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Article ; Online: The mechanism and energetics of the dynein priming stroke.

Golcuk, Mert / Yilmaz, Sema Zeynep / Yildiz, Ahmet / Gur, Mert

Structure (London, England : 1993)

2024

Abstract: Dyneins are an AAA+ motor responsible for motility and force generation toward the minus end of microtubules. Dynein motility is powered by nucleotide-dependent transitions of its linker domain, which transitions between straight (post-powerstroke) and ... ...

Abstract	Dyneins are an AAA+ motor responsible for motility and force generation toward the minus end of microtubules. Dynein motility is powered by nucleotide-dependent transitions of its linker domain, which transitions between straight (post-powerstroke) and bent (pre-powerstroke) conformations. To understand the dynamics and energetics of the linker, we performed all-atom molecular dynamics simulations of human dynein-2 primed for its power stroke. Simulations revealed that the linker can adopt either a bent conformation or a semi-bent conformation, separated by a 5.7 kT energy barrier. The linker cannot switch back to its straight conformation in the pre-powerstroke state due to a steric clash with the AAA+ ring. Simulations also showed that an isolated linker has a free energy minimum near the semi-bent conformation in the absence of the AAA+ ring, indicating that the linker stores energy as it bends and releases this energy during the powerstroke.
Language	English
Publishing date	2024-02-28
Publishing country	United States
Document type	Journal Article
ZDB-ID	1213087-4
ISSN	1878-4186 ; 0969-2126
ISSN (online)	1878-4186
ISSN	0969-2126
DOI	10.1016/j.str.2024.02.003
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Article ; Online: Omicron BA.1 and BA.2 variants increase the interactions of SARS-CoV-2 spike glycoprotein with ACE2.

Golcuk, Mert / Yildiz, Ahmet / Gur, Mert

Journal of molecular graphics & modelling

2022 Volume 117, Page(s) 108286

Abstract: SARS-CoV-2 infection is initiated by binding of the receptor-binding domain (RBD) of its spike glycoprotein to the peptidase domain (PD) of angiotensin-converting enzyme 2 (ACE2) receptors in host cells. Recently detected Omicron variant of SARS-CoV-2 (B. ...

Abstract	SARS-CoV-2 infection is initiated by binding of the receptor-binding domain (RBD) of its spike glycoprotein to the peptidase domain (PD) of angiotensin-converting enzyme 2 (ACE2) receptors in host cells. Recently detected Omicron variant of SARS-CoV-2 (B.1.1.529) is heavily mutated on RBD. First the BA.1 and later the BA.2 variant became the most dominant strains of the Omicron variant. To investigate how the mutations of these strains affect RBD-PD interactions, we performed all-atom molecular dynamics simulations of the BA.1 and BA.2 RBD-PD in the presence of full-length glycans, explicit water, and ions. Simulations revealed that RBDs of BA.1 and BA.2 variants exhibit a more dispersed interaction network and make an increased number of salt bridges and hydrophobic interactions with PD compared to wild-type RBD. Although BA.1 and BA.2 differ in two residues at the RBD-ACE2 interface, no major difference in RBD-PD interactions and binding strengths were observed between these variants. Using the conformations sampled in each trajectory, the Molecular Mechanics Poisson-Boltzmann Surface Area (MMPBSA) method estimated ∼34% and ∼51% stronger binding free energies to PD for BA.1 and BA.2 RBD, respectively, than wild-type RBD, which may result in higher binding efficiency of the Omicron variant to infect host cells.
MeSH term(s)	Angiotensin-Converting Enzyme 2/chemistry ; COVID-19 ; Humans ; Mutation ; Protein Binding ; Receptors, Virus/chemistry ; SARS-CoV-2/genetics ; Spike Glycoprotein, Coronavirus/chemistry
Chemical Substances	Receptors, Virus ; Spike Glycoprotein, Coronavirus ; spike protein, SARS-CoV-2 ; ACE2 protein, human (EC 3.4.17.23) ; Angiotensin-Converting Enzyme 2 (EC 3.4.17.23)
Language	English
Publishing date	2022-08-04
Publishing country	United States
Document type	Journal Article
ZDB-ID	1396450-1
ISSN	1873-4243 ; 1093-3263
ISSN (online)	1873-4243
ISSN	1093-3263
DOI	10.1016/j.jmgm.2022.108286
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Article ; Online: SARS-CoV-2 Delta Variant Decreases Nanobody Binding and ACE2 Blocking Effectivity.

