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Stewart AM, Shanmugam M, Kutta RJ, Scrutton NS, Lovett JE, Hay S. Combined Pulsed Electron Double Resonance EPR and Molecular Dynamics Investigations of Calmodulin Suggest Effects of Crowding Agents on Protein Structures. Biochemistry 2022; 61:1735-1742. [PMID: 35979922 PMCID: PMC9454100 DOI: 10.1021/acs.biochem.2c00099] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
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Calmodulin (CaM) is a highly dynamic Ca2+-binding
protein
that exhibits large conformational changes upon binding Ca2+ and target proteins. Although it is accepted that CaM exists in
an equilibrium of conformational states in the absence of target protein,
the physiological relevance of an elongated helical linker region
in the Ca2+-replete form has been highly debated. In this
study, we use PELDOR (pulsed electron–electron double resonance)
EPR measurements of a doubly spin-labeled CaM variant to assess the
conformational states of CaM in the apo-, Ca2+-bound, and
Ca2+ plus target peptide-bound states. Our findings are
consistent with a three-state conformational model of CaM, showing
a semi-open apo-state, a highly extended Ca2+-replete state,
and a compact target protein-bound state. Molecular dynamics simulations
suggest that the presence of glycerol, and potentially other molecular
crowding agents, has a profound effect on the relative stability of
the different conformational states. Differing experimental conditions
may explain the discrepancies in the literature regarding the observed
conformational state(s) of CaM, and our PELDOR measurements show good
evidence for an extended conformation of Ca2+-replete CaM
similar to the one observed in early X-ray crystal structures.
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Affiliation(s)
- Andrew M Stewart
- The Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames 50011, Iowa, United States.,Manchester Institute of Biotechnology and Department of Chemistry, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
| | - Muralidharan Shanmugam
- Manchester Institute of Biotechnology and Department of Chemistry, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
| | - Roger J Kutta
- Manchester Institute of Biotechnology and Department of Chemistry, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K.,Institute of Physical and Theoretical Chemistry, University of Regensburg, Regensburg 93040, Germany
| | - Nigel S Scrutton
- Manchester Institute of Biotechnology and Department of Chemistry, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
| | - Janet E Lovett
- SUPA School of Physics and Astronomy and BSRC, The University of St Andrews, St Andrews KY16 9SS, U.K
| | - Sam Hay
- Manchester Institute of Biotechnology and Department of Chemistry, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
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Siddiqui GA, Naeem A. Refolding of Hemoglobin Under Macromolecular Confinement: Impersonating In Vivo Volume Exclusion. J Fluoresc 2021; 31:1371-1377. [PMID: 34156613 DOI: 10.1007/s10895-021-02751-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 05/20/2021] [Indexed: 11/27/2022]
Abstract
Biomacromolecules evolve and function inside the cell under crowded conditions. The effect of macromolecular crowding and confinement on nature and interactions of biomacromolecules cannot be ruled out. This study demonstrates the effect of volume exclusion due to macromolecular crowding on refolding rate of Gn-HCl induced unfolded hemoglobin. The in vivo like crowding milieu was created using dextran 70. Unfolding of Hb was followed by the absorbance at 280 nm and intrinsic fluorescence intensity along with a bathochromic shift that shows the destabilization of Hb in the presence of the denaturing agent. This was supported by a decrease in soret absorbance, increased hydrodynamic radii and loss in secondary structure, evidenced from dynamic light scattering and circular dichroism experiments respectively. Refolding process of Hb was followed by an increase in soret absorbance, decrease in intrinsic fluorescence intensity with a hypsochromic shift, decreased hydrodynamic radii and gain in secondary structural content. The results revealed that the effect of confinement and volume exclusion is insignificant on the process of Hb refolding.
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Affiliation(s)
- Gufran Ahmed Siddiqui
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, 202002, UP, India
| | - Aabgeena Naeem
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, 202002, UP, India.
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Abstract
Bioelectrocatalysis using redox enzymes appears as a sustainable way for biosensing, electricity production, or biosynthesis of fine products. Despite advances in the knowledge of parameters that drive the efficiency of enzymatic electrocatalysis, the weak stability of bioelectrodes prevents large scale development of bioelectrocatalysis. In this review, starting from the understanding of the parameters that drive protein instability, we will discuss the main strategies available to improve all enzyme stability, including use of chemicals, protein engineering and immobilization. Considering in a second step the additional requirements for use of redox enzymes, we will evaluate how far these general strategies can be applied to bioelectrocatalysis.
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4
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Zheng H, Li J, Feng C. An isoform-specific pivot modulates the electron transfer between the flavin mononucleotide and heme centers in inducible nitric oxide synthase. J Biol Inorg Chem 2020; 25:1097-1105. [PMID: 33057871 PMCID: PMC7669679 DOI: 10.1007/s00775-020-01824-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Accepted: 09/24/2020] [Indexed: 11/25/2022]
Abstract
Intraprotein interdomain electron transfer (IET) between the flavin mononucleotide (FMN) and heme centers is an obligatory step in nitric oxide synthase (NOS) enzymes. An isoform-specific pivotal region near Leu406 in the heme domain of human inducible NOS (iNOS) was proposed to mediate the FMN-heme domain-domain alignment (J Inorg Biochem 153:186-196, 2015). The FMN-heme IET rate is a measure of the interdomain FMN/heme complex formation. In this work, the FMN-heme IET kinetics in the wild type (wt) human iNOS oxygenase/FMN (oxyFMN) construct were directly measured by laser flash photolysis with added synthetic peptide related to the pivotal region, in comparison with the wt construct alone. The IET rates were decreased by the iNOS HKL peptide in a dose-saturable fashion, and the inhibitory effect was abolished by a single L406 → E mutation in the peptide. A similar trend in change of the NO synthesis activity of wt iNOS holoenzyme by the peptides was observed. These data, along with the kinetics and modeling results for the L406T and L406F mutant oxyFMN proteins, indicated that the Leu406 residue modulates the FMN-heme IET through hydrophobic interactions. Moreover, the IET rates were analyzed for the wt iNOS oxyFMN protein in the presence of nNOS or eNOS-derived peptide related to the equivalent pivotal heme domain site. These results together indicate that the isoform-specific pivotal region at the heme domain specifically interacts with the conserved FMN domain surface, to facilitate proper interdomain docking for the FMN-heme IET in NOS.
