Esma ERYILMAZ | Selcuk University (Selçuk Üniversitesi) (original) (raw)

Papers by Esma ERYILMAZ

Medicine Science | International Medical Journal, 2021

Pinostrobin as a famous member of flavonoid family has been investigated in terms of its therapeu... more Pinostrobin as a famous member of flavonoid family has been investigated in terms of its therapeutic effect on a variety of diseases, and positive effect has been reported in many in vitro and in vivo studies. As one of the essential elements of blood plasma in human body, serum albumin functions a carrier protein for fatty acids, hormones, and drugs because of its abundance and strength in blood. For that, serum albumin plays an important role on the understanding of pharmacological effect of the promising therapeutic agent, pinostrobin. For providing insight into the preclinical studies of albumin targeted therapeutics, we, in this study, investigated the binding characteristics of human serum albumin – pinostrobin complex in terms of binding energy, bounded residues, and association constants, and compared them with various mammalian albumins such as goat, bovine, porcine, rabbit, sheep, and dog albumins. We used molecular modeling and molecular docking methods with the softwares PyRX and PyMol. We found that pinostrobin-human serum albumin had an association constant in between (10.26-20.16)105 M-1 with the interaction energy in a range of (-8.2(-8.6)) kcal/mol. Among animal proteins, porcine (5IIU) and sheep (4LUF) showing the interaction energy of -8.4 kcal/mol and -8.1 kcal/mol, respectively, were found to be the most appropriate animal models to be used in albumin based preclinical investigations.

Medicine Science | International Medical Journal, 2021

Estrogen receptor is a key feature of many complex disorders. Natural estrogen ligand, estradiol ... more Estrogen receptor is a key feature of many complex disorders. Natural estrogen ligand, estradiol has been investigated in the pharmaceutical aspect of breast cancer, Parkinson's, Alzheimer's, risk of stroke in postmenopausal women, and dementia. From the similar manner, synthetic selective estrogen receptor modulators (SERMs) have been investigated, and their pharmaceutical effects have been evaluated in compared to the natural ligand, estradiol, in literature. To design better alternatives to the approved SERMs and to improve the clinical observations, it is crucial to understand the molecular basis of drug-target interactions of estrogen receptor with the natural and synthetic ligands in a comparative manner. We used molecular modeling softwares PyRX, Avogadro, and Arguslab for in silico calculations. The results were analyzed using PyMol. We, in this study, provided a computational binding analysis of the estrogen receptor with the endogenous ligand estradiol and the FDA approved SERMs raloxifene, tamoxifen, and toremifene. We investigated the toxicity profile of the SERMs and estradiol and interpreted the results according to the reported clinical observations. We found that designing new molecules based on the estradiol structure instead of the approved tamoxifen analogs could result in better clinical observations for future estrogen targeting therapeutics.

Physical review letters, Jan 11, 2014

We study a broad class of epitaxial assembly of filament networks on lattice surfaces. Over time,... more We study a broad class of epitaxial assembly of filament networks on lattice surfaces. Over time, a scale-free behavior emerges with a 2.5-3 power-law exponent in filament length distribution. Partitioning between the power-law and exponential behaviors in a network can be used to find the stage and kinetic parameters of the assembly process. To analyze real-world networks, we develop a computer program that measures the network architecture in experimental images. Application to triaxial networks of collagen fibrils shows quantitative agreement with our model. Our unifying approach can be used for characterizing and controlling the network formation that is observed across biological and nonbiological systems.

Interdisciplinary Sciences: Computational Life Sciences, 2021

MicroRNA (miRNA) molecules, which are effective in the formation and progression of many differen... more MicroRNA (miRNA) molecules, which are effective in the formation and progression of many different diseases, are 18-22 nucleotides in length and make up a type of non-coding RNA. Predicting disease-related microRNAs is crucial for understanding the pathogenesis of disease and for diagnosis, treatment, and prevention of diseases. Many computational techniques have been studied and developed, as the experimental techniques used to find novel miRNA-disease associations in biology are costly. In this paper, a Kernelized Bayesian Matrix Factorization (KBMF) technique was suggested to predict new relations among miRNAs and diseases with several information such as miRNA functional similarity, disease semantic similarity, and known relations among miRNAs and diseases. AUC value of 0.9450 was obtained by implementing fivefold cross-validation for KBMF technique. We also carried out three kinds of case studies (breast, lung, and colon neoplasms) to prove the performance of KBMF technique, and the predictive reliability of this method was confirmed by the results. Thus, KBMF technique can be used as a reliable computational model to infer possible miRNA-disease associations.

