Unraveling the Mechanism of a LOV Domain Optogenetic Sensor: A Glutamine Lever Induces Unfolding of the Jα Helix

AbstractLight-activated protein domains provide a convenient, modular, and genetically encodable sensor for optogenetics and optobiology. Although these domains have now been deployed in numerous systems, the precise mechanism of photoactivation and the accompanying structural dynamics that modulate output domain activity remain to be fully elucidated. In the C-terminal light, oxygen, voltage (LOV) domain of plant phototropins (LOV2), blue light activation leads to formation of an adduct between a conserved Cys residue and the embedded FMN chromophore, rotation of a conserved Gln (Q513), and unfolding of a helix (Jα-helix) which is coupled to the output partner. In the present work, we focus on the allosteric pathways leading to Jα helix unfolding in Avena sativa LOV2 (AsLOV2) using an interdisciplinary approach involving molecular dynamics simulations extending to 7 μs, time-resolved infrared spectroscopy, solution NMR spectroscopy, and in-cell optogenetic experiments. In the dark state, the side chain of N414 is hydrogen bonded to the backbone N-H of Q513. The simulations predict a lever-like motion of Q513 after Cys adduct formation resulting in loss of the interaction between the side chain of N414 and the backbone C=O of Q513, and formation of a transient hydrogen bond between the Q513 and N414 side chains. The central role of N414 in signal transduction was evaluated by site-directed mutagenesis supporting a direct link between Jα helix unfolding dynamics and the cellular function of the Zdk2-AsLOV2 optogenetic construct. Through this multifaceted approach, we show that Q513 and N414 are critical mediators of protein structural dynamics, linking the ultrafast (sub-ps) excitation of the FMN chromophore to the microsecond conformational changes that result in photoreceptor activation and biological function.

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Protein Structural Dynamics of Wild-Type and Mutant Homodimeric Hemoglobin Studied by Time-Resolved X-Ray Solution Scattering

International Journal of Molecular Sciences ◽

10.3390/ijms19113633 ◽

2018 ◽

Vol 19 (11) ◽

pp. 3633 ◽

Cited By ~ 2

Author(s):

Cheolhee Yang ◽

Minseo Choi ◽

Jong Kim ◽

Hanui Kim ◽

Srinivasan Muniyappan ◽

...

Keyword(s):

Structural Dynamics ◽

Conformational Changes ◽

Structural Transition ◽

Quaternary Structure ◽

Heme Binding ◽

Wild Type ◽

Time Resolved ◽

X Ray ◽

Protein Structural Dynamics ◽

Cooperative Transition

The quaternary transition between the relaxed (R) and tense (T) states of heme-binding proteins is a textbook example for the allosteric structural transition. Homodimeric hemoglobin (HbI) from Scapharca inaequivalvis is a useful model system for investigating the allosteric behavior because of the relatively simple quaternary structure. To understand the cooperative transition of HbI, wild-type and mutants of HbI have been studied by using time-resolved X-ray solution scattering (TRXSS), which is sensitive to the conformational changes. Herein, we review the structural dynamics of HbI investigated by TRXSS and compare the results of TRXSS with those of other techniques.

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Regulation of Protein Structural Changes by Incorporation of a Small-Molecule Linker

International Journal of Molecular Sciences ◽

10.3390/ijms19123714 ◽

2018 ◽

Vol 19 (12) ◽

pp. 3714

Author(s):

Youngmin Kim ◽

Cheolhee Yang ◽

Tae Kim ◽

Kamatchi Thamilselvan ◽

Yonggwan Kim ◽

...

