12 hasil untuk "Turkan Haliloglu"

Cooperative Transition between Open and Closed Conformations in Potassium Channels

Turkan Haliloglu; Nir Ben-Tal

PLoS Computational Biology, Vol. 4 No. 8 · 2008 · Inggris · PLOS Scopus

Potassium (K+) ion channels switch between open and closed conformations. The nature of this important transition was revealed by comparing the X-ray crystal structures of the MthK channel from Methanobacterium thermoautotrophicum, obtained in its open conformation, and the KcsA channel from…

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Hot Spots in a Network of Functional Sites

Pemra Ozbek; Seren Soner; Turkan Haliloglu

PLoS ONE, Vol. 8 No. 9 · 2013 · Inggris · PLOS Scopus

It is of significant interest to understand how proteins interact, which holds the key phenomenon in biological functions. Using dynamic fluctuations in high frequency modes, we show that the Gaussian Network Model (GNM) predicts hot spot residues with success rates ranging between S 8–58%, C…

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Predicting Important Residues and Interaction Pathways in Proteins Using Gaussian Network Model: Binding and Stability of HLA Proteins

Turkan Haliloglu; Ahmet Gul; Burak Erman

PLoS Computational Biology, Vol. 6 No. 7 · 2010 · Inggris · PLOS Scopus

A statistical thermodynamics approach is proposed to determine structurally and functionally important residues in native proteins that are involved in energy exchange with a ligand and other residues along an interaction pathway. The structure-function relationships, ligand binding and allosteric…

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Structure, Dynamics and Implied Gating Mechanism of a Human Cyclic Nucleotide-Gated Channel

Yana Gofman; Charlotta Schärfe; Debora S. Marks dkk.

PLoS Computational Biology, Vol. 10 No. 12 · 2014 · Inggris · PLOS Scopus

Cyclic nucleotide-gated (CNG) ion channels are nonselective cation channels, essential for visual and olfactory sensory transduction. Although the channels include voltage-sensor domains (VSDs), their conductance is thought to be independent of the membrane potential, and their gating regulated by…

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DynaFace: Discrimination between Obligatory and Non-obligatory Protein-Protein Interactions Based on the Complex’s Dynamics

Seren Soner; Pemra Ozbek; Jose Ignacio Garzon dkk.

PLOS Computational Biology, Vol. 11 No. 10 · 2015 · Inggris · PLOS Scopus

Protein-protein interfaces have been evolutionarily-designed to enable transduction between the interacting proteins. Thus, we hypothesize that analysis of the dynamics of the complex can reveal details about the nature of the interaction, and in particular whether it is obligatory, i.e., persists…

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Computational analysis of long-range allosteric communications in CFTR

Ayca Ersoy; Bengi Altintel; Nurit Livnat Levanon dkk.

eLife, Vol. 12 · 2023 · Inggris · DOAJ

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…

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

Halilibrahim Ciftci; Hiroshi Tateishi; Kotaro Koiwai dkk.

Scientific Reports, Vol. 11 No. 1 · 2021 · Inggris · DOAJ Scopus

Abstract Oligomerization of Pr55Gag is a critical step of the late stage of the HIV life cycle. It has been known that the binding of IP6, an abundant endogenous cyclitol molecule at the MA domain, has been linked to the oligomerization of Pr55Gag. However, the exact binding site of IP6 on MA…