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Article ; Online: Single-Molecule Force Spectroscopy: Experiments, Analysis, and Simulations.

Sumbul, Fidan / Rico, Felix

Methods in molecular biology (Clifton, N.J.)

2018 Volume 1886, Page(s) 163–189

Abstract: The mechanical properties of cells and of subcellular components are important to obtain a mechanistic molecular understanding of biological processes. The quantification of mechanical resistance of cells and biomolecules using biophysical methods ... ...

Abstract	The mechanical properties of cells and of subcellular components are important to obtain a mechanistic molecular understanding of biological processes. The quantification of mechanical resistance of cells and biomolecules using biophysical methods matured thanks to the development of nanotechnologies such as optical and magnetic tweezers, the biomembrane force probe, and atomic force microscopy (AFM). The quantitative nature of force spectroscopy measurements has converted AFM into a valuable tool in biophysics. Force spectroscopy allows the determination of the forces required to unfold protein domains and to disrupt individual receptor/ligand bonds. Molecular simulations as a computational microscope allow investigation of similar biological processes with an atomistic detail. In this chapter, we first provide a step-by-step protocol of force spectroscopy experiments using AFM, including sample preparation, measurements, and analysis and interpretation of the resulting dynamic force spectrum in terms of available theories. Next, we present the background for molecular dynamics (MD) simulations focusing on steered molecular dynamics (SMD) and the importance of bridging computational tools with experimental techniques.
MeSH term(s)	Data Analysis ; Image Processing, Computer-Assisted ; Ligands ; Microscopy, Atomic Force/methods ; Molecular Dynamics Simulation ; Protein Binding ; Receptors, Cell Surface/metabolism ; Single Molecule Imaging/methods
Chemical Substances	Ligands ; Receptors, Cell Surface
Language	English
Publishing date	2018-10-29
Publishing country	United States
Document type	Journal Article
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-4939-8894-5_9
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Article ; Online: Oncogenic mutations on Rac1 affect global intrinsic dynamics underlying GTP and PAK1 binding.

Acuner, Saliha Ece / Sumbul, Fidan / Torun, Hamdi / Haliloglu, Turkan

Biophysical journal

2021 Volume 120, Issue 5, Page(s) 866–876

Abstract: Rac1 is a small member of the Rho GTPase family. One of the most important downstream effectors of Rac1 is a serine/threonine kinase, p21-activated kinase 1 (PAK1). Mutational activation of PAK1 by Rac1 has oncogenic signaling effects. Here, although we ... ...

Abstract	Rac1 is a small member of the Rho GTPase family. One of the most important downstream effectors of Rac1 is a serine/threonine kinase, p21-activated kinase 1 (PAK1). Mutational activation of PAK1 by Rac1 has oncogenic signaling effects. Here, although we focus on Rac1-PAK1 interaction by atomic-force-microscopy-based single-molecule force spectroscopy experiments, we explore the effect of active mutations on the intrinsic dynamics and binding interactions of Rac1 by Gaussian network model analysis and molecular dynamics simulations. We observe that Rac1 oncogenic mutations are at the hinges of three global modes of motion, suggesting the mechanical changes as potential markers of oncogenicity. Indeed, the dissociation of wild-type Rac1-PAK1 complex shows two distinct unbinding dynamic states that are reduced to one with constitutively active Q61L and oncogenic Y72C mutant Rac1, as revealed by single-molecule force spectroscopy experiments. Q61L and Y72C mutations change the mechanics of the Rac1-PAK1 complex by increasing the elasticity of the protein and slowing down the transition to the unbound state. On the other hand, Rac1's intrinsic dynamics reveal more flexible GTP and PAK1-binding residues on switches I and II with Q61L, Y72C, oncogenic P29S and Q61R, and negative T17N mutations. The cooperativity in the fluctuations of GTP-binding sites around the p-loop and switch I decreases in all mutants, mostly in Q61L, whereas some PAK1-binding residues display enhanced coupling with GTP-binding sites in Q61L and Y72C and within each other in P29S. The predicted binding free energies of the modeled Rac1-PAK1 complexes show that the change in the dynamic behavior likely means a more favorable PAK1 interaction. Overall, these findings suggest that the active mutations affect intrinsic functional dynamic events and alter the mechanics underlying the binding of Rac1 to GTP and upstream and downstream partners including PAK1.
MeSH term(s)	Guanosine Triphosphate ; Mutation ; Signal Transduction ; p21-Activated Kinases/genetics ; p21-Activated Kinases/metabolism ; rac1 GTP-Binding Protein/genetics ; rac1 GTP-Binding Protein/metabolism
Chemical Substances	Guanosine Triphosphate (86-01-1) ; p21-Activated Kinases (EC 2.7.11.1) ; rac1 GTP-Binding Protein (EC 3.6.5.2)
Language	English
Publishing date	2021-01-28
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	218078-9
ISSN	1542-0086 ; 0006-3495
ISSN (online)	1542-0086
ISSN	0006-3495
DOI	10.1016/j.bpj.2021.01.016
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Article: High-speed force spectroscopy: microsecond force measurements using ultrashort cantilevers.