Keyword(s):

Structural Dynamics ◽

Small Molecule ◽

Conformational Changes ◽

Structural Changes ◽

Transient Absorption ◽

Structural Characteristics ◽

Site Directed Mutagenesis ◽

Photoactive Yellow Protein ◽

Fine Control ◽

Protein Structural Dynamics

Proteins have the potential to serve as nanomachines with well-controlled structural movements, and artificial control of their conformational changes is highly desirable for successful applications exploiting their dynamic structural characteristics. Here, we demonstrate an experimental approach for regulating the degree of conformational change in proteins by incorporating a small-molecule linker into a well-known photosensitive protein, photoactive yellow protein (PYP), which is sensitized by blue light and undergoes a photo-induced N-terminal protrusion coupled with chromophore-isomerization-triggered conformational changes. Specifically, we introduced thiol groups into specific sites of PYP through site-directed mutagenesis and then covalently conjugated a small-molecule linker into these sites, with the expectation that the linker is likely to constrain the structural changes associated with the attached positions. To investigate the structural dynamics of PYP incorporated with the small-molecule linker (SML-PYP), we employed the combination of small-angle X-ray scattering (SAXS), transient absorption (TA) spectroscopy and experiment-restrained rigid-body molecular dynamics (MD) simulation. Our results show that SML-PYP exhibits much reduced structural changes during photo-induced signaling as compared to wild-type PYP. This demonstrates that incorporating an external molecular linker can limit photo-induced structural dynamics of the protein and may be used as a strategy for fine control of protein structural dynamics in nanomachines.

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Structural dynamics of P-type ATPase ion pumps

Biochemical Society Transactions ◽

10.1042/bst20190124 ◽

2019 ◽

Vol 47 (5) ◽

pp. 1247-1257 ◽

Cited By ~ 17

Author(s):

Mateusz Dyla ◽

Sara Basse Hansen ◽

Poul Nissen ◽

Magnus Kjaergaard

Keyword(s):

Structural Dynamics ◽

Single Molecule ◽

New Technologies ◽

Atp Hydrolysis ◽

Resonance Energy Transfer ◽

Resonance Energy ◽

Time Resolved ◽

Dynamics Simulations ◽

Types Of Information ◽

P Type

Abstract P-type ATPases transport ions across biological membranes against concentration gradients and are essential for all cells. They use the energy from ATP hydrolysis to propel large intramolecular movements, which drive vectorial transport of ions. Tight coordination of the motions of the pump is required to couple the two spatially distant processes of ion binding and ATP hydrolysis. Here, we review our current understanding of the structural dynamics of P-type ATPases, focusing primarily on Ca2+ pumps. We integrate different types of information that report on structural dynamics, primarily time-resolved fluorescence experiments including single-molecule Förster resonance energy transfer and molecular dynamics simulations, and interpret them in the framework provided by the numerous crystal structures of sarco/endoplasmic reticulum Ca2+-ATPase. We discuss the challenges in characterizing the dynamics of membrane pumps, and the likely impact of new technologies on the field.

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Molecular Basis of Glucose Transport Mechanism in Plants

10.26434/chemrxiv.8049848.v1 ◽

2019 ◽

Cited By ~ 2

Author(s):

Balaji Selvam ◽

Ya-Chi Yu ◽

Liqing Chen ◽

Diwakar Shukla

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Molecular Dynamics Simulations ◽

Conformational Changes ◽

Transport Mechanism ◽

Conformational Dynamics ◽

Site Directed Mutagenesis ◽

Free Energy Barrier ◽

Transport Cycle ◽

Dynamics Simulations

<p>The SWEET family belongs to a class of transporters in plants that undergoes large conformational changes to facilitate transport of sugar molecules across the cell membrane. However, the structures of their functionally relevant conformational states in the transport cycle have not been reported. In this study, we have characterized the conformational dynamics and complete transport cycle of glucose in OsSWEET2b transporter using extensive molecular dynamics simulations. Using Markov state models, we estimated the free energy barrier associated with different states as well as 1 for the glucose the transport mechanism. SWEETs undergoes structural transition to outward-facing (OF), Occluded (OC) and inward-facing (IF) and strongly support alternate access transport mechanism. The glucose diffuses freely from outside to inside the cell without causing major conformational changes which means that the conformations of glucose unbound and bound snapshots are exactly same for OF, OC and IF states. We identified a network of hydrophobic core residues at the center of the transporter that restricts the glucose entry to the cytoplasmic side and act as an intracellular hydrophobic gate. The mechanistic predictions from molecular dynamics simulations are validated using site-directed mutagenesis experiments. Our simulation also revealed hourglass like intermediate states making the pore radius narrower at the center. This work provides new fundamental insights into how substrate-transporter interactions actively change the free energy landscape of the transport cycle to facilitate enhanced transport activity.</p>