European Journal of Science and Technology, 2021

Complex diseases such as cancer are mostly described by combining negative effects of multiple bi... more Complex diseases such as cancer are mostly described by combining negative effects of multiple biological factors or pathways. Based on that, multi-targeted approach for treating cancer is gaining interest. The aim of this study is to introduce a computational approach and to design new, multi-targeted drug candidates for treatment of bone cancer. In this approach, the FDA approved drugs of bone cancer were evaluated in terms of their molecular pharmaceutical properties and their bioactivity parameters predicted by bioinformatics and cheminformatics softwares. Among them, Methotrexate was chosen as a lead molecule due to its broader spectrum of bioactivity on the most important drug targets reported in literature. The lead molecule was exposed to basic bioisosteric modifications to obtain a better drug compound with improved bioactivity and a stronger drug-likeness profile using the known drug structure. Design compounds produced by a number of bioisosteric modifications performed on the 2D structure of the lead compound were evaluated in terms of both criteria; bioactivity and drug-likeness. Silicone modified compounds M4, M13, M14, and M15 showed a much broader spectrum of biological activity than that of the approved compound Methotrexate. The interesting effect of silicone incorporation makes our compounds promising drug candidates for further pharmaceutical investigation.

Macromolecular self-assembly is a promising way of fabricating ordered structures with interestin... more Macromolecular self-assembly is a promising way of fabricating ordered structures with interesting mechanical and optical properties. Learning how to produce highly organized structures and how to mediate the organization provide technological and application wise opportunities at both macroscale and nanoscale. In this study, we worked with an extracellular matrix protein collagen onto different substrates and try to control and to manipulate the assembly process externally. The most attractive benefit of producing biomaterial via self-assembly is the ability of controlling the mechanism by external parameters from nanometer scale to millimeter. Due to the prevalence of collagen fibril in human tissue and its self-assembly ability in vitro, Collagen becomes an important bio-macro molecule frequently used in biomedical materials and tissue engineering applications in recent decades. In this work, by using two different substrates, we observed a direct influence of the surface symmetr...

European Journal of Science and Technology, 2021

MicroRNA (miRNA) molecules, which are effective on the initiation and progression of many differe... more MicroRNA (miRNA) molecules, which are effective on the initiation and progression of many different diseases, are a type of noncoding RNA with a length of about 22 nucleotides. Scientists have reported the importance of miRNAs in the prevention, diagnosis, and treatment of complex human diseases. Therefore, in the last decade, researchers have been working hard to find potential miRNAdisease associations. Many computational techniques have been developed because of the experimental techniques are time-consuming and expensive used to find new relationships between miRNAs and diseases. In this study, we suggested Kernelized Bayesian matrix factorization (KBMF) technique to predict new miRNA-disease relationships. We applied 5-fold cross validation technique and obtained an average value AUC of 0.9450. Also, we applied case studies based on breast, lung, and colon neoplasms to prove the performance of KBMF technique. The results showed that KBMF can be used as a reliable computational model to reveal possible miRNA-disease relationships.

Biomedical Physics & Engineering Express, 2019

Collagens have remarkable ability to self-assemble into ordered fibrils. Assembly of collagens on... more Collagens have remarkable ability to self-assemble into ordered fibrils. Assembly of collagens on 2-dimensional surfaces serves as amodel system to study the dynamics of assembly process and the resultingfibrilar structure has potential biotechnological and biomedical applications. However, intermolecular forces driving the self-assembly of collagen are not well understood.Here, we apply the Derjaguin-Landau-Verwey-Overbeek (DLVO) theory to investigate the interactions between collagens and between collagen and themica surface. Interactions are found to be attractive at all distances, which is consistent with literature. To further investigate the sequence-dependent organization of collagenmolecules, we examined interaction near contact distances when collagen molecules are staggered to different degrees.We compared electrostatic, hydrophobic, and polar hydration interaction, and found that hydrophilic interaction plays a significant role on themolecular assembly by protecting themolecule from random collapsewith a consistent repulsion barrier. Electrostatic interaction, on the other hand, exhibits local energymaxima andminima onD-periodic arrangements throughout themolecule leading to an oscillation effect on the axial self-assembly. Our approaches, in bothmacromolecular and nanoscale, provide insights into the factors that determine interactions among collagens and between collagen andmica.

