Biology subjects

DeMirci, H.

Publications and source records attributed to DeMirci, H..

At least 19 recordsLinked to original sources

bioRxiv2025

A Novel Unorthodox Dimeric Primary Enoyl-CoA Reductase Structure

Enoyl-CoA carboxylases/reductases (ECRs) are enzymes with the fastest carbon dioxide (CO2) fixation capabilities, yet the precise mechanisms behind their assembly and catalytic activity are structurally not yet fully understood. Here, we employed cryo X-ray crystallography to reveal the dimeric structural organization of a novel ECR, isolated from mesophilic Mesorhizobium metallidurans (M. metallidurans). We examined the interactions in silico and compared oligomerization of our dimeric ECR from M. metallidurans (ECRMm_Dim) with tetrameric ECR from Burkholderia ambifaria (ECRBa_Tet)by using size exclusion chromatography in solution. Our in silico analysis revealed that specific residues in the M. metallidurans ECR that preclude tetramer formation, which could affect the enzymes catalytic activity. Additionally, we compared primary ECR sequences and structural variations between K. setae and M. metallidurans to explore their evolutionary relationships, along with their functional diversity. Our study presents the first example of a dimeric ECR structure which may provide new insights into how dimerization versus tetramerization may have an impact on catalytic function. By detailing how different oligomeric states influence enzyme activity and exploring active site conformational changes, we may offer a further understanding of ECR assembly. This work paves the way for future research into the precise molecular mechanisms that drive ECRs exceptional overall catalytic activity, efficiency and efficacy.

biochemistry↗

bioRxiv2025

Crystal Structure of 3-Hydroxypropionyl-CoA Synthetase (ADP-forming) from Nitrosopumilus maritimus

The 3-hydroxypropionate/4-hydroxybutyrate (3HP/4HB) cycle in thaumarchaeota contributes significantly to global organic carbon fixation as the most energetically efficient aerobic carbon fixation pathway. The thaumarchaeal 3-Hydroxypropionyl-CoA Synthetase (ADP-forming; Nmar_1309) is crucial to this efficiency, utilizing ATP to ADP catalysis. This first reported structure of Nmar_1309 reveals a homodimer with a unique subdomain organization ([3-4-1-2-5]) and a distinct linker between subdomains 4 and 1. The presence of bound substrates including 3-hydroxypropionate, non-hydrolyzable ATP (ADPNP), and a phosphate suggests an intermediate state mimicking a reaction step immediately preceding the formation of a 3-hydroxypropionyl-phosphohistidine. Conformational differences were observed between the two chains of the homodimer, likely influenced by the binding of a single ADPNP molecule in one chain. Phylogenetic analysis suggests that while 4HB synthetases may have evolved earlier in the evolutionary timeline, 3HP synthetases in Thaumarchaeota may have occurred after the Great Oxygenation Event. These structural data provide further characterization of the 3HP/4HB cycle and, in conjunction with the structure of 4-hydroxybutyryl-CoA synthetase, Nmar_0206, provide baseline structures of the key ADP-forming Acyl-CoA synthetases within this pathway.

biophysics↗

bioRxiv2025

Deciphering the altered conformational states of bifunctional thaumarchaeal crotonyl-CoA hydratase and 3-hydroxypropionyl-CoA dehydratase from Nitrosopumilus maritimus

The thaumarchaeal 3-hydroxypropionate/4-hydroxybutyrate (3HP/4HB) cycle represents one of the most efficient mechanisms for CO2 fixation discovered to date. Within this cycle, the enzyme encoded by Nmar_1308 from Nitrosopumilus maritimus SCM1 plays a crucial role due to its dual functionality as both a crotonyl-CoA hydratase (CCAH) and a 3-hydroxypropionyl-CoA dehydratase (3HPD). Although the importance of a bifunctional enzyme for lowering the cost of biosynthesis, the details of structural dynamics are still missing. Here, in addition to our cryogenic temperature structures, we determined the first ambient temperature structures of the Nmar_1308 protein by Serial Femtosecond X-ray Crystallography (SFX). The determined structures capture previously unobserved conformational dynamics of the Nmar_1308 protein, providing invaluable information for future synthetic biology applications.

