1
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Schweitzer-Stenner R. Probing the versatility of cytochrome c by spectroscopic means: A Laudatio on resonance Raman spectroscopy. J Inorg Biochem 2024; 259:112641. [PMID: 38901065 DOI: 10.1016/j.jinorgbio.2024.112641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Revised: 06/03/2024] [Accepted: 06/12/2024] [Indexed: 06/22/2024]
Abstract
Over the last 50 years resonance Raman spectroscopy has become an invaluable tool for the exploration of chromophores in biological macromolecules. Among them, heme proteins and metal complexes have attracted considerable attention. This interest results from the fact that resonance Raman spectroscopy probes the vibrational dynamics of these chromophores without direct interference from the surrounding. However, the indirect influence via through-bond and through-space chromophore-protein interactions can be conveniently probed and analyzed. This review article illustrates this point by focusing on class 1 cytochrome c, a comparatively simple heme protein generally known as electron carrier in mitochondria. The article demonstrates how through selective excitation of resonance Raman active modes information about the ligation, the redox state and the spin state of the heme iron can be obtained from band positions in the Raman spectra. The investigation of intensities and depolarization ratios emerged as tools for the analysis of in-plane and out-of-plane deformations of the heme macrocycle. The article further shows how resonance Raman spectroscopy was used to characterize partially unfolded states of oxidized cytochrome c. Finally, it describes its use for exploring structural changes due to the protein's binding to anionic surfaces like cardiolipin containing membranes.
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2
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Hossain M, Huda N, Bhuyan AK. A surprisingly simple three-state generic process for reversible protein denaturation by trifluoroethanol. Biophys Chem 2022; 291:106895. [PMID: 36182744 DOI: 10.1016/j.bpc.2022.106895] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 09/12/2022] [Accepted: 09/14/2022] [Indexed: 12/30/2022]
Abstract
Despite the rich knowledge of the influence of 2,2,2-trifluoroethanol (TFE) on the structure and conformation of peptides and proteins, the mode(s) of TFE-protein interactions and the mechanism by which TFE reversibly denatures a globular protein remain elusive. This study systematically examines TFE-induced equilibrium transition curves for six paradigmatic globular proteins by using basic fluorescence and circular dichroism measurements under neutral pH conditions. The results are remarkably simple. Low TFE invariably unfolds the tertiary structure of all proteins to produce the obligate intermediate (I) which retains nearly all of native-state secondary structure, but enables the formation of extra α-helices as the level of TFE is raised higher. Inspection of the transitions at once reveals that the tertiary structure unfolding is always a distinct process, necessitating the inclusion of at least one obligate intermediate in the TFE-induced protein denaturation. It appears that the intermediate in the minimal unfolding mechanism N⇌I⇌D somehow acquires higher α-helical propensity to generate α-helices in excess of that in the native state to produce the denatured state (D), also called the TFE state. The low TFE-populated intermediate I may be called a universal intermediate by virtue of its α-helical propensity. Contrary to many earlier suggestions, this study dismisses molten globule (MG)-like attribute of I or D.
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Affiliation(s)
- Mujahid Hossain
- School of Chemistry, University of Hyderabad, Hyderabad 500046, India
| | - Noorul Huda
- School of Chemistry, University of Hyderabad, Hyderabad 500046, India
| | - Abani K Bhuyan
- School of Chemistry, University of Hyderabad, Hyderabad 500046, India.
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3
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A single-molecule stochastic theory of protein-ligand binding in the presence of multiple unfolding/folding and ligand binding pathways. Biophys Chem 2022; 285:106803. [DOI: 10.1016/j.bpc.2022.106803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 03/17/2022] [Accepted: 03/17/2022] [Indexed: 11/19/2022]
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4
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Exploring the folding energy landscapes of heme proteins using a hybrid AWSEM-heme model. J Biol Phys 2022; 48:37-53. [PMID: 35000062 PMCID: PMC8866609 DOI: 10.1007/s10867-021-09596-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 11/03/2021] [Indexed: 10/29/2022] Open
Abstract
Heme is an active center in many proteins. Here we explore computationally the role of heme in protein folding and protein structure. We model heme proteins using a hybrid model employing the AWSEM Hamiltonian, a coarse-grained forcefield for the protein chain along with AMBER, an all-atom forcefield for the heme. We carefully designed transferable force fields that model the interactions between the protein and the heme. The types of protein-ligand interactions in the hybrid model include thioester covalent bonds, coordinated covalent bonds, hydrogen bonds, and electrostatics. We explore the influence of different types of hemes (heme b and heme c) on folding and structure prediction. Including both types of heme improves the quality of protein structure predictions. The free energy landscape shows that both types of heme can act as nucleation sites for protein folding and stabilize the protein folded state. In binding the heme, coordinated covalent bonds and thioester covalent bonds for heme c drive the heme toward the native pocket. The electrostatics also facilitates the search for the binding site.
