cryptochrome proteinleri arasındaki etkileşimin hesaplamalı araştırması
Circadian rhythms are oscillations in the biochemical, physiological, and behavioralfunctions of organisms that occur with a periodicity of approximately 24 hours. Inmammals, circadian rhythm is generated by a molecular clock. The molecular clock,which is located at suprachiasmatic nuclei (SCN) part of brain, is synchronized byenvironmental light-dark cycle.The cryptochromes are the mammalian circadian photoreceptors; they absorb light andtransmit the signal to the molecular clock. The cryptochromes and melanopsin (andpossibly other opsin family pigments) have been proposed as circadian photoreceptorpigments that exist in the inner retina. Experimental studies imply that there is mostprobably an interaction between melanopsin and cryptochromes for molecular clock tofunction normally. In order to uncover this interaction; the tertiary structures ofMelanopsin and Cryptochrome; the possible interaction between those two proteins havebeen predicted by usage of different computational means.The results of this study imply that mammalian Melanopsin and Cryptochrome proteinsinteract. The N-termini of Cryptchrome protein interacts with C-termini and cytoplasmictails of Melanopsin protein. The in vivo interaction is supported by preliminaryflourescent microscopy technique.
Protein dönme açılarını tahmin etmek için bilgi tabanlı yöntem
The three dimensional structure of a protein can be identified in terms of its torsion angles. These torsion angles can be considered as the degrees of freedom of a protein. In this study, a method grouping these torsion angles in different rotational isomeric states and estimating their probabilities is developed. Specifically, the probabilities of the various torsion angle states in Ramachandran maps is proposed and the accuracy of the method is examined using a knowledge based approach. Statistical independence and dependence of the states of different residues along the peptide chain are analyzed. The Flory isolated pair hypothesis, near neighbor correlations, context effects and long-range correlations are discussed. In the knowledge based approach, two different protein libraries i) coil library ii) full libarary are constructed and information from both these libraries is used. Results showed that amino acids have propensities for some rotational isomeric states that favor the choice of the native state torsion angles and they are context dependent, preferring different torsion states determined by the amino acid sequence of the protein. Context dependency is also related to chameleon sequences and the effect of chameleon sequences is also integrated into the method.
Yapı odaklı ilaç tasarımı
The aim of this study is to target two possible pathways of cancer which are (i) p65p50 protein heterodimer from NF-?B protein family and (ii) Fgfr2 from fibroblastic growth hormone receptors. A structure-based screening approach, based on a data set of 236 natural products for each protein is adopted. Docking analysis is performed for structure-based screening. Three scoring functions are used for docking. Docking results of both proteins and their ranking are compared using known scoring functions. It is shown that scoring functions have a tendency to rank specific structural groups selectively. AutoDock, which is based on a semi-empirical function, performs the rankings according to the properties of the ligands in the data set. Hence, AutoDock ranks via selecting a specific group from the data set. The two other scoring functions, Gold Score and Chem Score that come with the software GOLD (Genetic Optimization for Ligand Docking) show that specific groups of molecules are ranked selectively according to the properties of both the system and the ligand. Variation between selectivity of different scoring functions is based on the main equations used within each scoring function. On the other hand, as also reported in recent studies, although the ranking of a docked protein-ligand pair depends on the scoring function used, the orientation and interaction modes of docking performed with different scoring functions are similar.
JMJD2A enziminin metilasyon spesifisitesinin karşılaştırmalı moleküler dinamik çalışması
Specific patterns of post-translational modifications of histones act as a molecular ?code? recognized and used by non-histone proteins to regulate specific chromatin functions. K9 methylation on Histone 3 (H3) tail, mainly trimethylation, induces formation of constitutive heterochromatin via a well-known pathway, which employs heterochromatin formation protein (HP1) and DNA methyl transferase (DNMT). Jumonji domain containing 2A (JMJD2A) is a histone demethylase that specifically removes K9 and K36 trimethyl marks on H3 tail. This enzyme does not function on monomethyl marks and has almost 20-fold reduced activity on dimethyl forms compared to trimethyl forms.In order to gain insight into how JMJD2A discriminates between its substrates, we performed molecular dynamics simulations of mono-, di- and trimethylated histone tails in complex with JMJD2A catalytic domain and analyzed positional fluctuations, located the hydrogen bonds and calculated some critical distances. We revealed the importance of water molecules and the oxygen-enclosed environment in appropriate orientation of methylammonium head in the active site. We also calculated binding free energy and energy contribution of each residue. We found out that recognition is mostly driven by van der Waals and Coulombic interactions in enzyme-substrate interface. We also revealed the role of Arg8 on the H3 tail in binding and stabilizing the necessary conformation of substrate peptide.