biochemistry↗

bioRxiv2025

Production, Purification, and Crystallization of Recombinant HER2 Tyrosine Kinase Domain (HER2-TKD) as a Platform for Structure-Based Drug Screening

The human epidermal growth factor receptor 2 tyrosine kinase domain (HER2-TKD) plays a central role in signal transduction and is a significant therapeutic target in cancer. This study aimed to produce soluble recombinant HER2-TKD in Escherichia coli to enable structural studies for drug screening applications. The HER2-TKD gene was cloned into the pET28a(+) expression vector and expressed in E. coli. Initial expression led to the formation of inclusion bodies; thus, sarcosyl was used to solubilize the aggregated protein. Several induction durations were tested to optimize soluble expression. SDS-PAGE analysis was used to monitor expression and solubilization efficiency. The recombinant protein was purified using size-exclusion chromatography and reverse affinity chromatography to remove the SUMO tag. Crystallization trials were initiated using commercial screens to obtain diffraction-quality crystals. Soluble HER2-TKD was successfully obtained after optimization of induction and solubilization conditions. Crystallization efforts are ongoing to improve crystal quality for future structural analysis. These results provide a foundation for structure-based drug discovery studies targeting HER2.

biochemistry↗

bioRxiv2025

Expression, Purification, and Crystallization of Recombinant Human ABL-1 Kinase for Structure-Based Drug Screening Applications

Abelson-1 (ABL-1) is a non-receptor tyrosine kinase that plays essential roles in various cellular processes, including proliferation, survival, differentiation and its kinase activity is tightly regulated. The dysregulated ABL-1 kinase activity is linked to disease pathogenesis like Chronic Myeloid Leukemia (CML), where the BCR::ABL-1 fusion oncoprotein drives oncogenic signaling. Due to its central role in CML pathogenesis, understanding the structure of ABL-1 is crucial for the effective management of the disease and drug development studies. This study focuses on optimizing the expression, purification and crystallization of the recombinant human ABL-1 kinase domain for its structural analysis via X-ray crystallography and structure-based drug screening applications. The human ABL-1 kinase domain, fused with a SUMO-tag, was expressed in Escherichia coli Rosetta2 BL21 using the pET28(a)+ expression vector. The ABL-1 aggregates seen under native culture conditions were successfully solubilized by mild ionic detergent sarkosyl. After obtaining soluble expression of the protein, Ni-NTA affinity chromatography was performed and high tiled of purified ABL-1 was obtained. The 6X-His-SUMO-tag of purified ABL1 was cleaved by ULP1 protease. The recombinant ABL-1 was subsequently used in crystallization trials for enlightening structural features of ABL-1 that could guide the development of novel therapeutics and drug screening platforms targeting ABL-1 in CML.

biochemistry↗

bioRxiv2025

Structural Categorization and identification of electrostatic interactions in two proposed Human Serum Albumin dimerization patterns and dipyridamole interaction.

Human serum albumin (HSA) is a ubiquitous, multifunctional protein responsible for the systemic distribution of both endogenous metabolites and exogenous pharmaceuticals. Its inherent properties, mainly its ability to seep into the tissues and multiple ligand-binding sites, have rendered HSA an attractive vehicle in nanoparticle-based drug delivery systems, particularly in cancer targeting. In this study, we present high-resolution crystallographic data revealing two distinct dimerization patterns of HSA (PDB ID: 9V61), obtained under high-concentration crystallization conditions, in addition to results from dipyridamole dockings. Both dimer types demonstrate extensive interface areas and a significant number of electrostatic interactions. Comparative analysis with previously reported dimer structure (PDB ID: 3JQZ) and other high-interface-area structures, (PDB ID: 5Z0B, PDB ID: 8CKS) indicates similarities in contact regions, but unique residue-level differences in bonding interactions. Interface surface area distribution and space group histograms further support the rarity and potential physiological relevance of the identified dimer forms. Importantly, these dimer configurations do not disrupt Sudlows drug-binding sites, which is important as the dipyridamole docking analysis presents strong affinity to Sudlow site I and Sudlow site III, not affecting their utility in engineered drug delivery. Our findings open new avenues for structure-based mutagenesis and nanoparticle design strategies centered on HSA dimerization dynamics.