Cellular and Molecular Bioengineering, 2016

fibrils, the main constituents of the extracellular matrix, are "biological alloys" that contain ... more fibrils, the main constituents of the extracellular matrix, are "biological alloys" that contain many additive molecules for fine-tuning the dynamical and biological properties. A representative example is the type-I collagen fibril, the most abundant among the 28 collagen types, which also contains type-III collagen. We perform atomic force microscopy (AFM) to elucidate the coassembly of these two important members into heterotypic fibrils on mica surfaces. Time-lapse AFM imaging of samples at different ratios of type-I and type-III collagen molecules revealed that type-III assembles and nucleates fibrils slower than type-I. Furthermore, in the type-I/III mixture, nucleation appeared to be enhanced, resulting in formation of more fibrils compared to cases with either type-I or III only. We discuss possible mechanisms for the enhanced fibril nucleation in the co-assembly process of the two molecules that differ slightly in physical properties.

European Journal of Science and Technology, 2021

This article is an open access article distributed under the terms and conditions of the Creative... more This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY

Journal of Selcuk University Natural and Applied Science, 2016

Ab initio calculations have been performed for a doublet H 2 COH --> H 3 CO and a singlet sys... more Ab initio calculations have been performed for a doublet H 2 COH --> H 3 CO and a singlet system of SiH 4 -->H 2 +H 2 reactions. Geometry optimization including frequency analysis have been accomplished at the HF/6-31G(d) level of theory for reactants, transition states (TS), and products of the reactions studied. The physico-chemical properties of the compounds including zero-point energy, multiplicity, dipole moment, and point group symmetries have been calculated at the same level of theory. Upon obtaining TS geometry, the reaction paths following for the reactions have been generated with the IRC keyword and the TS structures have been confirmed to belong to the reactions desired. The activation energies and the formation of reaction have been calculated by using the total energy graph along the IRC reaction coordinate. The reaction paths generated by the program exhibit the exothermic/endothermic characteristics of the reactions.

We study a broad class of epitaxial assembly of filament networks on lattice surfaces. Over time,... more We study a broad class of epitaxial assembly of filament networks on lattice surfaces. Over time, a scale-free behavior emerges with a 2.5-3 power-law exponent in filament length distribution. Partitioning between the power-law and exponential behaviors in a network can be used to find the stage and kinetic parameters of the assembly process. To analyze real-world networks, we develop a computer program that measures the network architecture in experimental images. Application to triaxial networks of collagen fibrils shows quantitative agreement with our model. Our unifying approach can be used for characterizing and controlling the network formation that is observed across biological and nonbiological systems.

European Journal of Science and Technology

Biomedical Physics & Engineering Express

Collagens have remarkable ability to self-assemble into ordered fibrils. Assembly of collagens on... more Collagens have remarkable ability to self-assemble into ordered fibrils. Assembly of collagens on 2-dimensional surfaces serves as amodel system to study the dynamics of assembly process and the resultingfibrilar structure has potential biotechnological and biomedical applications. However, intermolecular forces driving the self-assembly of collagen are not well understood.Here, we apply the Derjaguin-Landau-Verwey-Overbeek (DLVO) theory to investigate the interactions between collagens and between collagen and themica surface. Interactions are found to be attractive at all distances, which is consistent with literature. To further investigate the sequence-dependent organization of collagenmolecules, we examined interaction near contact distances when collagen molecules are staggered to different degrees.We compared electrostatic, hydrophobic, and polar hydration interaction, and found that hydrophilic interaction plays a significant role on themolecular assembly by protecting themolecule from random collapsewith a consistent repulsion barrier. Electrostatic interaction, on the other hand, exhibits local energymaxima andminima onD-periodic arrangements throughout themolecule leading to an oscillation effect on the axial self-assembly. Our approaches, in bothmacromolecular and nanoscale, provide insights into the factors that determine interactions among collagens and between collagen andmica.