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5
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Yamaguchi T, Akao K, Koutsioubas A, Frielinghaus H, Kohzuma T. Open-Bundle Structure as the Unfolding Intermediate of Cytochrome c' Revealed by Small Angle Neutron Scattering. Biomolecules 2022; 12:95. [PMID: 35053243 PMCID: PMC8774185 DOI: 10.3390/biom12010095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 12/31/2021] [Accepted: 01/04/2022] [Indexed: 11/27/2022] Open
Abstract
The dynamic structure changes, including the unfolding, dimerization, and transition from the compact to the open-bundle unfolding intermediate structure of Cyt c', were detected by a small-angle neutron scattering experiment (SANS). The structure of Cyt c' was changed into an unstructured random coil at pD = 1.7 (Rg = 25 Å for the Cyt c' monomer). The four-α-helix bundle structure of Cyt c' at neutral pH was transitioned to an open-bundle structure (at pD ~13), which is given by a numerical partial scattering function analysis as a joint-clubs model consisting of four clubs (α-helices) connected by short loops. The compactly folded structure of Cyt c' (radius of gyration, Rg = 18 Å for the Cyt c' dimer) at neutral or mildly alkaline pD transited to a remarkably larger open-bundle structure at pD ~13 (Rg = 25 Å for the Cyt c' monomer). The open-bundle structure was also supported by ab initio modeling.
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Affiliation(s)
- Takahide Yamaguchi
- Institute of Quantum Beam Science, Graduate School of Science and Engineering, Ibaraki University, 2-1-1 Bunkyo, Mito 310-8512, Ibaraki, Japan; (T.Y.); (K.A.)
- Frontier Research Center of Applied Atomic Sciences, Ibaraki University, 162-1 Shirakata, Tokai 319-1106, Ibaraki, Japan
| | - Kouhei Akao
- Institute of Quantum Beam Science, Graduate School of Science and Engineering, Ibaraki University, 2-1-1 Bunkyo, Mito 310-8512, Ibaraki, Japan; (T.Y.); (K.A.)
| | - Alexandros Koutsioubas
- Jülich Centre for Neutron Science JCNS-4 at Heinz Maier-Leibnitz Zentrum, Forschungszentrum Jülich GmbH, Lichtenbergstrasse 1, D-85747 Garching, Germany; (A.K.); (H.F.)
| | - Henrich Frielinghaus
- Jülich Centre for Neutron Science JCNS-4 at Heinz Maier-Leibnitz Zentrum, Forschungszentrum Jülich GmbH, Lichtenbergstrasse 1, D-85747 Garching, Germany; (A.K.); (H.F.)
| | - Takamitsu Kohzuma
- Institute of Quantum Beam Science, Graduate School of Science and Engineering, Ibaraki University, 2-1-1 Bunkyo, Mito 310-8512, Ibaraki, Japan; (T.Y.); (K.A.)
- Frontier Research Center of Applied Atomic Sciences, Ibaraki University, 162-1 Shirakata, Tokai 319-1106, Ibaraki, Japan
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6
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Li J, Li H. New insights into the folding–unfolding mechanism and conformations of cytochrome C. Chem Sci 2022; 13:7498-7508. [PMID: 35872809 PMCID: PMC9241957 DOI: 10.1039/d2sc01126c] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 05/29/2022] [Indexed: 11/21/2022] Open
Abstract
Optical trapping experiments offer new insights into the folding and unfolding of cytochrome C.
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Affiliation(s)
- Jiayu Li
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1, Canada
| | - Hongbin Li
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1, Canada
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7
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Hirota S, Mashima T, Kobayashi N. Use of 3D domain swapping in constructing supramolecular metalloproteins. Chem Commun (Camb) 2021; 57:12074-12086. [PMID: 34714300 DOI: 10.1039/d1cc04608j] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Supramolecules, which are formed by assembling multiple molecules by noncovalent intermolecular interactions instead of covalent bonds, often show additional properties that cannot be exhibited by a single molecule. Supramolecules have evolved into molecular machines in the field of chemistry, and various supramolecular proteins are responsible for life activities in the field of biology. The design and creation of supramolecular proteins will lead to development of new enzymes, functional biomaterials, drug delivery systems, etc.; thus, the number of studies on the regulation of supramolecular proteins is increasing year by year. Several methods, including disulfide bond, metal coordination, and surface-surface interaction, have been utilized to construct supramolecular proteins. In nature, proteins have been shown to form oligomers by 3D domain swapping (3D-DS), a phenomenon in which a structural region is exchanged between molecules of the same protein. We have been studying the mechanism of 3D-DS and utilizing 3D-DS to construct supramolecular metalloproteins. Cytochrome c forms cyclic oligomers and polymers by 3D-DS, whereas other metalloproteins, such as various c-type cytochromes and azurin form small oligomers and myoglobin forms a compact dimer. We have also utilized 3D-DS to construct heterodimers with different active sites, a protein nanocage encapsulating a Zn-SO4 cluster in the internal cavity, and a tetrahedron with a designed building block protein. Protein oligomer formation was controlled for the 3D-DS dimer of a dimer-monomer transition protein. This article reviews our research on supramolecular metalloproteins.
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Affiliation(s)
- Shun Hirota
- Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan.
| | - Tsuyoshi Mashima
- Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan.
| | - Naoya Kobayashi
- Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan.