Golcuk, Mert / Hacisuleyman, Aysima / Yilmaz, Sema Zeynep / Taka, Elhan / Yildiz, Ahmet / Gur, Mert

Journal of chemical information and modeling

2022 Volume 62, Issue 10, Page(s) 2490–2498

Abstract: The Delta variant spreads more rapidly than previous variants of SARS-CoV-2. This variant comprises several mutations on the receptor-binding domain ( ... ...

Abstract	The Delta variant spreads more rapidly than previous variants of SARS-CoV-2. This variant comprises several mutations on the receptor-binding domain (RBD
MeSH term(s)	Angiotensin-Converting Enzyme 2 ; COVID-19/drug therapy ; Humans ; Molecular Dynamics Simulation ; Protein Binding ; SARS-CoV-2 ; Single-Domain Antibodies/metabolism ; Spike Glycoprotein, Coronavirus/genetics ; Spike Glycoprotein, Coronavirus/metabolism
Chemical Substances	Single-Domain Antibodies ; Spike Glycoprotein, Coronavirus ; spike protein, SARS-CoV-2 ; Angiotensin-Converting Enzyme 2 (EC 3.4.17.23)
Language	English
Publishing date	2022-05-09
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	190019-5
ISSN	1549-960X ; 0095-2338
ISSN (online)	1549-960X
ISSN	0095-2338
DOI	10.1021/acs.jcim.1c01523
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Article ; Online: Molecular dynamics simulations provide molecular insights into the role of HLA-B51 in Behçet's disease pathogenesis.

Gur, Mert / Golcuk, Mert / Gul, Ahmet / Erman, Burak

Chemical biology & drug design

2020 Volume 96, Issue 1, Page(s) 644–658

Abstract: Behçet's disease is an inflammatory disorder of unknown etiology. Genetic tendency has an important role in its pathogenesis, and HLA-B51, a class I MHC antigen, has been recognized as the strongest susceptibility factor for Behçet's disease. Despite the ...

Abstract	Behçet's disease is an inflammatory disorder of unknown etiology. Genetic tendency has an important role in its pathogenesis, and HLA-B51, a class I MHC antigen, has been recognized as the strongest susceptibility factor for Behçet's disease. Despite the confirmation of the association of HLA-B51 with Behçet's disease in different populations, its pathogenic mechanisms remain elusive. HLA-B51 differs in only two amino acids from HLA-B52, other split antigen of HLA-B5, which is not associated with Behçet's disease. These two amino acids are located in the B pocket of the antigen-binding groove, which occupies the second amino acids of the bound peptides. To understand the nature of the HLA-peptide interactions, differences in structure and dynamics of two HLA alleles were investigated by molecular dynamics simulations using YAYDGKDYI, LPRSTVINI, and IPYQDLPHL peptides. For HLA-B51, all bound peptides fluctuated to larger extent than HLA-B52. Free energy profiles of unbinding process for YAYDGKDYI by steered molecular dynamics simulations showed that unbinding from HLA-B52 results in greater free energy differences than HLA-B51. These results suggest the possibility of an instability of HLA-B51 associated with the repertoire of peptides, and this finding may provide significant insight to its pathogenic role in Behçet's disease.
MeSH term(s)	Alleles ; Amino Acid Sequence ; Behcet Syndrome/metabolism ; HLA-B51 Antigen/chemistry ; HLA-B51 Antigen/metabolism ; HLA-B52 Antigen/metabolism ; Humans ; Molecular Dynamics Simulation ; Peptides/chemistry ; Peptides/metabolism ; Protein Binding ; Protein Conformation ; Thermodynamics
Chemical Substances	HLA-B51 Antigen ; HLA-B52 Antigen ; Peptides
Language	English
Publishing date	2020-07-21
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2216600-2
ISSN	1747-0285 ; 1747-0277
ISSN (online)	1747-0285
ISSN	1747-0277
DOI	10.1111/cbdd.13658
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Article ; Online: Binding Mechanism of Neutralizing Nanobodies Targeting SARS-CoV-2 Spike Glycoprotein.