molecular biology↗

bioRxiv2025

Structural Analysis and Docking Studies of FK506-Binding Protein 1A

FK-binding protein 1A, a member of immunophilin family of proteins, is a protein with a wide variety of roles in cellular processes, including regulation of immune system, calcium intake metabolism through ryanodine receptors, TGF-{beta} signaling and EGFR regulation. As a protein originally defined as the cellular target of premier immunosuppresant drugs, FK506 and Rapamycin, it has been a protein studied for further pharmacological uses. In this study, we have overexpressed, purified and crystallized apo-FKBP1A. Here, we are showing the FKBP1A crystal structure, calculated at cryogenic temperature at a very high resolution of 1.05 [A], obtained with a home source X-ray Turkish DeLight. Docking studies, with drug repurposing in mind were carried out with Molegro Virtual Docker software. Docking results will prove useful in future pharmaceutical studies done on FKBP1A, and similar proteins.

biochemistry↗

bioRxiv2025

Structural Insights into the Dynamics of Water in SOD1 Catalysis and Drug Interactions

Superoxide dismutase 1 (SOD1) is a crucial enzyme that protects cells from oxidative damage by converting superoxide radicals into H2O2 and O2. This detoxification process, essential for cellular homeostasis, relies on a precisely orchestrated catalytic mechanism involving the copper cation, while the zinc cation contributes to the structural integrity of the enzyme. This study presents the 2.3 [A] crystal structure of human SOD1 (PDB ID: 9IYK), revealing an assembly of six homodimers and twelve distinct active sites. The water molecules form a complex hydrogen-bonding network that drives proton transfer and sustains active site dynamics. Our structure also uncovers subtle conformational changes that highlight the intrinsic flexibility of SOD1, which is essential for its function. Additionally, we observe how these dynamic structural features may be linked to pathological mutations associated with amyotrophic lateral sclerosis (ALS). By advancing our understanding of hSOD1s mechanistic intricacies and the influence of water coordination, this study offers valuable insights for developing therapeutic strategies targeting ALS. Our structures unique conformations and active site interactions illuminates new facets of hSOD1 function, underscoring the critical role of structural dynamics in enzyme catalysis. Besides, we conducted molecular docking analysis using SOD1 for potential radical scavengers and Abl1 inhibitors targeting misfolded SOD1 aggregation along with oxidative stress and apoptosis, respectively. The results showed that CHEMBL1075867, a free radical scavenger derivative, showed the most promising docking results and interactions in the binding site of hSOD1, highlighting its promising role for further studies against SOD1-mediated ALS.

molecular biology↗

bioRxiv2025

The N-terminal order-disorder transition is a critical determinant for a metamorphosis of IscU

IscU, a key scaffold protein mediating the biogenesis of iron-sulfur (Fe-S) clusters, exhibits metamorphic characteristics crucial for its versatile and efficient function. Previous studies have demonstrated that IscU has two interconverting conformations: the structured state (S-state) and the disordered state (D-state), each contributing to its distinct functionality and interaction network. Despite its physiological importance, the precise mechanism underpinning the maintenance of IscUs unique structural heterogeneity has remained elusive. In this study, we used computational and experimental approaches to reveal that the N-terminal order-disorder plays a critical role in the metamorphic modulation of IscU. We found that the N-terminal region displays greater structural plasticity, which is linked to other regions of IscU through coevolutionary relationships. Moreover, we demonstrated that the degree of orderliness in the N-terminal region correlates positively with the stabilization of IscUs S-state and negatively with its affinity for HscA. This indicates that the flexibility in the N-terminal region is finely tuned to optimize IscUs physiological efficiency and efficacy. Finally, our data suggest that a peptide mimicking the N-terminal motif can modulate IscUs metamorphic properties, suggesting a novel therapeutic potential for related pathogenic processes.