Proteinlerde bulunan ligand bağlanma yerlerinin ağ yapı modeli kullanarak tespit edilmesi
Biomolecular interactions play key roles in biological activity. Investigation of those interactions, including protein-ligand interactions, is crucial for understanding the way that nature designed its biological machinery. Ligand binding particularly requires, recognition of the ligand by the protein, which in turn arranges the three dimensional structure of the protein, mostly directed by the energetic interactions involved. Based on these requirements, ligand-binding has been considered as a local process. Yet, it has been recently shown that ligand binding depends not on the local structure, but rather on an interaction pathway, that takes part in rearrangement of the protein into the most favorable conformation upon binding.The nonlocal nature of the protein-ligand binding problem is investigated via the Gaussian Network Model with which the residues lying along interaction pathways in a protein and the residues at the binding site are predicted. The predictions of the binding site residues are verified by using several benchmark systems where the topology of the unbound protein and the bound protein-ligand complex are known. Predictions are made on the unbound protein. Agreement of results with the bound complexes indicates that the information for binding resides in the unbound protein. Cliques that consist of three or more residues that are far apart along the primary structure but are in contact in the folded structure are shown to be important determinants of the binding problem.Comparison with known structures shows that the predictive capability of the method is significant.
Alzheimer hastalığındaki amyloid beta birikimi için hesaplamalı olarak peptid inhibitör tasarlanması
The most common form of dementia, Alzheimer?s disease, that is neurodegenerative and incurable, is associated with tight packaging of amyloid fibrils. This packaging is caused by the compatibility of the ridges and grooves on the amyloid surface that are composed of ß-sheets orientation. The major factor which creates compatibility between two amyloid surfaces is GxMxG motif. Therefore, this motif is an important target in designing inhibitors for amyloid fibrillization. In this study, particular peptides that bind Aß40 fibrils according to amino acids groups were modified, and a small peptide library was composed. The peptide sequences that bind the surface via GxMxG motif were identified with the docking program GOLD. The sequence that had the highest docking score and binds to around MET35 was selected. Finally, the binding free energies of modified and unmodified peptides were calculated with Steered Molecular Dynamics by using the Jarzynski?s Equality.
Protein bağlanması ve proteinlerde mod bağlanması
In order to understand the the change in thermodynamic properties upon binding and determine the binding sides, two hexa-peptides and their bound complex structures were analyzed. In order to extract the thermodynamic properties and determine the binding side, a harmonic model was applied.The harmonic formulation is extended to large ? uctuations of residues in order to account for effects of anharmonicity. The ? uctuation probability function is constructed for this purpose as a tensorial Hermite series expansion with higher order moments of ? uctuations as coef ? cients.Mode coupling and anharmonicity in a native fluctuating protein is investigated in modal space. Molecular dynamics trajectories of Crambin are generated and used to evaluate the terms of the polynomials and to obtain the modal energies. Slowest modes have energies that are below that of the harmonic energy, kT/2 per mode, and a few fast modes have energies significantly larger than the harmonic which is a result of coupling. Detailed analysis of the lowest order two mode coupling terms is presented.It is was shown that mode coupling and anharmonicity are important for modeling the multidimensional energy landscape of Crambin. The effect of them on the fluctuational entropy is on the order of a few percent.The fluctuations and unbinding free energy profiles of two very similar proteins, HLA-B51 and HLA-B52, were investigated. HLA-B51 is related to the Behçet?s disease whereas HLA-B52 is not. Change in the dynamics of 1 helix were analyzed. Unbinding from HLA-B52 resulted in greater free energy differences than for HLA-B51.
