Biology subjects

Haliloglu, T.

Publications and source records attributed to Haliloglu, T..

6 recordsLinked to original sources

bioRxiv2026

GNMCADS: Sampling For Protein Conformation Diversity With Gaussian Network Model Guided Condition Annealed Diffusion Sampler

Proteins are dynamic molecules existing in diverse conformational states underlying their biological functions. Although recent approaches have enabled diverse conformational sampling by emulating molecular dynamics simulations, perturbing evolutionary information, or steering internal mechanisms of structure prediction models, predicting conformations resulting from major domain motions or motions that occur over long timescales still remains a challenge. To this end, we introduce GNMCADS, a conformational sampling strategy that enhances the diversity of protein diffusion models by selectively annealing the conditioning signal guided by the intrinsic dynamical organization of the sampled protein. Further, we implement GNMCADS in the diffusion module of AlphaFold3, enabling the generation of diverse protein conformations. When benchmarked across 92 proteins that include 54 class A GPCRs, 15 transporters, and 23 proteins with major domain movements, GNMCADS exhibits improved sampling diversity compared to other current conformational sampling methods.

bioinformatics↗

bioRxiv2026

Structure and Dynamics of a Long-Acting Insulin Analog in Hexameric and Dihexameric States

Elucidating the structure and dynamics of insulin and its analogs has been of broad interest, while presenting challenges due to the unique structural dynamics of insulin (composed itself of two multiply cross-linked peptides A and B) and its ability to assemble in a variety of oligomeric structures under physiological conditions. Here, we present two distinct X-ray crystallographic structures of the long-acting human insulin analog detemir (INSD) resolved in hexameric and dodecameric (or dihexameric) states at 2.85 [A] and 2.70 [A] resolution, respectively, using diffraction data collected under ambient temperature conditions. Characterization of the collective dynamics of these oligomers using the Gaussian Network Model (GNM) reveals several key features: (i) Oligomerization imparts high cooperativity in structural dynamics evidenced by dissection of the cross-correlations at various hierarchical levels; (ii) detemir monomers conformational flexibility is highly suppressed within oligomeric constructs, the effect being particularly strong in the dihexamer due to the asymmetric packing of the hexamers and the presence of myristoyl groups at B peptides termini whose interactions imparts further heterogeneities; and (iii) a number of key residues retain, however, their intrinsic dynamics, to be deployed upon release from the oligomers. We distinguish in particular residues serving as hinge sites that mediates the conformational dynamics of the asymmetric units (dimers) and monomers (I2A-V3A and Y19 A -C20A, and L11B-L15B and Y26B of the respective peptides A and B), or as anchors supporting structural stability (disulfide-bridge forming cysteines, plus selected residues such as L16A, G8B and R22B-F24B. Overall, this study provides a structural-dynamic framework for gaining new insights into the dynamics of long-acting analog INSD and helps identify actionable sites for modulating insulin (analogs) dynamics toward designing more effective therapeutics.

biophysics↗

bioRxiv2025

Mutation-Induced Effects on Rac1 Conformational Dynamics: Implications for Therapeutic Targeting

Understanding the conformational dynamics of proteins, particularly small GTPases like Rac1, is vital for elucidating their functional mechanisms and developing targeted therapies. Rac1, pivotal in cellular processes, toggles between inactive GDP-bound and active GTP-bound states, regulated by guanine nucleotide exchange factors (GEFs) and GTPase-activating proteins (GAPs). Mutations, such as Rac1s spontaneously activating oncogenic gain-of-function mutation P29S, associated with cancer, disrupt this equilibrium, leading to aberrant signaling. Traditional drug targeting of Rac1 is challenging due to its biological complexity and the lack of accessible active sites on its surface, necessitating alternative strategies. We propose a computational framework integrating Molecular Dynamics (MD) simulations and Elastic Network Models (ENM) to explore conformational dynamics. Our findings highlight the interplay between Mg2+ binding and conformational ensembles, revealing enhanced conformational heterogeneity in both inactive and active states upon P29S mutation. The critical location of P29S, Mg2+ coordination site, and GDP/GTP binding pocket with respect to global hinges provides mechanistic insight into how this mutation disrupts normal protein function through altered metal coordination dynamics. Furthermore, we identified strategic positions as potential "rescue mutation" sites, with T75A showing particular promise in mitigating the destabilizing conformational effects of P29S. Overall, this work provides insights into Rac1s dynamic behavior and offers a foundation for targeted drug design strategies.