biochemistry↗

bioRxiv2024

Experimental and Computational Insights into the Structural Dynamics of the Fc Fragment of IgG1 Subtype from Biosimilar VEGF-Trap

The constant fragment (Fc) of the Immunoglobulin G1 (IgG1) subtype is increasingly recognized as a crucial scaffold in the development of advanced therapeutics due to its enhanced specificity, efficacy, and extended half-life. A prime example is VEGF-Trap (Aflibercept), a recombinant fusion protein that merges the Fc region of the IgG1 subtype with the binding domains of vascular endothelial growth factor receptors (VEGFR)-1 and VEGFR-2. The Fc regions role in N-glycosylation is particularly important, as it significantly influences protein stability. In this study, we present the first near-physiological temperature structures of the N-glycan-bound Fc fragment of IgG1 subtype from a biosimilar VEGF-Trap, determined using the SPring-8 Angstrom Compact free electron LAser (SACLA) and the Turkish Light Source (Turkish DeLight). Comparative analysis with cryogenic structures, including our own data, reveals alternate conformations within the glycan-binding pocket. Furthermore, molecular dynamics (MD) simulations highlight an unexpected degree of structural plasticity. These findings offer new insights into the molecular basis of Fc-mediated functions and provide valuable information for the design of next-generation therapeutics.

molecular biology↗

bioRxiv2023

4D Crystallography Captures Transient IF1-Ribosome Dynamics in Translation Initiation

Initiation factor 1 (IF1) is one of multiple key ligands involved in the initiation of mRNA translation, a highly dynamic and carefully-orchestrated process. However, details surrounding IF1 transient interactions with the small 30S ribosomal subunit remain incompletely understood despite characterization of unbound and fully-bound 30S states. Improvements in X-ray light sources and crystallographic techniques are now enabling time-resolved structural studies at near-physiological temperature and near-atomic resolution and thus the structural investigation of such dynamic processes. Here, we employed time-resolved serial femtosecond X-ray crystallography (TR-SFX) to probe the binding of IF1 to the small 30S ribosomal subunit in real time. Our time-resolved structural data demonstrates transient cryptic short-, mid-, and long-range allostery among different regions of the small 30 ribosomal subunit during IF1 binding, revealing small- and large-scale protein-target interactions and dynamics within intermediate macromolecular states at unprecedented temporal and spatial resolution. These data represent one of the first such 4D crystallographic studies assessing protein-protein and protein-RNA interactions and could serve as the basis for subsequent studies of the ribosome and of the multitudinous dynamic processes which underpin biology, and therefore, of life.

biophysics↗

bioRxiv2023

Ambient Temperature Bacterial Large Ribosomal Subunit Structure Enabled by Serial Femtosecond X-ray Crystallography

Ribosomes are the supramolecular complexes responsible for protein synthesis. The large 50S ribosomal subunit catalyzes the peptidyl transferase reaction and peptide bond formation between amino acids. The 50S is targeted by many known clinically effective antibiotics. Available structures, obtained at cryogenic temperatures (CT), are used for drug discovery despite that active or important target sites may display a structural configuration that is CT-induced. The introduction of ultrafast and ultrabright X-ray free electron laser (XFEL) pulses has enabled the structural observation of biological macro- and supramolecules at previously unattainable, near-physiological temperatures. In this study, we use ultrafast and ultrabright XFEL pulses to solve the apo form of 50S ribosomal subunit isolated from the extremely thermophilic bacterium Thermus thermophilus at ambient temperature (AT). The dimeric structure of the 50S subunit presented in this work is among the largest ([~]3 megadalton) structures determined using an XFEL source to date. This study demonstrates the ability to obtain new information about ribosome structural dynamics at AT through serial femtosecond X-ray crystallography (SFX). This allowed us to capture previously unobserved dynamics of ribosomal protein uL23 and coordination by hexahydrated magnesium cations at a hitherto unseen resolution at near-physiological temperature. Also, residue A2602, at the core of the peptidyl transferase center (PTC), shows a rather different orientation of the sugar moiety if compared to CT structures. In addition, our structure highlights the importance of flexible residues at both the PTC and in the binding sites for antibiotics erythromycin and chloramphenicol. The method implemented here may also serve as a starting point for future structural research involving the 50S subunit complexes by employing time-resolved mix-inject and probe kineto-crystallography experiments at XFELs. Unveiling ligand-dependent 50S dynamics at physiological temperatures shall guide further development of next-generation antibiotics that target the translation machinery.