Valotteau, Claire / Sumbul, Fidan / Rico, Felix

Biophysical reviews

2019 Volume 11, Issue 5, Page(s) 689–699

Abstract: Complete understanding of the role of mechanical forces in biological processes requires knowledge of the mechanical properties of individual proteins and living cells. Moreover, the dynamic response of biological systems at the nano- and microscales ... ...

Abstract	Complete understanding of the role of mechanical forces in biological processes requires knowledge of the mechanical properties of individual proteins and living cells. Moreover, the dynamic response of biological systems at the nano- and microscales span over several orders of magnitude in time, from sub-microseconds to several minutes. Thus, access to force measurements over a wide range of length and time scales is required. High-speed atomic force microscopy (HS-AFM) using ultrashort cantilevers has emerged as a tool to study the dynamics of biomolecules and cells at video rates. The adaptation of HS-AFM to perform high-speed force spectroscopy (HS-FS) allows probing protein unfolding and receptor/ligand unbinding up to the velocity of molecular dynamics (MD) simulations with sub-microsecond time resolution. Moreover, application of HS-FS on living cells allows probing the viscoelastic response at short time scales providing deep understanding of cytoskeleton dynamics. In this mini-review, we assess the principles and recent developments and applications of HS-FS using ultrashort cantilevers to probe molecular and cellular mechanics.
Language	English
Publishing date	2019-10-07
Publishing country	Germany
Document type	Journal Article ; Review
ZDB-ID	2486483-3
ISSN	1867-2469 ; 1867-2450
ISSN (online)	1867-2469
ISSN	1867-2450
DOI	10.1007/s12551-019-00585-4
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Article ; Online: History, rare, and multiple events of mechanical unfolding of repeat proteins.

Sumbul, Fidan / Marchesi, Arin / Rico, Felix

The Journal of chemical physics

2018 Volume 148, Issue 12, Page(s) 123335

Abstract: Mechanical unfolding of proteins consisting of repeat domains is an excellent tool to obtain large statistics. Force spectroscopy experiments using atomic force microscopy on proteins presenting multiple domains have revealed that unfolding forces depend ...

Abstract	Mechanical unfolding of proteins consisting of repeat domains is an excellent tool to obtain large statistics. Force spectroscopy experiments using atomic force microscopy on proteins presenting multiple domains have revealed that unfolding forces depend on the number of folded domains (history) and have reported intermediate states and rare events. However, the common use of unspecific attachment approaches to pull the protein of interest holds important limitations to study unfolding history and may lead to discarding rare and multiple probing events due to the presence of unspecific adhesion and uncertainty on the pulling site. Site-specific methods that have recently emerged minimize this uncertainty and would be excellent tools to probe unfolding history and rare events. However, detailed characterization of these approaches is required to identify their advantages and limitations. Here, we characterize a site-specific binding approach based on the ultrastable complex dockerin/cohesin III revealing its advantages and limitations to assess the unfolding history and to investigate rare and multiple events during the unfolding of repeated domains. We show that this approach is more robust, reproducible, and provides larger statistics than conventional unspecific methods. We show that the method is optimal to reveal the history of unfolding from the very first domain and to detect rare events, while being more limited to assess intermediate states. Finally, we quantify the forces required to unfold two molecules pulled in parallel, difficult when using unspecific approaches. The proposed method represents a step forward toward more reproducible measurements to probe protein unfolding history and opens the door to systematic probing of rare and multiple molecule unfolding mechanisms.
MeSH term(s)	Cell Cycle Proteins/chemistry ; Chromosomal Proteins, Non-Histone/chemistry ; Mechanical Phenomena ; Protein Conformation ; Protein Denaturation ; Protein Folding ; Proteins/chemistry ; Reproducibility of Results ; Cohesins
Chemical Substances	Cell Cycle Proteins ; Chromosomal Proteins, Non-Histone ; Proteins
Language	English
Publishing date	2018-03-28
Publishing country	United States
Document type	Journal Article
ZDB-ID	3113-6
ISSN	1089-7690 ; 0021-9606
ISSN (online)	1089-7690
ISSN	0021-9606
DOI	10.1063/1.5013259
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Article ; Online: High-Speed Force Spectroscopy for Single Protein Unfolding.