biophysics↗

bioRxiv2023

Computational analysis of long-range allosteric communications in CFTR

Malfunction of the CFTR protein results in cystic fibrosis, one of the most common hereditary diseases. CFTR functions as an anion channel, the gating of which is controlled by long- range allosteric communications. Allostery also has direct bearings on CF treatment: the most effective CFTR drugs modulate its activity allosterically. Herein, we integrated Gaussian Network Model, Transfer Entropy, and Anisotropic Normal Mode-Langevin dynamics and investigated the allosteric communications network of CFTR. The results are in remarkable agreement with experimental observations and mutational analysis and provide extensive novel insight. We identified residues that serve as pivotal allosteric sources and transducers, many of which correspond to disease causing mutations. We find that in the ATP-free form, dynamic fluctuations of the residues that comprise the ATP binding sites facilitate the initial binding of the nucleotide. Subsequent binding of ATP then brings to the fore and focuses dynamic fluctuations that were present in a latent and diffuse form in the absence of ATP. We demonstrate that drugs that potentiate CFTRs conductance do so not by directly acting on the gating residues, but rather by mimicking the allosteric signal sent by the ATP binding sites. We have also uncovered a previously undiscovered allosteric "hotspot" located proximal to the docking site of the phosphorylated Regulatory (R) domain, thereby establishing a molecular foundation for its phosphorylation- dependent excitatory role. This study unveils the molecular underpinnings of allosteric connectivity within CFTR and highlights a novel allosteric "hotspot" that could serve as a promising target for the development of novel therapeutic interventions.

biophysics↗

bioRxiv2021

Structural insight into host plasma membrane association and assembly of HIV-1 Matrix protein

HIV-1 continues to be a global health concern since AIDS was first recognized by the World Health Organization (WHO). It is estimated that there were 38 million people infected with HIV-1 and 1.5 million deaths in 2019 alone. A better understanding of the details of the HIV late-stage life cycle, involving Pr55Gag attachment to the membrane for the further oligomerization to release virion, will provide us new avenues for potential treatment. Inositol hexakisphosphate (IP6) is an abundant endogenous cyclitol molecule and its binding was linked to the oligomerization of Pr55Gag via the MA domain. However, the binding site of IP6 on MA was unknown and the structural details of this interaction were missing. Here, we present three high-resolution crystal structures of the MA domain in complex with IP6 molecules to reveal its binding mode. Additionally, extensive Differential Scanning Fluorimetry analysis combined with cryo- and ambient-temperature X-ray crystallography and computational biology identify the key residues that participate in IP6 binding. Our data provide novel insights about the multilayered HIV-1 virion assembly process that involves the interplay of IP6 with PIP2, a phosphoinositide essential for the membrane binding of Pr55Gag. IP6 and PIP2 have neighboring alternate binding sites within the same highly basic region (residues 18-33). This indicates that IP6 and PIP2 bindings are not mutually exclusive and may play a key role in coordinating virion particles membrane localization. Based on our three different IP6-MA complex crystal structures, we propose a new model that involves the IP6 coordination of the oligomerization of outer MA and inner CA domain 2D layers during assembly and budding.

microbiology↗

bioRxiv2020

Dynamic Order in Allosteric Interactions

Allostery is an intrinsic dynamic phenomenon that underlies functional long-distance interactions in proteins, which we study here by stochastic calculus approach to elastic network models (ENMs). We show that once you drop the usually accepted high friction limit and include hydrodynamic interactions in ENMs, a simple measure that uses the pairwise difference in the time-delayed correlations of residue fluctuations provides insight about functional sites and their dynamical behaviour in allosteric communication. We present this with three exemplary cases Aspartate Carbamoyl transferase, Insulin Receptor and DNA-dependent Protein Kinase. We show that proteins possess characteristic pathways operating at different time-delay windows with slow to faster motions underlying the protein function. As these pathways help communication between key residues of functionality, they can also be used to identify their locations without any prior knowledge other than the protein crystal structure.

molecular biology↗