Cellular and Molecular Bioengineering, Aug 31, 2016

An important step towards achieving functional diversity of biomimetic surfaces is to better unde... more An important step towards achieving functional diversity of biomimetic surfaces is to better understand the co-assembly of the extracellular matrix components. For this, we study type-I and type-III collagen, the two major collagen types in the extracellular matrix. By using atomic force microscopy, custom image analysis, and kinetic modeling, we study their homotypic and heterotypic assembly. We find that the growth rate and thickness of heterotypic fibrils decrease as the fraction of type-III collagen increases, but the fibril nucleation rate is maximal at an intermediate fraction of type-III. This is because the more hydrophobic type-I collagen nucleates fast and grows in both longitudinal and lateral directions, whereas more hydrophilic type-III limits lateral growth of fibrils, driving more monomers to nucleate additional fibrils. This demonstrates that subtle differences in physico-chemical properties of similar molecules can be used to fine-tune their assembly behavior.Electr...

European Journal of Pharmaceutical Sciences

Acute Lymphoblastic Leukemia (ALL) represents 30% of all childhood cancers and children younger t... more Acute Lymphoblastic Leukemia (ALL) represents 30% of all childhood cancers and children younger than 5 years old have the highest risk for developing ALL. Existing ALL drugs do not respond in approximately 20% of treatment. Therefore, drug development studies against ALL must be continued with either developing existing drugs or discovering new ones. In this study, we evaluated the U.S Food and Drug Administration (FDA) approved ALL drugs according to their physicochemical and pharmaceutical properties, and Nelarabine was found to have the highest bioactivity score. Using the key strategy of bioisosterism commonly accepted by medicinal chemists, we investigated in silico ADME properties, drug-likeness, and biological activity of new designed twenty-four compounds including Nelarabine. The results were evaluated in terms of two classifications: broad spectrum biological activity and filtering of five different drug likeness criteria of the literature including Lipinski's rule of five. We interestingly observed that silicon incorporated compounds exhibited better performance on both criteria by targeting broader spectrum of drug receptors including G-protein coupled receptor (GPCR), ion channel modulator, kinase inhibitor, protease and enzyme inhibitor and by satisfying all of five different drug-likeness criteria reported in the literature. Design compound C19 appeared as a potential drug candidate for further pharmacological research.

Physical Review Letters, 2014

We study a broad class of epitaxial assembly of filament networks on lattice surfaces. Over time,... more We study a broad class of epitaxial assembly of filament networks on lattice surfaces. Over time, a scalefree behavior emerges with a 2.5-3 power-law exponent in filament length distribution. Partitioning between the power-law and exponential behaviors in a network can be used to find the stage and kinetic parameters of the assembly process. To analyze real-world networks, we develop a computer program that measures the network architecture in experimental images. Application to triaxial networks of collagen fibrils shows quantitative agreement with our model. Our unifying approach can be used for characterizing and controlling the network formation that is observed across biological and nonbiological systems.

Journal of Bioinformatics and Computational Biology

MicroRNAs (miRNA) are a type of non-coding RNA molecules that are effective on the formation and ... more MicroRNAs (miRNA) are a type of non-coding RNA molecules that are effective on the formation and the progression of many different diseases. Various researches have reported that miRNAs play a major role in the prevention, diagnosis, and treatment of complex human diseases. In recent years, researchers have made a tremendous effort to find the potential relationships between miRNAs and diseases. Since the experimental techniques used to find that new miRNA-disease relationships are time-consuming and expensive, many computational techniques have been developed. In this study, Weighted [Formula: see text]-Nearest Known Neighbors and Network Consistency Projection techniques were suggested to predict new miRNA-disease relationships using various types of knowledge such as known miRNA-disease relationships, functional similarity of miRNA, and disease semantic similarity. An average AUC of 0.9037 and 0.9168 were calculated in our method by 5-fold and leave-one-out cross validation, resp...