Sumbul, Fidan / Marchesi, Arin / Takahashi, Hirohide / Scheuring, Simon / Rico, Felix

Methods in molecular biology (Clifton, N.J.)

2018 Volume 1814, Page(s) 243–264

Abstract: Single-molecule force spectroscopy (SMFS) measurements allow for quantification of the molecular forces required to unfold individual protein domains. Atomic force microscopy (AFM) is one of the long-established techniques for force spectroscopy (FS). ... ...

Abstract	Single-molecule force spectroscopy (SMFS) measurements allow for quantification of the molecular forces required to unfold individual protein domains. Atomic force microscopy (AFM) is one of the long-established techniques for force spectroscopy (FS). Although FS at conventional AFM pulling rates provides valuable information on protein unfolding, in order to get a more complete picture of the mechanism, explore new regimes, and combine and compare experiments with simulations, we need higher pulling rates and μs-time resolution, now accessible via high-speed force spectroscopy (HS-FS). In this chapter, we provide a step-by-step protocol of HS-FS including sample preparation, measurements and analysis of the acquired data using HS-AFM with an illustrative example on unfolding of a well-studied concatamer made of eight repeats of the titin I91 domain.
MeSH term(s)	Calibration ; Connectin/chemistry ; Data Analysis ; Microscopy, Atomic Force/methods ; Protein Unfolding
Chemical Substances	Connectin
Language	English
Publishing date	2018-06-28
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-4939-8591-3_15
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Article ; Online: Modulation of SARS-CoV-2 spike binding to ACE2 through conformational selection

Saha, Prithwidip / Fernanadez, Ignacio / Sumbul, Fidan / Valotteau, Claire / Kostrz, Dorota / Meola, Annalisa / Baquero, Eduard / Sharma, Arvind / Portman, James R. / Stransky, Francois / Boudier, Thomas / Guardado Calvo, Pablo / Gosse, Charlie / Strick, Terence / Rey, Felix A. / Rico, Felix

bioRxiv

Abstract: The first step of SARS-CoV-2 infection involves the interaction between the trimeric viral spike protein () and the host angiotensin-converting enzyme 2 (2). The receptor binding domain () of adopts two conformations: open and closed, respectively, ... ...

Abstract	The first step of SARS-CoV-2 infection involves the interaction between the trimeric viral spike protein () and the host angiotensin-converting enzyme 2 (2). The receptor binding domain () of adopts two conformations: open and closed, respectively, accessible and inaccessible to 2. Therefore, motions are suspected to affect 2 binding; yet a quantitative description of the underlying mechanism has been elusive. Here, using single-molecule approaches, we visualize opening and closing and probe the /2 interaction. Our results show that RBD dynamics affect 2 binding but not unbinding. The resulting modulation is quantitatively predicted by a conformational selection model in which each protomer behaves independently. Our work reveals a general molecular mechanism affecting binding affinity without altering binding strength, helping to understand coronavirus infection and immune evasion.
Keywords	covid19
Language	English
Publishing date	2024-03-18
Publisher	Cold Spring Harbor Laboratory
Document type	Article ; Online
DOI	10.1101/2024.03.15.585207
Database	COVID19

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Article ; Online: Epistatic Effects Between Amino Acid Insertions and Substitutions Mediate Toxin resistance of Vertebrate Na+,K+-ATPases.

Mohammadi, Shabnam / Özdemir, Halil İbrahim / Ozbek, Pemra / Sumbul, Fidan / Stiller, Josefin / Deng, Yuan / Crawford, Andrew J / Rowland, Hannah M / Storz, Jay F / Andolfatto, Peter / Dobler, Susanne

Molecular biology and evolution

2022 Volume 39, Issue 12

Abstract: The recurrent evolution of resistance to cardiotonic steroids (CTS) across diverse animals most frequently involves convergent amino acid substitutions in the H1-H2 extracellular loop of Na+,K+-ATPase (NKA). Previous work revealed that hystricognath ... ...