biophysics↗

bioRxiv2023

Ambient temperature crystal structure of Escherichia coli CyaY protein displays alternate conformation

Frataxin is a 23 KDa mitochondrial iron-binding protein that is involved in biogenesis of iron sulfur clusters. A deficiency in frataxin leads to Friedreichs ataxia, a progressive neurodegenerative disorder. The bacterial ortholog of eukaryotic mitochondrial frataxin, CyaY, is thought to play a role in iron sulfur cluster assembly as an iron supplier, making it an important target for study. Here, we present the first ambient temperature crystal structure of CyaY protein from Escherichia coli, obtained using the Turkish Light Source "Turkish DeLight". This study reveals the dynamic structural characteristics of CyaY at near-physiological temperature and displays an alternate conformation, highlighting the importance of temperature considerations in protein structure characterization and providing new insights into the proteins flexibility.

biochemistry↗

bioRxiv2023

Structural Characterization of TRAF6 N-terminal for Therapeutic Uses

Tumor Necrosis Factor Receptor Associated Factors (TRAFs) are a protein family with a wide variety of roles and binding partners. Among them, TRAF6, a ubiquitin ligase, possesses unique receptor binding specificity and shows diverse functions in immune system regulation, cellular signaling, central nervous system (CNS), and tumor formation. TRAF6 consists of an N-terminal Really Interesting New Gene (RING) domain, multiple zinc fingers, and a C-terminal TRAF domain. RING domain and zinc fingers mediate the activation of nuclear factor kappa B (NF-{kappa}B), which has essential roles in the regulation of inflammatory responses, proliferation, differentiation, migration, cell adhesion, and apoptosis. Therefore, it has been found that TRAF6 is overexpressed in various types of cancer including pancreatic, liver, lung, head and neck, breast, colorectal cancers, and melanoma along with inflammatory, autoimmune and neurodegenerative disorders. Furthermore, TRAF6 is an important therapeutic target for numerous disorders and structural studies of this protein are crucial for the development of next-generation therapeutics. Here, we present a TRAF6 N-terminal structure determined at the Turkish Light Source "Turkish DeLight" to 2.6 [A] resolution at cryogenic temperature. This structure offers insight into the domain organization and zinc-binding, which are critical for protein function. Since the RING domain and the zinc fingers are key targets for TRAF6 therapeutics, structural insights are crucial for future research.

molecular biology↗

bioRxiv2022

Structural and Dynamic Characterization of Candida boidinii Formate Dehydrogenase by High-Resolution X-ray Crystallography

Candida boidinii NAD+-dependent formate dehydrogenase (CbFDH) has gained significant attention for its potential applications in the production of biofuels and various industrial chemicals from inorganic carbon dioxide. The present study reports the atomic X-ray crystal structures of the wild-type CbFDH at cryogenic and ambient temperatures as well as Val120Thr mutant at cryogenic temperature determined at the Turkish Light Source "Turkish DeLight". The structures reveal new hydrogen bonds between Thr120 and water molecules in the mutant CbFDHs active site, suggesting increased stability of the active site and more efficient electron transfer during the reaction. Further experimental data is needed to test these hypotheses. Collectively, our findings provide invaluable insights into future protein engineering efforts that could potentially enhance the efficiency and effectiveness of CbFDH.

biophysics↗

bioRxiv2022

Comparative Study of High-resolution LysB29(Nε-myristoyl) des(B30) Insulin Structures Display Novel Dynamic Causal Interrelations in Monomeric-Dimeric Motions