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8
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Jas GS, Childs EW, Middaugh CR, Kuczera K. Dissecting Multiple Pathways in the Relaxation Dynamics of Helix <==> Coil Transitions with Optimum Dimensionality Reduction. Biomolecules 2021; 11:1351. [PMID: 34572564 PMCID: PMC8471320 DOI: 10.3390/biom11091351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 09/07/2021] [Accepted: 09/09/2021] [Indexed: 11/16/2022] Open
Abstract
Fast kinetic experiments with dramatically improved time resolution have contributed significantly to understanding the fundamental processes in protein folding pathways involving the formation of a-helices and b-hairpin, contact formation, and overall collapse of the peptide chain. Interpretation of experimental results through application of a simple statistical mechanical model was key to this understanding. Atomistic description of all events observed in the experimental findings was challenging. Recent advancements in theory, more sophisticated algorithms, and a true long-term trajectory made way for an atomically detailed description of kinetics, examining folding pathways, validating experimental results, and reporting new findings for a wide range of molecular processes in biophysical chemistry. This review describes how optimum dimensionality reduction theory can construct a simplified coarse-grained model with low dimensionality involving a kinetic matrix that captures novel insights into folding pathways. A set of metastable states derived from molecular dynamics analysis generate an optimally reduced dimensionality rate matrix following transition pathway analysis. Analysis of the actual long-term simulation trajectory extracts a relaxation time directly comparable to the experimental results and confirms the validity of the combined approach. The application of the theory is discussed and illustrated using several examples of helix <==> coil transition pathways. This paper focuses primarily on a combined approach of time-resolved experiments and long-term molecular dynamics simulation from our ongoing work.
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Affiliation(s)
- Gouri S. Jas
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS 66047, USA;
| | - Ed W. Childs
- Department of Surgery, Morehouse School of Medicine, Atlanta, GA 30310, USA;
| | - C. Russell Middaugh
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS 66047, USA;
| | - Krzysztof Kuczera
- Department of Chemistry, The University of Kansas, Lawrence, KS 66045, USA;
- Department of Molecular Biosciences, The University of Kansas, Lawrence, KS 66045, USA
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9
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Pintér G, Hohmann K, Grün J, Wirmer-Bartoschek J, Glaubitz C, Fürtig B, Schwalbe H. Real-time nuclear magnetic resonance spectroscopy in the study of biomolecular kinetics and dynamics. MAGNETIC RESONANCE (GOTTINGEN, GERMANY) 2021; 2:291-320. [PMID: 37904763 PMCID: PMC10539803 DOI: 10.5194/mr-2-291-2021] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 04/07/2021] [Indexed: 11/01/2023]
Abstract
The review describes the application of nuclear magnetic resonance (NMR) spectroscopy to study kinetics of folding, refolding and aggregation of proteins, RNA and DNA. Time-resolved NMR experiments can be conducted in a reversible or an irreversible manner. In particular, irreversible folding experiments pose large requirements for (i) signal-to-noise due to the time limitations and (ii) synchronising of the refolding steps. Thus, this contribution discusses the application of methods for signal-to-noise increases, including dynamic nuclear polarisation, hyperpolarisation and photo-CIDNP for the study of time-resolved NMR studies. Further, methods are reviewed ranging from pressure and temperature jump, light induction to rapid mixing to induce rapidly non-equilibrium conditions required to initiate folding.
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Affiliation(s)
- György Pintér
- Institute for Organic Chemistry and Chemical Biology, Center for
Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang
Goethe-Universität Frankfurt, Frankfurt 60438, Germany
| | - Katharina F. Hohmann
- Institute for Organic Chemistry and Chemical Biology, Center for
Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang
Goethe-Universität Frankfurt, Frankfurt 60438, Germany
| | - J. Tassilo Grün
- Institute for Organic Chemistry and Chemical Biology, Center for
Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang
Goethe-Universität Frankfurt, Frankfurt 60438, Germany
| | - Julia Wirmer-Bartoschek
- Institute for Organic Chemistry and Chemical Biology, Center for
Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang
Goethe-Universität Frankfurt, Frankfurt 60438, Germany
| | - Clemens Glaubitz
- Institute for Biophysical Chemistry, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-Universität Frankfurt, Frankfurt 60438, Germany
| | - Boris Fürtig
- Institute for Organic Chemistry and Chemical Biology, Center for
Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang
Goethe-Universität Frankfurt, Frankfurt 60438, Germany
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology, Center for
Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang
Goethe-Universität Frankfurt, Frankfurt 60438, Germany
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10
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Electrical unfolding of cytochrome c during translocation through a nanopore constriction. Proc Natl Acad Sci U S A 2021; 118:2016262118. [PMID: 33883276 DOI: 10.1073/pnas.2016262118] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Many small proteins move across cellular compartments through narrow pores. In order to thread a protein through a constriction, free energy must be overcome to either deform or completely unfold the protein. In principle, the diameter of the pore, along with the effective driving force for unfolding the protein, as well as its barrier to translocation, should be critical factors that govern whether the process proceeds via squeezing, unfolding/threading, or both. To probe this for a well-established protein system, we studied the electric-field-driven translocation behavior of cytochrome c (cyt c) through ultrathin silicon nitride (SiNx) solid-state nanopores of diameters ranging from 1.5 to 5.5 nm. For a 2.5-nm-diameter pore, we find that, in a threshold electric-field regime of ∼30 to 100 MV/m, cyt c is able to squeeze through the pore. As electric fields inside the pore are increased, the unfolded state of cyt c is thermodynamically stabilized, facilitating its translocation. In contrast, for 1.5- and 2.0-nm-diameter pores, translocation occurs only by threading of the fully unfolded protein after it transitions through a higher energy unfolding intermediate state at the mouth of the pore. The relative energies between the metastable, intermediate, and unfolded protein states are extracted using a simple thermodynamic model that is dictated by the relatively slow (∼ms) protein translocation times for passing through the nanopore. These experiments map the various modes of protein translocation through a constriction, which opens avenues for exploring protein folding structures, internal contacts, and electric-field-induced deformability.