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New insights into structure and function of bis-phosphinic acid derivatives and implications for CFTR modulation

Scientific Reports ◽

10.1038/s41598-021-83240-x ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Sara Bitam ◽

Ahmad Elbahnsi ◽

Geordie Creste ◽

Iwona Pranke ◽

Benoit Chevalier ◽

...

Keyword(s):

Phosphinic Acid ◽

Site Directed Mutagenesis ◽

Side Chain ◽

Transmembrane Conductance Regulator ◽

Intracellular Loop ◽

Respiratory Cells ◽

Cftr Protein ◽

Dynamics Simulations ◽

And Function ◽

Molecular Mode

AbstractC407 is a compound that corrects the Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) protein carrying the p.Phe508del (F508del) mutation. We investigated the corrector effect of c407 and its derivatives on F508del-CFTR protein. Molecular docking and dynamics simulations combined with site-directed mutagenesis suggested that c407 stabilizes the F508del-Nucleotide Binding Domain 1 (NBD1) during the co-translational folding process by occupying the position of the p.Phe1068 side chain located at the fourth intracellular loop (ICL4). After CFTR domains assembly, c407 occupies the position of the missing p.Phe508 side chain. C407 alone or in combination with the F508del-CFTR corrector VX-809, increased CFTR activity in cell lines but not in primary respiratory cells carrying the F508del mutation. A structure-based approach resulted in the synthesis of an extended c407 analog G1, designed to improve the interaction with ICL4. G1 significantly increased CFTR activity and response to VX-809 in primary nasal cells of F508del homozygous patients. Our data demonstrate that in-silico optimized c407 derivative G1 acts by a mechanism different from the reference VX-809 corrector and provide insights into its possible molecular mode of action. These results pave the way for novel strategies aiming to optimize the flawed ICL4–NBD1 interface.

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Insights into the roles of charged residues in substrate binding and mode of action of mannuronan C-5 epimerase AlgE4

Glycobiology ◽

10.1093/glycob/cwab025 ◽

2021 ◽

Author(s):

Margrethe Gaardløs ◽

Sergey A Samsonov ◽

Marit Sletmoen ◽

Maya Hjørnevik ◽

Gerd Inger Sætrom ◽

...

Keyword(s):

Optical Tweezers ◽

Conformational Changes ◽

Molecular Mechanisms ◽

Hydrophobic Interactions ◽

Substrate Binding ◽

Interdisciplinary Approach ◽

Product Formation ◽

Titration Calorimetry ◽

Binding Groove ◽

Dynamics Simulations

Abstract Mannuronan C-5 epimerases catalyse the epimerization of monomer residues in the polysaccharide alginate, changing the physical properties of the biopolymer. The enzymes are utilized to tailor alginate to numerous biological functions by alginate-producing organisms. The underlying molecular mechanisms that control the processive movement of the epimerase along the substrate chain is still elusive. To study this, we have used an interdisciplinary approach combining molecular dynamics simulations with experimental methods from mutant studies of AlgE4, where initial epimerase activity and product formation were addressed with NMR spectroscopy, and characteristics of enzyme-substrate interactions were obtained with isothermal titration calorimetry and optical tweezers. Positive charges lining the substrate-binding groove of AlgE4 appear to control the initial binding of poly-mannuronate, and binding also seems to be mediated by both electrostatic and hydrophobic interactions. After the catalytic reaction, negatively charged enzyme residues might facilitate dissociation of alginate from the positive residues, working like electrostatic switches, allowing the substrate to translocate in the binding groove. Molecular simulations show translocation increments of two monosaccharide units before the next productive binding event resulting in MG-block formation, with the epimerase moving with its N-terminus towards the reducing end of the alginate chain. Our results indicate that the charge pair R343-D345 might be directly involved in conformational changes of a loop that can be important for binding and dissociation. The computational and experimental approaches used in this study complement each other, allowing for a better understanding of individual residues’ roles in binding and movement along the alginate chains.