Fibroblast büyüme faktörü reseptörü (FGFR3) IIIB için hesaplamalı yöntemlerle pentapeptid inhibitör tasarımı
Fibroblast growth factor receptor (FGFR) is a cell membrane protein, a member of tyrosine kinase family, which has extracellular domains activated by ligand binding, followed by receptor dimerization. FGFR3 has two isoforms, IIIb and IIIc. The IIIb isoforom of FGFR3 is a highly expressed epithelial cell protein, whose R248C mutation causes different kinds of dermatological diseases like seborrheic keratoses (SK), acanthosis nigricans (AN) and epidermal nevi (EN). This mutation leads to ligand independent receptor dimerization, which increases intracellular signaling, resulting in skin diseases. In order to prevent R248C mutation-caused cellular signaling, a pentapeptide ligand is designed that recognizes the mutation and binds to the receptor dimerization site. For this purpose molecular docking and molecular dynamics simulations are conducted. Binding free energy is calculated with Steered Molecular Dynamics (SMD) and Molecular mechanics ? Generalized Born Surface Area (MM-GBSA) methods. The found pentapeptide sequence appears to be a possible drug candidate for FGFR3 IIIb R248C mutation related skin diseases.
Kaspaz-1 için peptit bazlı ilaç tasarımı ve metabolik yol analizi
As one of the mostly studied protein in the literature, caspase-1 (ICE) attracts the attention of many scientists due to its crucial roles in inflammatory responses. It has other roles in the apoptotic path, for example, because of having more than 40 substrates. Increased expression of its substrates such as pro-IL-1beta results in inflammatory disorders. Consequently, inhibition and pathway studies related to caspase-1 have gained importance.Peptide based drug design for caspase-1 is performed and potent inhibitors are determined computationally. Bicylic (a molecule that contains two fused rings) and ketone structures with Asp and D-enantiomeric aminoacids are obtained as good inhibitors in accordance with previous experimental work. Moreover, multi-target drug determination in the caspase-1 pathway is made. Conformational factors in tripeptides are also taken into consideration with Viterbi Algorithm, which indicates whether a peptide can change its conformation from minimized state to bound state.Knockout analysis on the ICE pathway by Gaussian Network Model (GNM) shows knockouts of NLRP3, ASC, caspase-1, NF-kappaB, pro-IL-33, TLR4, TLR2, TRIF and MyD88 are effective.?
İnterlökin 1 beta (IL-1ß) için peptid kökenli inhibitör dizaynı
Interleukin 1 beta (IL-1ß) is a pro-inflammatory cytokine which is activated intracellularly by the cleavage of Caspase-1 (Interleukin converting enzyme, ICE). Upon activation, IL-1ß is secreted to the extracellular region. Increased expression of IL-1ß is associated with several diseases such as rheumatoid arthritis and intestinal inflammation. Thus in controlling these kinds of diseases, blocking IL-1ß has great importance. IL-1ß has an embedded receptor (IL-1R) and an accessory protein (IL-1RAcP) in the cell surface. IL-1ß binds to its receptor and to the accessory protein which juxtaposes the intracellular domains of its receptors and causes more expression of IL-1ß. In this study, inhibition of active IL-1ß has been studied extensively by using computational docking tools and techniques. Binding residues of IL-1ß to its receptor were accepted as docking regions. Genetic Algorithm (GA) and Viterbi algorithm (VA) based on the Hidden Markov Model were applied to obtain the most suitable inhibitor candidate by considering its binding free energy and secondary structure conformation. As a result, tripeptide and pentapeptide candidates from Genetic Algorithm and thirty heptapeptide candidates from the Viterbi Algorithm were obtained. Elimination of the candidates was achieved by Molecular Dynamics Simulations by calculating binding free energies of the ligands. Most potent inhibitor for IL-1ß was observed to inhibit IL-1? as well. The unbinding process of ligands was investigated and their probability distribution graphs were examined.
Bir moleküler dinamik analizi: Kolşisinin kaspaz-1 aktivasyonu üzerindeki etkisi
Caspase-1 is a member of a family of aspartate-specific cysteine proteases. Since there is a large number of studies of caspase-1 in inflammation processes, this enzyme became an important drug target in order to prevent the disorders which are associated with caspase-1. Colchicine, which is a common drug used for Familial Mediterranean Fever and gouty arthritis disorders, inhibits caspase-1 activation, but the mechanism of inhibition is not clearly known. Procaspase-1 is activated through oligomerization in inflammasome and then becomes auto-activated. Some studies show that caspase-1 is regulated by allosteric regulation through a hydrogen bonding network passing dimer-dimer interface and has two conformational states which are controlled by active-site and allosteric-site inhibitors. In this study, colchicine is bound to dimer-dimer interface of procaspase-1 enzyme. By using Molecular Dynamics simulations, the changes of distances and correlations between residue pairs before and after colchicine bound was calculated. Since the structural changes on active site were observed after colchicine binding to allosteric site -dimer-dimer interface-, the inhibitory effect of colchicine on caspase-1 enzyme may be through the allosteric regulation. This outcome may be guide for further drug discoveries.