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11
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Wilkinson JA, Silvera S, LeBlanc PJ. The effect of cardiolipin side chain composition on cytochrome c protein conformation and peroxidase activity. Physiol Rep 2021; 9:e14772. [PMID: 33667034 PMCID: PMC7934914 DOI: 10.14814/phy2.14772] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 01/21/2021] [Accepted: 02/01/2021] [Indexed: 12/26/2022] Open
Abstract
Skeletal muscle, a highly active tissue, makes up 40% of the total body weight. This tissue relies on mitochondria for ATP production, calcium homeostasis, and programed cell death. Mitochondrial phospholipid composition, namely, cardiolipin (CL), influences the functional efficiency of mitochondrial proteins, specifically cytochrome c. The interaction of CL with cytochrome c in the presence of free radicals induces structural and functional changes promoting peroxidase activity and cytochrome c release, a key event in the initiation of apoptosis. The CL acyl chain degree of saturation has been implicated in the cytochrome c to cytochrome c peroxidase transition in liposomal models. However, mitochondrial membranes are composed of differing CL acyl chain composition. Currently, it is unclear how differing CL acyl chain composition utilizing liposomes will influence the cytochrome c form and function as a peroxidase. Thus, this study examined the role of CL acyl chain saturation within liposomes broadly reflecting the relative CL composition of mitochondrial membranes from healthy and dystrophic mouse muscle on cytochrome c conformation and function. Despite no differences in protein conformation or function between healthy and dystrophic liposomes, cytochrome c's affinity to CL increased with greater unsaturation. These findings suggest that increasing CL acyl chain saturation, as implicated in muscle wasting diseases, may not influence cytochrome c transformation and function as a peroxidase but may alter its interaction with CL, potentially impacting further downstream effects.
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Affiliation(s)
- Jennifer A Wilkinson
- Center for Bone and Muscle Health, Faculty of Applied Health Sciences, Brock University, 1812 Sir Isaac Brock Way, St. Catharines, Ontario, L2S 3A1, Canada
| | - Sebastian Silvera
- Center for Bone and Muscle Health, Faculty of Applied Health Sciences, Brock University, 1812 Sir Isaac Brock Way, St. Catharines, Ontario, L2S 3A1, Canada
| | - Paul J LeBlanc
- Center for Bone and Muscle Health, Faculty of Applied Health Sciences, Brock University, 1812 Sir Isaac Brock Way, St. Catharines, Ontario, L2S 3A1, Canada
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12
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Milorey B, Schweitzer-Stenner R, Kurbaj R, Malyshka D. pH-Induced Switch between Different Modes of Cytochrome c Binding to Cardiolipin-Containing Liposomes. ACS OMEGA 2019; 4:1386-1400. [PMID: 31459406 PMCID: PMC6647999 DOI: 10.1021/acsomega.8b02574] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 01/02/2019] [Indexed: 05/28/2023]
Abstract
Fluorescence, visible circular dichroism (CD), absorption, and resonance Raman spectroscopy techniques were combined to explore structural changes of ferricytochrome c upon its binding to cardiolipin-containing liposomes (20% 1,1',1,2'-tetraoleyolcardiolipin and 1,2-deoleyol-sn-glycero-3-phosphocholine) at acidic pH (6.5). According to the earlier work of Kawai [J. Biol. Chem.2005, 280, 34709-347171],cytochrome c binding at this pH is governed by interactions between the phosphate head groups of cardiolipin and amino acid side chains of the so-called L-site, which contains the charged residues K22, K25, K27, and potentially H26 and H33. We found that L-site binding causes a conformational transition that involves a change of the protein's ligation and spin state. In this paper, we report spectroscopic responses to an increasing number of cardiolipin-containing liposomes at pH 6.5 in the absence and presence of NaCl. The latter was found to mostly inhibit protein binding already with 50 mM concentration. The inhibition effect can be quantitatively reproduced by applying the electrostatic theory of Heimburg [Biophys. J.1995, 68, 536-546]. A comparison with corresponding spectroscopic response data obtained at pH 7.4 reveals major differences in that the latter indicates hydrophobic binding, followed by an electrostatically driven conformational change. Visible CD data suggest that structural changes in the heme pocket of liposome-bound ferricytochrome c resemble to some extent those in the denatured protein in urea at neutral and acidic pH. The measured noncoincidence between absorption and CD Soret band of cytochrome c in the presence of a large access of cardiolipin is caused by the electric field at the membrane surface. The very fact that its contribution to the internal electric field in the heme pocket is detectable by spectroscopic means suggests some penetration of the protein into membrane surface.