Medicine Science | International Medical Journal, 2021

Pinostrobin as a famous member of flavonoid family has been investigated in terms of its therapeu... more Pinostrobin as a famous member of flavonoid family has been investigated in terms of its therapeutic effect on a variety of diseases, and positive effect has been reported in many in vitro and in vivo studies. As one of the essential elements of blood plasma in human body, serum albumin functions a carrier protein for fatty acids, hormones, and drugs because of its abundance and strength in blood. For that, serum albumin plays an important role on the understanding of pharmacological effect of the promising therapeutic agent, pinostrobin. For providing insight into the preclinical studies of albumin targeted therapeutics, we, in this study, investigated the binding characteristics of human serum albumin – pinostrobin complex in terms of binding energy, bounded residues, and association constants, and compared them with various mammalian albumins such as goat, bovine, porcine, rabbit, sheep, and dog albumins. We used molecular modeling and molecular docking methods with the softwares PyRX and PyMol. We found that pinostrobin-human serum albumin had an association constant in between (10.26-20.16)105 M-1 with the interaction energy in a range of (-8.2(-8.6)) kcal/mol. Among animal proteins, porcine (5IIU) and sheep (4LUF) showing the interaction energy of -8.4 kcal/mol and -8.1 kcal/mol, respectively, were found to be the most appropriate animal models to be used in albumin based preclinical investigations.

Medicine Science | International Medical Journal, 2021

Estrogen receptor is a key feature of many complex disorders. Natural estrogen ligand, estradiol ... more Estrogen receptor is a key feature of many complex disorders. Natural estrogen ligand, estradiol has been investigated in the pharmaceutical aspect of breast cancer, Parkinson's, Alzheimer's, risk of stroke in postmenopausal women, and dementia. From the similar manner, synthetic selective estrogen receptor modulators (SERMs) have been investigated, and their pharmaceutical effects have been evaluated in compared to the natural ligand, estradiol, in literature. To design better alternatives to the approved SERMs and to improve the clinical observations, it is crucial to understand the molecular basis of drug-target interactions of estrogen receptor with the natural and synthetic ligands in a comparative manner. We used molecular modeling softwares PyRX, Avogadro, and Arguslab for in silico calculations. The results were analyzed using PyMol. We, in this study, provided a computational binding analysis of the estrogen receptor with the endogenous ligand estradiol and the FDA approved SERMs raloxifene, tamoxifen, and toremifene. We investigated the toxicity profile of the SERMs and estradiol and interpreted the results according to the reported clinical observations. We found that designing new molecules based on the estradiol structure instead of the approved tamoxifen analogs could result in better clinical observations for future estrogen targeting therapeutics.

Physical review letters, Jan 11, 2014

We study a broad class of epitaxial assembly of filament networks on lattice surfaces. Over time,... more We study a broad class of epitaxial assembly of filament networks on lattice surfaces. Over time, a scale-free behavior emerges with a 2.5-3 power-law exponent in filament length distribution. Partitioning between the power-law and exponential behaviors in a network can be used to find the stage and kinetic parameters of the assembly process. To analyze real-world networks, we develop a computer program that measures the network architecture in experimental images. Application to triaxial networks of collagen fibrils shows quantitative agreement with our model. Our unifying approach can be used for characterizing and controlling the network formation that is observed across biological and nonbiological systems.

Interdisciplinary Sciences: Computational Life Sciences, 2021

MicroRNA (miRNA) molecules, which are effective in the formation and progression of many differen... more MicroRNA (miRNA) molecules, which are effective in the formation and progression of many different diseases, are 18-22 nucleotides in length and make up a type of non-coding RNA. Predicting disease-related microRNAs is crucial for understanding the pathogenesis of disease and for diagnosis, treatment, and prevention of diseases. Many computational techniques have been studied and developed, as the experimental techniques used to find novel miRNA-disease associations in biology are costly. In this paper, a Kernelized Bayesian Matrix Factorization (KBMF) technique was suggested to predict new relations among miRNAs and diseases with several information such as miRNA functional similarity, disease semantic similarity, and known relations among miRNAs and diseases. AUC value of 0.9450 was obtained by implementing fivefold cross-validation for KBMF technique. We also carried out three kinds of case studies (breast, lung, and colon neoplasms) to prove the performance of KBMF technique, and the predictive reliability of this method was confirmed by the results. Thus, KBMF technique can be used as a reliable computational model to infer possible miRNA-disease associations.