K-Ras proteini ve onkojenik mutasyonları üzerine kapsamlı bir çalışma: Dinamik bir bakış açısı
K-Ras is the most frequently mutated protein in human cancers driving cancer initiation, progression and drug resistance, directly leading to nearly a million deaths per year. Sadly, there are still no drugs in that directly target mutant K-Ras in the clinic. Recent studies utilizing dynamics information show promising results for selectively targeting it. However, despite extensive characterization, the regulatory mechanisms of K-Ras dynamics remain elusive. Since protein function is related to its dynamics, understanding these mechanisms can present novel opportunities for identifying target sites on mutant K-Ras surface. In this work, we investigate the regulation mechanisms of K-Ras dynamics and the effects of nucleotide binding and mutations on these mechanisms using extensive molecular dynamics (MD) simulations. We applied different MD simulation data analysis techniques to compare the dynamic characteristics of both active and inactive forms of wild-type K-RasWT and mutant K-RasG12D, the most recurrent mutant in cancer patients. Our results on K-RasWT showed excellent agreement with experimental data and served as a reference point for K-RasG12D analysis. Then, we demonstrated how G12D mutation induces structural and conformational changes that result in characteristic correlated motions in active K-RasG12D. Moreover, we developed a novel conditional time-delayed correlations (CTC) based approach to predict causal relationships in regulation of K-Ras dynamics. CTC analysis identified the regulatory sites that control K-Ras dynamics. Finally, we identified a novel drug target pocket in active K-RasG12D and screened a small molecule library against it using docking techniques. Our study draws a complete picture of the regulation of K-Ras dynamics. We anticipate that the identified regulatory sites on active K-RasG12D can present novel opportunities for direct targeting of K-RasG12D in future drug discovery efforts.
Proteinler içindeki iletişim ağını ve ligand bağlama, mutasyon ve çeviri sonrası değişiklikler üzerindeki dinamiklerindeki değişimi inceleyen hesaplamalı bir çalışma
The thesis analyses the dynamic and structure changes in biomolecules upon ligand or protein binding, mutation and post translational modifications such as phosphorylation or methylation by using computational methods. The computational methods utilized throughout this study are biophysics based; harmonic interaction and molecular dynamics (MD)-based approaches. The entropy transfer concept is used to detect allosteric communication network in proteins in first chapter and the driver-driven relationships between residue pairs are introduced, by using Molecular Dynamics based and Gaussian Network Model based approaches. In second chapter, a special derivative of antibodies produced by camelids named as nanobodies are optimized for humans and specific design criteria and methods are introduced to optimize a given nanobody to a specific antigen. Longer simulations must be conducted in order to get reliable results from a Molecular dynamics simulation. To enhance sampling by running several short MD simulations, most important motions must be filtered out by removing the noise in the simulations by a Latent Semantic Indexing analysis. This method is used to enhance conformational sampling quality from three short MD simulations of MEK1 protein and residue fluctuations of the filtered and unfiltered trajectories are compared. In the following chapter the activation mechanism of MEK1 protein upon Raf binding and following phosphorylation are investigated. The effect of ligand binding and mutation on MEK1 dynamics are revealed and the effects of these events on MEK1 and dual phosphorylated MEK1 are compared. In the final chapter the effect of DNA methylation on methyl binding protein affinities are investigated and the effect of hydration of the binding site is explained. MeCP2 and MBD2 proteins are used to investigate these effects and the binding affinities are compared by using Steered Molecular Dynamics simulations. Biology adapted itself to computer and computational methods makes biological concepts easily testable. With the integration of mathematics, physics, statistics and computational methods the ideas will shape into hypotheses and large amount of data produced by computational methods will direct and shape experimental studies.