Golcuk, Mert / Hacisuleyman, Aysima / Erman, Burak / Yildiz, Ahmet / Gur, Mert

Journal of chemical information and modeling

2021 Volume 61, Issue 10, Page(s) 5152–5160

Abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) enters human cells upon binding of its spike (S) glycoproteins to ACE2 receptors. Several nanobodies neutralize SARS-CoV-2 infection by binding to the receptor-binding domain (RBD) of the S ... ...

Abstract	Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) enters human cells upon binding of its spike (S) glycoproteins to ACE2 receptors. Several nanobodies neutralize SARS-CoV-2 infection by binding to the receptor-binding domain (RBD) of the S protein, but how their binding antagonizes S-ACE2 interactions is not well understood. Here, we identified interactions between the RBD and nanobodies H11-H4, H11-D4, and Ty1 by performing all-atom molecular dynamics simulations. H11-H4 and H11-D4 can bind to RBD without overlapping with ACE2. H11-H4, and to a lesser extent H11-D4, binding dislocates ACE2 from its binding site due to electrostatic repulsion. In comparison, Ty1 overlaps with ACE2 on RBD and has a similar binding strength to ACE2. Mutations in the Alpha variant of SARS-CoV-2 had a minor effect in RBD binding strengths of ACE2 and nanobodies, but reduced the ability of H11-H4 and H11-D4 to dislocate ACE2 from RBD. In comparison, the Beta variant weakened the RBD binding strengths of H11-H4 and H11-D4, which were less effective to dislocate ACE2 binding. Unexpectedly, mutations in Beta strengthened Ty1 binding to RBD, suggesting that this nanobody may be more effective to neutralize the Beta variant of SARS-CoV-2.
MeSH term(s)	Antibodies, Neutralizing/immunology ; Antibodies, Viral/immunology ; Binding Sites ; COVID-19 ; Humans ; Protein Binding ; SARS-CoV-2 ; Single-Domain Antibodies/immunology ; Spike Glycoprotein, Coronavirus/immunology
Chemical Substances	Antibodies, Neutralizing ; Antibodies, Viral ; Single-Domain Antibodies ; Spike Glycoprotein, Coronavirus ; spike protein, SARS-CoV-2
Language	English
Publishing date	2021-09-28
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	190019-5
ISSN	1549-960X ; 0095-2338
ISSN (online)	1549-960X
ISSN	0095-2338
DOI	10.1021/acs.jcim.1c00695
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Article: A force-sensitive mutation reveals a spindle assembly checkpoint-independent role for dynein in anaphase progression.

Salvador-Garcia, David / Jin, Li / Hensley, Andrew / Gölcük, Mert / Gallaud, Emmanuel / Chaaban, Sami / Port, Fillip / Vagnoni, Alessio / Planelles-Herrero, Vicente José / McClintock, Mark A / Derivery, Emmanuel / Carter, Andrew P / Giet, Régis / Gür, Mert / Yildiz, Ahmet / Bullock, Simon L

bioRxiv : the preprint server for biology

2023

Abstract: The cytoplasmic dynein-1 (dynein) motor organizes cells by shaping microtubule networks and moving a large variety of cargoes along them. However, dynein's diverse roles ... ...