The treatment of insulin-dependent diabetes mellitus is characterized by artificial supplementation of pancreatic {beta}-cell ability to regulate sugar levels in the blood. Even though various insulin analogs are crucial for reasonable glycemic control, understanding the dynamic mechanism of the insulin analogs may help to improve the best-protracted insulin analog to assist people with Type 1 Diabetes (T1D) to live comfortably while maintaining tight glycemic control. Here we present the high-resolution crystal structure of NN304, known as insulin detemir, to 1.7 [A] resolution at cryogenic temperature. We computationally further investigated our crystal structures monomeric-dimeric conformation and dynamic profile by comparing it with a previously available detemir structure (PDB ID: 1XDA). Our structure (PDB ID: 8HGZ) obtained at elevated pH provides electrostatically triggered minor movements in the equilibrium between alternate conformational substates compared to the previous structure, suggesting it might induce an intermediate state in the dissociation pathway of the insulin detemirs hexamer:dihexamer equilibrium. Supplemented with orientational cross-correlation analysis by Gaussian Network Model (GNM), this alternate oligomeric conformation offers the distinct cooperative motions originated by loose coupling of distant conformational substates of a protracted insulin analog that has not been previously observed.

biophysics↗

bioRxiv2022

Rapid and High Resolution Ambient Temperature Structure Determination at Turkish Light Source

High-resolution biomacromolecular structure determination is essential to better understand protein function and dynamics. Serial crystallography is an emerging structural biology technique which has fundamental limitations due to either sample volume requirements or immediate access to the competitive X-ray beamtime. Obtaining a high volume of well-diffracting, sufficient-size crystals while mitigating radiation damage remains a critical bottleneck of serial crystallography. As an alternative, we introduce the plate-reader module adapted for using a 72-well Terasaki plate for biomacromolecule structure determination at a convenience of a home X-ray source. We also present the first ambient temperature lysozyme structure determined at the Turkish Light Source (Turkish DeLight). The complete dataset was collected in 18.5 mins with resolution extending to 2.39 [A] and 100% completeness. Combined with our previous cryogenic structure (PDB ID: 7Y6A), the ambient temperature structure provides invaluable information about the structural dynamics of the lysozyme. Turkish DeLight provides robust and rapid ambient temperature biomacromolecular structure determination with limited radiation damage.

biophysics↗

bioRxiv2022

Crystal structure of Vibrio cholerae (6-4) photolyase with DNA binding region

Photolyases (PLs) reverse UV-induced DNA damage using blue light as an energy source. Of these photolyases, (6-4) PLs repair (6-4)-lesioned photoproducts. We recently identified a gene from Vibrio cholerae (Vc) encoding a (6-4) PL, but structural characterization is needed to elucidate specific interactions with the chromophore cofactors. Here, we determined the crystal structure of Vc(6-4) PL at 2.5 [A] resolution. Our high-resolution structure revealed that the two well-known cofactors, flavin adenine dinucleotide (FAD) and the photoantenna 6,7-dimethyl 8-ribityl-lumazin (DMRL), stably interact with an -helical and an /{beta} domain, respectively. Additionally, the structure has a third cofactor with distinct electron clouds corresponding to a [4Fe-4S] cluster. Moreover, we identified that Asp106 makes a hydrogen bond with the water and DMRL, which indicates further stabilization of the photoantenna DMRL within Vc(6-4) PL. Further analysis of the Vc(6-4) PL structure revealed a possible region responsible for DNA binding. The region located between residues 478-484 may bind the lesioned DNA, with Arg483 potentially forming a salt bridge with DNA to stabilize further the interaction of Vc(6-4) PL with its substrate. Our comparative analysis revealed that the DNA lesion could not bind to the Vc(6-4) PL in a similar fashion to the Drosophila melanogaster Dm(6-4) PL without a significant conformational change of the protein. The 23rd helix of the bacterial (6-4) PLs seems to have remarkable plasticity, and conformational changes facilitate DNA binding. In conclusion, our structure provides further insight into DNA repair by a (6-4) PL containing three cofactors.

molecular biology↗