Abstract	The recurrent evolution of resistance to cardiotonic steroids (CTS) across diverse animals most frequently involves convergent amino acid substitutions in the H1-H2 extracellular loop of Na+,K+-ATPase (NKA). Previous work revealed that hystricognath rodents (e.g., chinchilla) and pterocliform birds (sandgrouse) have convergently evolved amino acid insertions in the H1-H2 loop, but their functional significance was not known. Using protein engineering, we show that these insertions have distinct effects on CTS resistance in homologs of each of the two species that strongly depend on intramolecular interactions with other residues. Removing the insertion in the chinchilla NKA unexpectedly increases CTS resistance and decreases NKA activity. In the sandgrouse NKA, the amino acid insertion and substitution Q111R both contribute to an augmented CTS resistance without compromising ATPase activity levels. Molecular docking simulations provide additional insight into the biophysical mechanisms responsible for the context-specific mutational effects on CTS insensitivity of the enzyme. Our results highlight the diversity of genetic substrates that underlie CTS insensitivity in vertebrate NKA and reveal how amino acid insertions can alter the phenotypic effects of point mutations at key sites in the same protein domain.
MeSH term(s)	Animals ; Sodium-Potassium-Exchanging ATPase/genetics ; Sodium-Potassium-Exchanging ATPase/metabolism ; Amino Acids/genetics ; Molecular Docking Simulation ; Chinchilla/metabolism ; Cardiac Glycosides/chemistry ; Cardiac Glycosides/pharmacology ; Vertebrates/genetics ; Vertebrates/metabolism
Chemical Substances	Sodium-Potassium-Exchanging ATPase (EC 7.2.2.13) ; Amino Acids ; Cardiac Glycosides
Language	English
Publishing date	2022-12-02
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	998579-7
ISSN	1537-1719 ; 0737-4038
ISSN (online)	1537-1719
ISSN	0737-4038
DOI	10.1093/molbev/msac258
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Article ; Online: Cullin neddylation may allosterically tune polyubiquitin chain length and topology.

Onel, Melis / Sumbul, Fidan / Liu, Jin / Nussinov, Ruth / Haliloglu, Turkan

The Biochemical journal

2017 Volume 474, Issue 5, Page(s) 781–795

Abstract: Conjugation of Nedd8 (neddylation) to Cullins (Cul) in Cul-RING E3 ligases (CRLs) stimulates ubiquitination and polyubiquitination of protein substrates. CRL is made up of two Cul-flanked arms: one consists of the substrate-binding and adaptor proteins ... ...

Abstract	Conjugation of Nedd8 (neddylation) to Cullins (Cul) in Cul-RING E3 ligases (CRLs) stimulates ubiquitination and polyubiquitination of protein substrates. CRL is made up of two Cul-flanked arms: one consists of the substrate-binding and adaptor proteins and the other consists of E2 and Ring-box protein (Rbx). Polyubiquitin chain length and topology determine the substrate fate. Here, we ask how polyubiquitin chains are accommodated in the limited space available between the two arms and what determines the polyubiquitin linkage topology. We focus on Cul5 and Rbx1 in three states: before Cul5 neddylation (closed state), after neddylation (open state), and after deneddylation, exploiting molecular dynamics simulations and the Gaussian Network Model. We observe that regulation of substrate ubiquitination and polyubiquitination takes place through Rbx1 rotations, which are controlled by Nedd8-Rbx1 allosteric communication. Allosteric propagation proceeds from Nedd8 via Cul5 dynamic hinges and hydrogen bonds between the C-terminal domain of Cul5 (Cul5
MeSH term(s)	Allosteric Regulation ; Allosteric Site ; Carrier Proteins/chemistry ; Carrier Proteins/metabolism ; Cullin Proteins/chemistry ; Cullin Proteins/metabolism ; Humans ; Hydrogen Bonding ; Kinetics ; Molecular Dynamics Simulation ; NEDD8 Protein ; Polyubiquitin ; Protein Binding ; Protein Interaction Domains and Motifs ; Protein Processing, Post-Translational ; Protein Structure, Secondary ; Substrate Specificity ; Ubiquitination ; Ubiquitins/chemistry ; Ubiquitins/metabolism
Chemical Substances	CUL5 protein, human ; Carrier Proteins ; Cullin Proteins ; NEDD8 Protein ; NEDD8 protein, human ; RBX1 protein, human ; Ubiquitins ; Polyubiquitin (120904-94-1)
Language	English
Publishing date	2017-02-20
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Intramural ; Research Support, N.I.H., Extramural
ZDB-ID	2969-5
ISSN	1470-8728 ; 0006-2936 ; 0306-3275 ; 0264-6021
ISSN (online)	1470-8728
ISSN	0006-2936 ; 0306-3275 ; 0264-6021
DOI	10.1042/BCJ20160748
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Article ; Online: Allosteric Dynamic Control of Binding.