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Conformational Changes Generated in GroEL during ATP Hydrolysis as Seen by Time-resolved Infrared Spectroscopy

Journal of Biological Chemistry ◽

10.1074/jbc.274.9.5508 ◽

1999 ◽

Vol 274 (9) ◽

pp. 5508-5513 ◽

Cited By ~ 19

Author(s):

Frithjof von Germar ◽

Asier Galán ◽

Oscar Llorca ◽

Jose L. Carrascosa ◽

Jose M. Valpuesta ◽

...

Keyword(s):

Infrared Spectroscopy ◽

Conformational Changes ◽

Atp Hydrolysis ◽

Time Resolved ◽

Time Resolved Infrared Spectroscopy

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The intercalation of imidazoacridinones into DNA induces conformational changes in their side chain.

Acta Biochimica Polonica ◽

10.18388/abp.2000_4063 ◽

2000 ◽

Vol 47 (1) ◽

pp. 65-78 ◽

Cited By ~ 10

Author(s):

J Mazerski ◽

K Muchewicz

Keyword(s):

Conformational Changes ◽

Ring System ◽

Van Der Waals Interactions ◽

Side Chain ◽

Intercalation Complex ◽

Highly Active ◽

Antitumor Compounds ◽

Chemical Constitution ◽

Modelling Techniques ◽

Dynamics Simulations

Imidazoacridinones (IAs) are a new group of highly active antitumor compounds. The intercalation of the IA molecule into DNA is the preliminary step in the mode of action of these compounds. There are no experimental data about the structure of an intercalation complex formed by imidazoacridinones. Therefore the design of new potentially better compounds of this group should employ the molecular modelling techniques. The results of molecular dynamics simulations performed for four IA analogues are presented. Each of the compounds was studied in two systems: i) in water, and ii) in the intercalation complex with dodecamer duplex d(GCGCGCGCGCGC)2. Significant differences in the conformation of the side chain in the two environments were observed for all studied IAs. These changes were induced by electrostatic as well as van der Waals interactions between the intercalator and DNA. Moreover, the results showed that the geometry of the intercalation complex depends on: i) the chemical constitution of the side chain, and ii) the substituent in position 8 of the ring system.

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Structural dynamics of the Ca2+-ATPase studied by time-resolved infrared spectroscopy

Spectroscopy An International Journal ◽

10.1155/2008/489739 ◽

2008 ◽

Vol 22 (2-3) ◽

pp. 63-82 ◽

Cited By ~ 7

Author(s):

Andreas Barth

Keyword(s):

Infrared Spectroscopy ◽

Structural Dynamics ◽

Ground State ◽

Transfer Reaction ◽

High Reactivity ◽

Acetyl Phosphate ◽

Time Resolved ◽

Closed Conformation ◽

Sarcoplasmic Reticulum Membrane ◽

Time Resolved Infrared Spectroscopy

This review discusses the contribution of time-resolved infrared spectroscopy to the understanding of the Ca2+pump in the sarcoplasmic reticulum membrane of skeletal muscle cells (SERCA1a). The focus is on interactions of the substrate ATP with the ATPase and on the bond parameters of the phosphoenzyme phosphate group. Functional groups throughout the ATP molecule are important for stabilising the closed conformation of the ATP–ATPase complex and for fast phosphorylation of the ATPase. Dissociation of the reaction product ADP after phosphorylation leads to a more open average conformation of the enzyme and does not trigger the transition from the first phosphoenzyme Ca2E1P to the second E2P. The P–O bond between phosphate and aspartyl moieties is weaker in Ca2E1P and E2P than in acetyl phosphate in aqueous solution, which explains the high reactivity of the phosphoenzymes. This ground state property of the phosphoenzymes prepares for a phosphate transfer reaction with dissociative character.

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