European Journal of Science and Technology, 2021

Complex diseases such as cancer are mostly described by combining negative effects of multiple bi... more Complex diseases such as cancer are mostly described by combining negative effects of multiple biological factors or pathways. Based on that, multi-targeted approach for treating cancer is gaining interest. The aim of this study is to introduce a computational approach and to design new, multi-targeted drug candidates for treatment of bone cancer. In this approach, the FDA approved drugs of bone cancer were evaluated in terms of their molecular pharmaceutical properties and their bioactivity parameters predicted by bioinformatics and cheminformatics softwares. Among them, Methotrexate was chosen as a lead molecule due to its broader spectrum of bioactivity on the most important drug targets reported in literature. The lead molecule was exposed to basic bioisosteric modifications to obtain a better drug compound with improved bioactivity and a stronger drug-likeness profile using the known drug structure. Design compounds produced by a number of bioisosteric modifications performed on the 2D structure of the lead compound were evaluated in terms of both criteria; bioactivity and drug-likeness. Silicone modified compounds M4, M13, M14, and M15 showed a much broader spectrum of biological activity than that of the approved compound Methotrexate. The interesting effect of silicone incorporation makes our compounds promising drug candidates for further pharmaceutical investigation.

Macromolecular self-assembly is a promising way of fabricating ordered structures with interestin... more Macromolecular self-assembly is a promising way of fabricating ordered structures with interesting mechanical and optical properties. Learning how to produce highly organized structures and how to mediate the organization provide technological and application wise opportunities at both macroscale and nanoscale. In this study, we worked with an extracellular matrix protein collagen onto different substrates and try to control and to manipulate the assembly process externally. The most attractive benefit of producing biomaterial via self-assembly is the ability of controlling the mechanism by external parameters from nanometer scale to millimeter. Due to the prevalence of collagen fibril in human tissue and its self-assembly ability in vitro, Collagen becomes an important bio-macro molecule frequently used in biomedical materials and tissue engineering applications in recent decades. In this work, by using two different substrates, we observed a direct influence of the surface symmetr...

European Journal of Science and Technology, 2021

MicroRNA (miRNA) molecules, which are effective on the initiation and progression of many differe... more MicroRNA (miRNA) molecules, which are effective on the initiation and progression of many different diseases, are a type of noncoding RNA with a length of about 22 nucleotides. Scientists have reported the importance of miRNAs in the prevention, diagnosis, and treatment of complex human diseases. Therefore, in the last decade, researchers have been working hard to find potential miRNAdisease associations. Many computational techniques have been developed because of the experimental techniques are time-consuming and expensive used to find new relationships between miRNAs and diseases. In this study, we suggested Kernelized Bayesian matrix factorization (KBMF) technique to predict new miRNA-disease relationships. We applied 5-fold cross validation technique and obtained an average value AUC of 0.9450. Also, we applied case studies based on breast, lung, and colon neoplasms to prove the performance of KBMF technique. The results showed that KBMF can be used as a reliable computational model to reveal possible miRNA-disease relationships.

Biomedical Physics & Engineering Express, 2019

Collagens have remarkable ability to self-assemble into ordered fibrils. Assembly of collagens on... more Collagens have remarkable ability to self-assemble into ordered fibrils. Assembly of collagens on 2-dimensional surfaces serves as amodel system to study the dynamics of assembly process and the resultingfibrilar structure has potential biotechnological and biomedical applications. However, intermolecular forces driving the self-assembly of collagen are not well understood.Here, we apply the Derjaguin-Landau-Verwey-Overbeek (DLVO) theory to investigate the interactions between collagens and between collagen and themica surface. Interactions are found to be attractive at all distances, which is consistent with literature. To further investigate the sequence-dependent organization of collagenmolecules, we examined interaction near contact distances when collagen molecules are staggered to different degrees.We compared electrostatic, hydrophobic, and polar hydration interaction, and found that hydrophilic interaction plays a significant role on themolecular assembly by protecting themolecule from random collapsewith a consistent repulsion barrier. Electrostatic interaction, on the other hand, exhibits local energymaxima andminima onD-periodic arrangements throughout themolecule leading to an oscillation effect on the axial self-assembly. Our approaches, in bothmacromolecular and nanoscale, provide insights into the factors that determine interactions among collagens and between collagen andmica.