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13
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Konno S, Doi K, Ishimori K. Uncovering dehydration in cytochrome c refolding from urea- and guanidine hydrochloride-denatured unfolded state by high pressure spectroscopy. Biophys Physicobiol 2019; 16:18-27. [PMID: 30775200 PMCID: PMC6373425 DOI: 10.2142/biophysico.16.0_18] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Accepted: 12/16/2018] [Indexed: 12/01/2022] Open
Abstract
To investigate the dehydration associated with protein folding, the partial molar volume changes for protein unfolding (ΔVu) in cytochrome c (Cyt c) were determined using high pressure absorption spectroscopy. ΔVu values for the unfolding to urea- and guanidine hydrochloride (GdnHCl)-denatured Cyt c were estimated to be 56±5 and 29±1 mL mol−1, respectively. Considering that the volume change for hydration of hydrophobic groups is positive and that Cyt c has a covalently bonded heme, a positive ΔVu reflects the primary contribution of the hydration of heme. Because of the marked tendency of guanidium ions to interact with hydrophobic groups, a smaller number of water molecules were hydrated with hydrophobic groups in GdnHCl-denatured Cyt c than in urea-denatured Cyt c, resulting in the smaller positive ΔVu. On the other hand, urea is a relatively weak denaturant and urea-denatured Cyt c is not completely hydrated, which retains the partially folded structures. To unfold such partial structures, we introduced a mutation near the heme binding site, His26, to Gln, resulting in a negatively shifted ΔVu (4±2 mL mol−1) in urea-denatured Cyt c. The formation of the more solvated and less structured state in the urea-denatured mutant enhanced hydration to the hydrophilic groups in the unfolding process. Therefore, we confirmed the hydration of amino acid residues in the protein unfolding of Cyt c by estimating ΔVu, which allows us to discuss the hydrated structures in the denatured states of proteins.
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Affiliation(s)
- Shohei Konno
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, Hokkaido 060-8628, Japan
| | - Kentaro Doi
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, Hokkaido 060-8628, Japan
| | - Koichiro Ishimori
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, Hokkaido 060-8628, Japan.,Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
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14
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Schweitzer-Stenner R. Relating the multi-functionality of cytochrome c to membrane binding and structural conversion. Biophys Rev 2018; 10:1151-1185. [PMID: 29574621 PMCID: PMC6082307 DOI: 10.1007/s12551-018-0409-4] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 02/23/2018] [Indexed: 12/16/2022] Open
Abstract
Cytochrome c is known as an electron-carrying protein in the respiratory chain of mitochondria. Over the last 20 years, however, alternative functions of this very versatile protein have become the focus of research interests. Upon binding to anionic lipids such as cardiolipin, the protein acquires peroxidase activity. Multiple lines of evidence suggest that this requires a conformational change of the protein which involves partial unfolding of its tertiary structure. This review summarizes the current state of knowledge of how cytochrome c interacts with cardiolipin-containing surfaces and how this affects its structure and function. In this context, we delineate partially conflicting results regarding the affinity of cytochrome c binding to cardiolipin-containing liposomes of different size and its influence on the structure of the protein and the morphology of the membrane.
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15
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Refolding kinetics of cytochrome c studied with microsecond timescale continuous-flow UV–vis spectroscopy and rapid freeze-quench EPR. J Inorg Biochem 2018; 184:42-49. [DOI: 10.1016/j.jinorgbio.2018.04.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 03/21/2018] [Accepted: 04/09/2018] [Indexed: 11/18/2022]
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16
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Rimmerman D, Leshchev D, Hsu DJ, Hong J, Abraham B, Henning R, Kosheleva I, Chen LX. Probing Cytochrome c Folding Transitions upon Phototriggered Environmental Perturbations Using Time-Resolved X-ray Scattering. J Phys Chem B 2018; 122:5218-5224. [PMID: 29709179 DOI: 10.1021/acs.jpcb.8b03354] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Direct tracking of protein structural dynamics during folding-unfolding processes is important for understanding the roles of hierarchic structural factors in the formation of functional proteins. Using cytochrome c (cyt c) as a platform, we investigated its structural dynamics during folding processes triggered by local environmental changes (i.e., pH or heme iron center oxidation/spin/ligation states) with time-resolved X-ray solution scattering measurements. Starting from partially unfolded cyt c, a sudden pH drop initiated by light excitation of a photoacid caused a structural contraction in microseconds, followed by active site restructuring and unfolding in milliseconds. In contrast, the reduction of iron in the heme via photoinduced electron transfer did not affect conformational stability at short timescales (<1 ms), despite active site coordination geometry changes. These results demonstrate how different environmental perturbations can change the nature of interaction between the active site and protein conformation, even within the same metalloprotein, which will subsequently affect the folding structural dynamics.