Sumbul, Fidan / Acuner-Ozbabacan, Saliha Ece / Haliloglu, Turkan

Biophysical journal

2015 Volume 109, Issue 6, Page(s) 1190–1201

Abstract: Proteins have a highly dynamic nature and there is a complex interrelation between their structural dynamics and binding behavior. By assuming various conformational ensembles, they perform both local and global fluctuations to interact with other ... ...

Abstract	Proteins have a highly dynamic nature and there is a complex interrelation between their structural dynamics and binding behavior. By assuming various conformational ensembles, they perform both local and global fluctuations to interact with other proteins in a dynamic infrastructure adapted to functional motion. Here, we show that there is a significant association between allosteric mutations, which lead to high-binding-affinity changes, and the hinge positions of global modes, as revealed by a large-scale statistical analysis of data in the Structural Kinetic and Energetic Database of Mutant Protein Interactions (SKEMPI). We further examined the mechanism of allosteric dynamics by conducting studies on human growth hormone (hGH) and pyrin domain (PYD), and the results show how mutations at the hinge regions could allosterically affect the binding-site dynamics or induce alternative binding modes by modifying the ensemble of accessible conformations. The long-range dissemination of perturbations in local chemistry or physical interactions through an impact on global dynamics can restore the allosteric dynamics. Our findings suggest a mechanism for the coupling of structural dynamics to the modulation of protein interactions, which remains a critical phenomenon in understanding the effect of mutations that lead to functional changes in proteins.
MeSH term(s)	Allosteric Regulation ; Cytoskeletal Proteins/genetics ; Cytoskeletal Proteins/metabolism ; Human Growth Hormone/genetics ; Human Growth Hormone/metabolism ; Humans ; Hydrogen Bonding ; Kinetics ; Molecular Dynamics Simulation ; Mutation ; Protein Binding ; Pyrin
Chemical Substances	Cytoskeletal Proteins ; MEFV protein, human ; Pyrin ; Human Growth Hormone (12629-01-5)
Language	English
Publishing date	2015-09-15
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	218078-9
ISSN	1542-0086 ; 0006-3495
ISSN (online)	1542-0086
ISSN	0006-3495
DOI	10.1016/j.bpj.2015.08.011
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Article ; Online: Structural and dynamics aspects of ASC speck assembly.

Sahillioglu, Ali Can / Sumbul, Fidan / Ozoren, Nesrin / Haliloglu, Turkan

Structure (London, England : 1993)

2014 Volume 22, Issue 12, Page(s) 1722–1734

Abstract: Activation of the inflammasome is accompanied by rapid formation of a micrometer-sized perinuclear structure called the ASC speck, a platform for caspase-1 activity. The ASC speck is often referred to as an aggregate and shares certain features with ... ...

Abstract	Activation of the inflammasome is accompanied by rapid formation of a micrometer-sized perinuclear structure called the ASC speck, a platform for caspase-1 activity. The ASC speck is often referred to as an aggregate and shares certain features with aggresomes. It is thus an open question whether the ASC speck formation takes place via nonspecific aggregation of hydrophobic patches or specific interactions of its domains; PYD and CARD, which belong to the death fold superfamily. Bringing together structure and dynamics studies using the Gaussian network model of PYD and CARD, and molecular dynamics simulations of the wild-type and in silico mutated PYD, with the mutational analysis on the ASC structure and its separate domains in human cells, we show that the ASC speck is an organized structure with at least two levels of distinct compaction mechanisms based on the specific interactions of PYD and CARD.
MeSH term(s)	CARD Signaling Adaptor Proteins ; Caspase 1/metabolism ; Cytoskeletal Proteins/metabolism ; HEK293 Cells ; Humans ; Inflammasomes/metabolism ; Models, Molecular ; Molecular Dynamics Simulation ; Protein Conformation ; Protein Multimerization
Chemical Substances	CARD Signaling Adaptor Proteins ; Cytoskeletal Proteins ; Inflammasomes ; PYCARD protein, human ; Caspase 1 (EC 3.4.22.36)
Language	English
Publishing date	2014-12-02
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1213087-4
ISSN	1878-4186 ; 0969-2126
ISSN (online)	1878-4186
ISSN	0969-2126
DOI	10.1016/j.str.2014.09.011
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