Cellular and Molecular Bioengineering, 2016

fibrils, the main constituents of the extracellular matrix, are "biological alloys" that contain ... more fibrils, the main constituents of the extracellular matrix, are "biological alloys" that contain many additive molecules for fine-tuning the dynamical and biological properties. A representative example is the type-I collagen fibril, the most abundant among the 28 collagen types, which also contains type-III collagen. We perform atomic force microscopy (AFM) to elucidate the coassembly of these two important members into heterotypic fibrils on mica surfaces. Time-lapse AFM imaging of samples at different ratios of type-I and type-III collagen molecules revealed that type-III assembles and nucleates fibrils slower than type-I. Furthermore, in the type-I/III mixture, nucleation appeared to be enhanced, resulting in formation of more fibrils compared to cases with either type-I or III only. We discuss possible mechanisms for the enhanced fibril nucleation in the co-assembly process of the two molecules that differ slightly in physical properties.

European Journal of Science and Technology, 2021

This article is an open access article distributed under the terms and conditions of the Creative... more This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY

Journal of Selcuk University Natural and Applied Science, 2016

Ab initio calculations have been performed for a doublet H 2 COH --> H 3 CO and a singlet sys... more Ab initio calculations have been performed for a doublet H 2 COH --> H 3 CO and a singlet system of SiH 4 -->H 2 +H 2 reactions. Geometry optimization including frequency analysis have been accomplished at the HF/6-31G(d) level of theory for reactants, transition states (TS), and products of the reactions studied. The physico-chemical properties of the compounds including zero-point energy, multiplicity, dipole moment, and point group symmetries have been calculated at the same level of theory. Upon obtaining TS geometry, the reaction paths following for the reactions have been generated with the IRC keyword and the TS structures have been confirmed to belong to the reactions desired. The activation energies and the formation of reaction have been calculated by using the total energy graph along the IRC reaction coordinate. The reaction paths generated by the program exhibit the exothermic/endothermic characteristics of the reactions.

We study a broad class of epitaxial assembly of filament networks on lattice surfaces. Over time,... more We study a broad class of epitaxial assembly of filament networks on lattice surfaces. Over time, a scale-free behavior emerges with a 2.5-3 power-law exponent in filament length distribution. Partitioning between the power-law and exponential behaviors in a network can be used to find the stage and kinetic parameters of the assembly process. To analyze real-world networks, we develop a computer program that measures the network architecture in experimental images. Application to triaxial networks of collagen fibrils shows quantitative agreement with our model. Our unifying approach can be used for characterizing and controlling the network formation that is observed across biological and nonbiological systems.

European Journal of Science and Technology

Biomedical Physics & Engineering Express

Collagens have remarkable ability to self-assemble into ordered fibrils. Assembly of collagens on... more Collagens have remarkable ability to self-assemble into ordered fibrils. Assembly of collagens on 2-dimensional surfaces serves as amodel system to study the dynamics of assembly process and the resultingfibrilar structure has potential biotechnological and biomedical applications. However, intermolecular forces driving the self-assembly of collagen are not well understood.Here, we apply the Derjaguin-Landau-Verwey-Overbeek (DLVO) theory to investigate the interactions between collagens and between collagen and themica surface. Interactions are found to be attractive at all distances, which is consistent with literature. To further investigate the sequence-dependent organization of collagenmolecules, we examined interaction near contact distances when collagen molecules are staggered to different degrees.We compared electrostatic, hydrophobic, and polar hydration interaction, and found that hydrophilic interaction plays a significant role on themolecular assembly by protecting themolecule from random collapsewith a consistent repulsion barrier. Electrostatic interaction, on the other hand, exhibits local energymaxima andminima onD-periodic arrangements throughout themolecule leading to an oscillation effect on the axial self-assembly. Our approaches, in bothmacromolecular and nanoscale, provide insights into the factors that determine interactions among collagens and between collagen andmica.