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Affiliation(s)
- Dolev Rimmerman
- Department of Chemistry , Northwestern University , Evanston , Illinois 60208 , United States
| | - Denis Leshchev
- Department of Chemistry , Northwestern University , Evanston , Illinois 60208 , United States
| | - Darren J Hsu
- Department of Chemistry , Northwestern University , Evanston , Illinois 60208 , United States
| | - Jiyun Hong
- Department of Chemistry , Northwestern University , Evanston , Illinois 60208 , United States
| | - Baxter Abraham
- Department of Chemistry and Biochemistry , University of Delaware , Newark , Delaware 19716 , United States
| | - Robert Henning
- Center for Advanced Radiation Sources , The University of Chicago , Chicago , Illinois 60637 , United States
| | - Irina Kosheleva
- Center for Advanced Radiation Sources , The University of Chicago , Chicago , Illinois 60637 , United States
| | - Lin X Chen
- Department of Chemistry , Northwestern University , Evanston , Illinois 60208 , United States.,Chemical Sciences and Engineering Division , Argonne National Laboratory , Argonne , Illinois 60439 , United States
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17
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Gu J, Shin DW, Pletneva EV. Remote Perturbations in Tertiary Contacts Trigger Ligation of Lysine to the Heme Iron in Cytochrome c. Biochemistry 2017; 56:2950-2966. [PMID: 28474881 DOI: 10.1021/acs.biochem.6b01187] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Perturbations in protein structure define the mechanism of allosteric regulation and biological information transfer. In cytochrome c (cyt c), ligation of Met80 to the heme iron is critical for the protein's electron-transfer (ET) function in oxidative phosphorylation and for suppressing its peroxidase activity in apoptosis. The hard base Lys is a better match for the hard ferric iron than the soft base Met is, suggesting the key role of the protein scaffold in favoring Met ligation. To probe the role of the protein structure in the maintenance of Met ligation, mutations T49V and Y67R/M80A were designed to disrupt hydrogen bonding and packing of the heme coordination loop, respectively. Electronic absorption, nuclear magnetic resonance, and electron paramagnetic resonance spectra reveal that ferric forms of both variants are Lys-ligated at neutral pH. A minor change in the tertiary contacts in T49V, away from the heme coordination loop, appears to be sufficient to execute a change in ligation, suggesting a cross-talk between the different regions of the protein structure and a possibility of built-in conformational switches in cyt c. Analyses of thermodynamic stability, kinetics of Lys binding and dissociation, and the pH-dependent changes in ligation provide a detailed characterization of the Lys coordination in these variants and relate these properties to the extent of structural perturbations. The findings emphasize the importance of the hydrogen-bonding network in controlling ligation of the native Met80 to the heme iron.
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Affiliation(s)
- Jie Gu
- Department of Chemistry, Dartmouth College , Hanover, New Hampshire 03755, United States
| | - Dong-Woo Shin
- Department of Chemistry, Dartmouth College , Hanover, New Hampshire 03755, United States
| | - Ekaterina V Pletneva
- Department of Chemistry, Dartmouth College , Hanover, New Hampshire 03755, United States
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18
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Milorey B, Malyshka D, Schweitzer-Stenner R. pH Dependence of Ferricytochrome c Conformational Transitions during Binding to Cardiolipin Membranes: Evidence for Histidine as the Distal Ligand at Neutral pH. J Phys Chem Lett 2017; 8:1993-1998. [PMID: 28418677 DOI: 10.1021/acs.jpclett.7b00597] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The conformational changes of ferricytochrome c upon binding to cardiolipin-containing small unilamellar vesicles were studied at slightly acidic pH using fluorescence, visible circular dichroism, UV-visible absorption, and resonance Raman spectroscopy. The obtained spectroscopic response data suggest a mode of interaction, which is clearly distinct from the binding process observed at neutral pH. Evidence of a reversible and electrostatic binding mechanism under these conditions is provided through binding inhibition in the presence of 150 mM NaCl. Moreover, UV-visible absorption and resonance Raman spectra reveal that the conformational ensemble of membrane bound cytochrome c is dominated by a mixture of conformers with pentacoordinated and hexacoordinated high-spin heme irons, which contrast with the dominance of low-spin species at neutral pH. While our results confirm the L-site binding proposed by Kawai et al., they point to the protonation of a histidine ligand (H33) as conformational trigger.
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Affiliation(s)
- Bridget Milorey
- Department of Chemistry, Drexel University , Philadelphia, Pennsylvania 19104, United States
| | - Dmitry Malyshka
- Department of Chemistry, Drexel University , Philadelphia, Pennsylvania 19104, United States
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19
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20
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Preimesberger MR, Majumdar A, Lecomte JTJ. Dynamics of Lysine as a Heme Axial Ligand: NMR Analysis of the Chlamydomonas reinhardtii Hemoglobin THB1. Biochemistry 2017; 56:551-569. [DOI: 10.1021/acs.biochem.6b00926] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Matthew R. Preimesberger
- T.
C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Ananya Majumdar
- Biomolecular
NMR Center, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Juliette T. J. Lecomte
- T.
C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, United States
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21
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Word TA, Larsen RW. Time resolved calorimetry of photo-induced folding in horse heart cytochrome c at high pH. Arch Biochem Biophys 2016; 615:10-14. [PMID: 28041937 DOI: 10.1016/j.abb.2016.12.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Revised: 12/27/2016] [Accepted: 12/28/2016] [Indexed: 10/20/2022]
Abstract
Here the molar volume and enthalpy changes associated with the early events in the folding of ferrocytochrome c (Cc) at high pH have been examined using time resolved photoacoustic calorimetry (PAC). The data reveal an overall volume change of 1.3 ± 0.3 mL mol-1 and an enthalpy change of 13 ± 7 kcal mol -1 occurring subsequent to photodissociation of the unfolded CO bound Cc species in <∼20 ns. Two additional kinetic phases are observed that are associated with non-native His binding (ΔH and ΔV of 2 ± 4 kcal mol-1 and -0.5 mL mol-1, τ ∼ 2.5 μs ) and Met binding (ΔH and ΔV -0.4 ± 2 kcal mol-1 and -0.1 ± 0.1 mL mol-1, τ∼ 660 ns). Considering only protein conformational changes (excluding volume and enthalpies associated with heme ligation events) the initial conformational event exhibits a ΔH and ΔV of 6 ± 3 kcal mol-1 and -3±0.1 mL mol-1, respectively, that are attributed to a small contraction of the unfolded protein. The corresponding enthalpy associated with both native and non-native ligand binding are found to be -5±4 kcal mol-1 (Fe-Met) and +20 ± 4 kcal mol-1 (Fe-His) with the change in volume for both phases being essential negligible. This would indicate that non-native ligand binding likely occurs from an already collapsed conformation.