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Affiliation(s)
- Huayu Zheng
- College of Pharmacy, University of New Mexico, Albuquerque, NM, 87131, USA
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, NM, 87131, USA
| | - Jinghui Li
- College of Pharmacy, University of New Mexico, Albuquerque, NM, 87131, USA
| | - Changjian Feng
- College of Pharmacy, University of New Mexico, Albuquerque, NM, 87131, USA.
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, NM, 87131, USA.
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Zheng H, Li J, Feng C. Heat shock protein 90 enhances the electron transfer between the FMN and heme cofactors in neuronal nitric oxide synthase. FEBS Lett 2020; 594:2904-2913. [PMID: 32573772 DOI: 10.1002/1873-3468.13870] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Revised: 05/30/2020] [Accepted: 06/04/2020] [Indexed: 11/05/2022]
Abstract
Heat shock protein 90 (Hsp90) is a key regulator of nitric oxide synthase (NOS) in vivo. Despite its functional importance, little is known about the underlying molecular mechanism. Here, purified dimeric human Hsp90α was used to investigate whether (and if so, how) Hsp90 affects the FMN-heme interdomain electron transfer (IET) step in NOS. Hsp90α increases the IET rate for rat neuronal NOS (nNOS) in a dose-saturable manner, and a single charge-neutralization mutation at conserved Hsp90 K585 abolishes the effect. The kinetic results with added Ficoll 70, a crowder, further indicate that Hsp90 enhances the FMN-heme IET through specific association with nNOS. The Hsp90-nNOS docking models provide hints on the putative role of Hsp90 in constraining the available conformational space for the FMN domain motions.
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Affiliation(s)
- Huayu Zheng
- College of Pharmacy, University of New Mexico, Albuquerque, NM, USA.,Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, NM, USA
| | - Jinghui Li
- College of Pharmacy, University of New Mexico, Albuquerque, NM, USA
| | - Changjian Feng
- College of Pharmacy, University of New Mexico, Albuquerque, NM, USA.,Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, NM, USA
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Das N, Sen P. Shape-Dependent Macromolecular Crowding on the Thermodynamics and Microsecond Conformational Dynamics of Protein Unfolding Revealed at the Single-Molecule Level. J Phys Chem B 2020; 124:5858-5871. [DOI: 10.1021/acs.jpcb.0c03897] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Nilimesh Das
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208 016, UP India
| | - Pratik Sen
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208 016, UP India
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Astashkin AV, Li J, Zheng H, Feng C. Positional Distributions of the Tethered Modules in Nitric Oxide Synthase: Monte Carlo Calculations and Pulsed EPR Measurements. J Phys Chem A 2019; 123:7075-7086. [PMID: 31310526 DOI: 10.1021/acs.jpca.9b05388] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The nitric oxide synthase (NOS) enzyme consists of multiple domains connected by flexible random coil tethers. In a catalytic cycle, the NOS domains move within the limits determined by the length and flexibility of the interdomain tethers and form docking complexes with each other. This process represents a key component of the electron transport from the flavin adenine dinucleotide/reduced nicotinamide adenine dinucleotide phosphate binding domain to the catalytic heme centers located in the oxygenase domain. Studying the conformational behavior of NOS is therefore imperative for a full understanding of the overall catalytic mechanism. In this work, we have investigated the equilibrium positional distributions of the NOS domains and the bound calmodulin (CaM) by using Monte Carlo calculations of the NOS conformations. As a main experimental reference, we have used the magnetic dipole interaction between a bifunctional spin label attached to T34C/S38C mutant CaM and the NOS heme centers, which was measured by pulsed electron paramagnetic resonance. In general, the calculations of the conformational distributions allow one to determine the range and statistics of positions occupied by the tethered protein domains, assess the crowding effect of the multiple domains on each other, evaluate the accessibility of various potential domain docking sites, and estimate the interaction energies required to achieve target populations of the docked states. In the particular application described here, we have established the specific mechanisms by which the bound CaM facilitates the flavin mononucleotide (FMN)/heme interdomain docking in NOS. We have also shown that the intersubunit FMN/heme domain docking and electron transfer in the homodimeric NOS protein are dictated by the existing structural makeup of the protein. Finally, from comparison of the calculated and experimental docking probabilities, the characteristic stabilization energies for the CaM/heme domain and the FMN domain/heme domain docking complexes have been estimated as -4.5kT and -10.5kT, respectively.
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Affiliation(s)
- Andrei V Astashkin
- Department of Chemistry and Biochemistry , University of Arizona , Tucson , Arizona 85721 , United States
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