Abstract	The cytoplasmic dynein-1 (dynein) motor organizes cells by shaping microtubule networks and moving a large variety of cargoes along them. However, dynein's diverse roles complicate
Language	English
Publishing date	2023-08-04
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.08.03.551815
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Article ; Online: The Omicron Variant Increases the Interactions of SARS-CoV-2 Spike Glycoprotein with ACE2

Golcuk, Mert / Yildiz, Ahmet / Gur, Mert

bioRxiv

Abstract: The Omicron variant (B.1.1.529) comprises 30 mutations on the spike glycoprotein (S), 15 of which are located on its receptor-binding domain (RBD_Omicron). RBD interacts with the peptidase domain (PD) of angiotensin-converting enzyme 2 (ACE2) receptors ... ...

Abstract	The Omicron variant (B.1.1.529) comprises 30 mutations on the spike glycoprotein (S), 15 of which are located on its receptor-binding domain (RBD_Omicron). RBD interacts with the peptidase domain (PD) of angiotensin-converting enzyme 2 (ACE2) receptors and plays a critical role in the host cell entry of the virus. We performed all-atom simulations of the RBD_Omicron-PD in the presence of explicit water and ions. Simulations showed a considerably more extensive interactions network between RBD_Omicron and PD compared to RBD_WT, comprising a 250%, 10% and -25% change in the total number of salt bridges, hydrophobic interactions, hydrogen bonds at the S-ACE2 interface, respectively. Using the conformations sampled in each our MD trajectories, binding energies of two sets of RBD_WT-PD and four sets of RBD_Omicron-PD simulations were calculated via the Molecular Mechanics Poisson-Boltzmann Surface Area (MMPBSA) method, estimating ~44% stronger binding energy for RBD_Omicron compared to RBD_WT. Our results suggest that an increase in the number of salt bridges in the S-ACE2 interface result in a higher binding strength of RBD to PD, which may result in a higher efficiency of the SARS-CoV-2 virus to infect host cells. Furthermore, RBD_Omicron exhibits a more dispersed interaction network on both sides of the RBD-PD interaction surface compared to WT.
Keywords	covid19
Language	English
Publishing date	2021-12-07
Publisher	Cold Spring Harbor Laboratory
Document type	Article ; Online
DOI	10.1101/2021.12.06.471377
Database	COVID19

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Article ; Online: Thermodynamic first law efficiency of membrane proteins.

Gur, Mert / Golcuk, Mert / Yilmaz, Sema Zeynep / Taka, Elhan

Journal of biomolecular structure & dynamics

2019 Volume 38, Issue 2, Page(s) 439–449

Abstract: Proteins are nature's biomolecular machines. Proteins, such as transporters, pumps and motors, have complex function/operating-machinery/mechanisms, comparable to the macro-scaled machines that we encounter in our daily life. These proteins, as it is for ...

Abstract	Proteins are nature's biomolecular machines. Proteins, such as transporters, pumps and motors, have complex function/operating-machinery/mechanisms, comparable to the macro-scaled machines that we encounter in our daily life. These proteins, as it is for their macro-scaled counterparts, convert (part of) other/various forms of energy into work. In this study, we are performing the first law analysis on a set of proteins, including the dopamine transporter, glycine transporters I and II, glutamate transporter, sodium-potassium pump and Ca
MeSH term(s)	Adenosine Triphosphatases/metabolism ; Adenosine Triphosphate/metabolism ; Ions ; Membrane Proteins/chemistry ; Neuroglia/metabolism ; Neurons/metabolism ; Neurotransmitter Agents/metabolism ; Synapses/metabolism ; Thermodynamics
Chemical Substances	Ions ; Membrane Proteins ; Neurotransmitter Agents ; Adenosine Triphosphate (8L70Q75FXE) ; Adenosine Triphosphatases (EC 3.6.1.-)
Language	English
Publishing date	2019-03-04
Publishing country	England
Document type	Journal Article
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2019.1577759
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Zs.A 2093: Show issues

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Article ; Online: Immersive virtual reality on childbirth experience for women: a randomized controlled trial.

Carus, Elif Gizem / Albayrak, Nazli / Bildirici, Halit Mert / Ozmen, Selen Gur

BMC pregnancy and childbirth

2022 Volume 22, Issue 1, Page(s) 354

Abstract: Objective: To evaluate the effectiveness of immersive virtual reality (VR) on patient satisfaction as a distractive tool and pain relief among laboring women.: Methods: This was a randomized, controlled clinical trial with 42 laboring women allocated ...