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Affiliation(s)
- Tarah A Word
- Department of Chemistry, University of South Florida, 4202 East Fowler Ave., Tampa, FL 33602 USA
| | - Randy W Larsen
- Department of Chemistry, University of South Florida, 4202 East Fowler Ave., Tampa, FL 33602 USA.
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22
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Serpas L, Milorey B, Pandiscia LA, Addison AW, Schweitzer-Stenner R. Autoxidation of Reduced Horse Heart Cytochrome c Catalyzed by Cardiolipin-Containing Membranes. J Phys Chem B 2016; 120:12219-12231. [PMID: 27934230 DOI: 10.1021/acs.jpcb.6b05620] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Visible circular dichroism, absorption, and fluorescence spectroscopy were used to probe the binding of horse heart ferrocytochrome c to anionic cardiolipin (CL) head groups on the surface of 1,1',2,2'-tetraoleoyl cardiolipin (TOCL)/1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) (20%:80%) liposomes in an aerobic environment. We found that ferrocytochrome c undergoes a conformational transition upon binding that leads to complete oxidation of the protein at intermediate and high CL concentrations. At low lipid concentrations, the protein maintains a structure that is only slightly different from its native one, whereas an ensemble of misligated predominantly hexacoordinated low-spin states become increasingly populated at high lipid concentrations. A minor fraction of conformations with either high- or quantum-mixed-spin states were detected at a CL to protein ratio of 200 (the largest one investigated). The population of the non-native state is less pronounced than that found for cytochrome c-CL interactions initiated with oxidized cytochrome c. Under anaerobic conditions, the protein maintains its reduced state but still undergoes some conformational change upon binding to CL head groups on the liposome surface. Our data suggest that CL-containing liposomes function as catalysts by reducing the activation barrier for a Fe2+ → O2 electron transfer. Adding NaCl to the existing cytochrome-liposome mixtures under aerobic conditions inhibits protein autoxidation of ferrocytochrome c and stabilizes the reduced state of the membrane-bound protein.
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Affiliation(s)
- Lee Serpas
- Department of Chemistry, Drexel University , 3141 Chestnut Street, Philadelphia, Pennsylvania 19104, United States
| | - Bridget Milorey
- Department of Chemistry, Drexel University , 3141 Chestnut Street, Philadelphia, Pennsylvania 19104, United States
| | - Leah A Pandiscia
- Department of Chemistry, Drexel University , 3141 Chestnut Street, Philadelphia, Pennsylvania 19104, United States
| | - Anthony W Addison
- Department of Chemistry, Drexel University , 3141 Chestnut Street, Philadelphia, Pennsylvania 19104, United States
| | - Reinhard Schweitzer-Stenner
- Department of Chemistry, Drexel University , 3141 Chestnut Street, Philadelphia, Pennsylvania 19104, United States
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23
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Paul SS, Sil P, Chakraborty R, Haldar S, Chattopadhyay K. Molecular Crowding Affects the Conformational Fluctuations, Peroxidase Activity, and Folding Landscape of Yeast Cytochrome c. Biochemistry 2016; 55:2332-43. [DOI: 10.1021/acs.biochem.6b00053] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Simanta Sarani Paul
- Protein
Folding and Dynamics Laboratory, Structural Biology and Bioinformatics
Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C.
Mullick Road, Kolkata 700032, India
| | - Pallabi Sil
- Protein
Folding and Dynamics Laboratory, Structural Biology and Bioinformatics
Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C.
Mullick Road, Kolkata 700032, India
| | - Ritobrita Chakraborty
- Protein
Folding and Dynamics Laboratory, Structural Biology and Bioinformatics
Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C.
Mullick Road, Kolkata 700032, India
| | - Shubhasis Haldar
- Department
of Cellular Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz
18, 82152 Martinsried, Germany
| | - Krishnananda Chattopadhyay
- Protein
Folding and Dynamics Laboratory, Structural Biology and Bioinformatics
Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C.