Cellular and Molecular Bioengineering, Aug 31, 2016

An important step towards achieving functional diversity of biomimetic surfaces is to better unde... more An important step towards achieving functional diversity of biomimetic surfaces is to better understand the co-assembly of the extracellular matrix components. For this, we study type-I and type-III collagen, the two major collagen types in the extracellular matrix. By using atomic force microscopy, custom image analysis, and kinetic modeling, we study their homotypic and heterotypic assembly. We find that the growth rate and thickness of heterotypic fibrils decrease as the fraction of type-III collagen increases, but the fibril nucleation rate is maximal at an intermediate fraction of type-III. This is because the more hydrophobic type-I collagen nucleates fast and grows in both longitudinal and lateral directions, whereas more hydrophilic type-III limits lateral growth of fibrils, driving more monomers to nucleate additional fibrils. This demonstrates that subtle differences in physico-chemical properties of similar molecules can be used to fine-tune their assembly behavior.Electr...

European Journal of Pharmaceutical Sciences

Acute Lymphoblastic Leukemia (ALL) represents 30% of all childhood cancers and children younger t... more Acute Lymphoblastic Leukemia (ALL) represents 30% of all childhood cancers and children younger than 5 years old have the highest risk for developing ALL. Existing ALL drugs do not respond in approximately 20% of treatment. Therefore, drug development studies against ALL must be continued with either developing existing drugs or discovering new ones. In this study, we evaluated the U.S Food and Drug Administration (FDA) approved ALL drugs according to their physicochemical and pharmaceutical properties, and Nelarabine was found to have the highest bioactivity score. Using the key strategy of bioisosterism commonly accepted by medicinal chemists, we investigated in silico ADME properties, drug-likeness, and biological activity of new designed twenty-four compounds including Nelarabine. The results were evaluated in terms of two classifications: broad spectrum biological activity and filtering of five different drug likeness criteria of the literature including Lipinski's rule of five. We interestingly observed that silicon incorporated compounds exhibited better performance on both criteria by targeting broader spectrum of drug receptors including G-protein coupled receptor (GPCR), ion channel modulator, kinase inhibitor, protease and enzyme inhibitor and by satisfying all of five different drug-likeness criteria reported in the literature. Design compound C19 appeared as a potential drug candidate for further pharmacological research.

Physical Review Letters, 2014

We study a broad class of epitaxial assembly of filament networks on lattice surfaces. Over time,... more We study a broad class of epitaxial assembly of filament networks on lattice surfaces. Over time, a scalefree behavior emerges with a 2.5-3 power-law exponent in filament length distribution. Partitioning between the power-law and exponential behaviors in a network can be used to find the stage and kinetic parameters of the assembly process. To analyze real-world networks, we develop a computer program that measures the network architecture in experimental images. Application to triaxial networks of collagen fibrils shows quantitative agreement with our model. Our unifying approach can be used for characterizing and controlling the network formation that is observed across biological and nonbiological systems.

Journal of Bioinformatics and Computational Biology

MicroRNAs (miRNA) are a type of non-coding RNA molecules that are effective on the formation and ... more MicroRNAs (miRNA) are a type of non-coding RNA molecules that are effective on the formation and the progression of many different diseases. Various researches have reported that miRNAs play a major role in the prevention, diagnosis, and treatment of complex human diseases. In recent years, researchers have made a tremendous effort to find the potential relationships between miRNAs and diseases. Since the experimental techniques used to find that new miRNA-disease relationships are time-consuming and expensive, many computational techniques have been developed. In this study, Weighted [Formula: see text]-Nearest Known Neighbors and Network Consistency Projection techniques were suggested to predict new miRNA-disease relationships using various types of knowledge such as known miRNA-disease relationships, functional similarity of miRNA, and disease semantic similarity. An average AUC of 0.9037 and 0.9168 were calculated in our method by 5-fold and leave-one-out cross validation, resp...