Abstract	Objective: To evaluate the effectiveness of immersive virtual reality (VR) on patient satisfaction as a distractive tool and pain relief among laboring women. Methods: This was a randomized, controlled clinical trial with 42 laboring women allocated to VR intervention and control groups. Among women in the VR group, patient satisfaction with the use of VR was assessed by a Virtual Reality Satisfaction Survey, measured by a Visual Analog Scale (VAS) score and evaluated by questioning them about whether they would choose VR in future labor. As a primary outcome, patient satisfaction scores regarding the overall childbirth experience were compared between women in the two groups. A secondary outcome was pain assessed by a visual pain rating scale in the early and active phases of labor in women in both groups. Psychometric information was also collected from participants in each group using the Beck Anxiety Inventory and Beck Depression Inventory. Results: We observed a high level of patient satisfaction with the use of immersive VR during labor. The VAS revealed a mean satisfaction score of 87.7 ± 12.9 out of a maximum of 100. Twenty out of 21 (95%) women in the VR group stated that they would like to use VR again in future labor. VR improved pain scores in early labor and contributed positively to the overall childbirth experience. The mean pain score pre-VR was 2.6 ± 1.2 compared to 2.0 ± 1.3 post-VR (p < 0.01). Anxiety and depression scores were similar in participants in the intervention and control groups (p = 0.103 and p = 0.13, respectively). Conclusion: Immersive VR application during labor was associated with higher patient satisfaction based on our study findings. VR also improved participants' pain scores in early labor before epidural administration. Immersive VR may find a place as an adjunct in labor and delivery units to improve lengthy labor experiences for women. Studies with larger groups of participants are needed to confirm these observations. Trial registration: ClinicalTrials.gov: NCT05032456.
MeSH term(s)	Anxiety/etiology ; Female ; Humans ; Male ; Pain ; Pain Management ; Pain Measurement ; Pregnancy ; Virtual Reality
Language	English
Publishing date	2022-04-23
Publishing country	England
Document type	Journal Article ; Randomized Controlled Trial
ZDB-ID	2059869-5
ISSN	1471-2393 ; 1471-2393
ISSN (online)	1471-2393
ISSN	1471-2393
DOI	10.1186/s12884-022-04598-y
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Article ; Online: Binding mechanism of neutralizing Nanobodies targeting SARS-CoV-2 Spike Glycoprotein

Golcuk, Mert / Hacisuleyman, Aysima / Erman, Burak / Yildiz, Ahmet / Gur, Mert

bioRxiv

Abstract	Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) enters human cells upon binding of its spike (S) glycoproteins to ACE2 receptors. Several nanobodies neutralize SARS-CoV-2 infection by binding to the receptor-binding domain (RBD) of S protein, but the underlying mechanism is not well understood. Here, we identified an extended network of pairwise interactions between RBD and nanobodies H11-H4, H11-D4, and Ty1 by performing all-atom molecular dynamics (MD) simulations. Simulations of the nanobody-RBD-ACE2 complex revealed that H11-H4 more strongly binds to RBD without overlapping with ACE2 and triggers dissociation of ACE2 due to electrostatic repulsion. In comparison, Ty1 binding results in dissociation of ACE2 from RBD due to an overlap with the ACE2 binding site, whereas H11-D4 binding does not trigger ACE2 dissociation. Mutations in SARS-CoV-2 501Y.V1 and 501.V2 variants resulted in a negligible effect on RBD-ACE2 binding. However, the 501.V2 variant weakened H11-H4 and H11-D4 binding while strengthening Ty1 binding to RBD. Our simulations indicate that all three nanobodies can neutralize 501Y.V1 while Ty1 is more effective against the 501.V2 variant.
Keywords	covid19
Language	English
Publishing date	2021-04-26
Publisher	Cold Spring Harbor Laboratory
Document type	Article ; Online
DOI	10.1101/2021.04.23.441186
Database	COVID19

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