Mullick Road, Kolkata 700032, India
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24
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Hannibal L, Tomasina F, Capdevila DA, Demicheli V, Tórtora V, Alvarez-Paggi D, Jemmerson R, Murgida DH, Radi R. Alternative Conformations of Cytochrome c: Structure, Function, and Detection. Biochemistry 2016; 55:407-28. [DOI: 10.1021/acs.biochem.5b01385] [Citation(s) in RCA: 89] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Luciana Hannibal
- Departamento
de Bioquímica, Facultad de Medicina, Universidad de la República, Avda. General Flores 2125, 11800 Montevideo, Uruguay
- Centro
de Investigaciones Biomédicas (CEINBIO), Facultad de Medicina, Universidad de la República, Avda. General Flores 2125, 11800 Montevideo, Uruguay
- Center
for Pediatrics and Adolescent Medicine, Medical Center, University of Freiburg, Mathildenstrasse 1, Freiburg D-79106, Germany
| | - Florencia Tomasina
- Departamento
de Bioquímica, Facultad de Medicina, Universidad de la República, Avda. General Flores 2125, 11800 Montevideo, Uruguay
- Centro
de Investigaciones Biomédicas (CEINBIO), Facultad de Medicina, Universidad de la República, Avda. General Flores 2125, 11800 Montevideo, Uruguay
| | - Daiana A. Capdevila
- Departamento
de Química Inorgánica, Analítica y Química
Física/INQUIMAE, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Pabellón 2, Ciudad Universitaria, C1428EHA Buenos Aires, Argentina
| | - Verónica Demicheli
- Departamento
de Bioquímica, Facultad de Medicina, Universidad de la República, Avda. General Flores 2125, 11800 Montevideo, Uruguay
- Centro
de Investigaciones Biomédicas (CEINBIO), Facultad de Medicina, Universidad de la República, Avda. General Flores 2125, 11800 Montevideo, Uruguay
| | - Verónica Tórtora
- Departamento
de Bioquímica, Facultad de Medicina, Universidad de la República, Avda. General Flores 2125, 11800 Montevideo, Uruguay
- Centro
de Investigaciones Biomédicas (CEINBIO), Facultad de Medicina, Universidad de la República, Avda. General Flores 2125, 11800 Montevideo, Uruguay
| | - Damián Alvarez-Paggi
- Departamento
de Química Inorgánica, Analítica y Química
Física/INQUIMAE, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Pabellón 2, Ciudad Universitaria, C1428EHA Buenos Aires, Argentina
| | - Ronald Jemmerson
- Department
of Microbiology and Immunology, University of Minnesota, MMC 196,
420 Delaware Street, Southeast, Minneapolis, Minnesota 55455, United States
| | - Daniel H. Murgida
- Departamento
de Química Inorgánica, Analítica y Química
Física/INQUIMAE, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Pabellón 2, Ciudad Universitaria, C1428EHA Buenos Aires, Argentina
| | - Rafael Radi
- Departamento
de Bioquímica, Facultad de Medicina, Universidad de la República, Avda. General Flores 2125, 11800 Montevideo, Uruguay
- Centro
de Investigaciones Biomédicas (CEINBIO), Facultad de Medicina, Universidad de la República, Avda. General Flores 2125, 11800 Montevideo, Uruguay
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25
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Karunakaran V. Ultrafast Heme Dynamics of Ferric Cytochrome c in Different Environments: Electronic, Vibrational, and Conformational Relaxation. Chemphyschem 2015; 16:3974-83. [DOI: 10.1002/cphc.201500672] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Revised: 09/23/2015] [Indexed: 12/17/2022]
Affiliation(s)
- Venugopal Karunakaran
- Photosciences and Photonics Section; Chemical Sciences and Technology Division; CSIR-National Institute for Interdisciplinary Science and Technology; Thiruvananthapuram 695 019 Kerala India
- Academy of Scientific and Innovative Research (AcSIR); New Delhi 110 001 India
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26
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Varhač R, Sedláková D, Stupák M, Sedlák E. Non-two-state thermal denaturation of ferricytochrome c at neutral and slightly acidic pH values. Biophys Chem 2015; 203-204:41-50. [DOI: 10.1016/j.bpc.2015.05.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Revised: 05/08/2015] [Accepted: 05/11/2015] [Indexed: 12/19/2022]
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27
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Zaidi S, Hassan MI, Islam A, Ahmad F. The role of key residues in structure, function, and stability of cytochrome-c. Cell Mol Life Sci 2014; 71:229-55. [PMID: 23615770 PMCID: PMC11113841 DOI: 10.1007/s00018-013-1341-1] [Citation(s) in RCA: 105] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2013] [Revised: 04/05/2013] [Accepted: 04/08/2013] [Indexed: 02/06/2023]
Abstract
Cytochrome-c (cyt-c), a multi-functional protein, plays a significant role in the electron transport chain, and thus is indispensable in the energy-production process. Besides being an important component in apoptosis, it detoxifies reactive oxygen species. Two hundred and eighty-five complete amino acid sequences of cyt-c from different species are known. Sequence analysis suggests that the number of amino acid residues in most mitochondrial cyts-c is in the range 104 ± 10, and amino acid residues at only few positions are highly conserved throughout evolution. These highly conserved residues are Cys14, Cys17, His18, Gly29, Pro30, Gly41, Asn52, Trp59, Tyr67, Leu68, Pro71, Pro76, Thr78, Met80, and Phe82. These are also known as "key residues", which contribute significantly to the structure, function, folding, and stability of cyt-c. The three-dimensional structure of cyt-c from ten eukaryotic species have been determined using X-ray diffraction studies. Structure analysis suggests that the tertiary structure of cyt-c is almost preserved along the evolutionary scale. Furthermore, residues of N/C-terminal helices Gly6, Phe10, Leu94, and Tyr97 interact with each other in a specific manner, forming an evolutionary conserved interface. To understand the role of evolutionary conserved residues on structure, stability, and function, numerous studies have been performed in which these residues were substituted with different amino acids. In these studies, structure deals with the effect of mutation on secondary and tertiary structure measured by spectroscopic techniques; stability deals with the effect of mutation on T m (midpoint of heat denaturation), ∆G D (Gibbs free energy change on denaturation) and folding; and function deals with the effect of mutation on electron transport, apoptosis, cell growth, and protein expression. In this review, we have compiled all these studies at one place. This compilation will be useful to biochemists and biophysicists interested in understanding the importance of conservation of certain residues throughout the evolution in preserving the structure, function, and stability in proteins.
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Affiliation(s)
- Sobia Zaidi
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025 India
| | - Md. Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025 India
| | - Asimul Islam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025 India
| | - Faizan Ahmad
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025 India
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28
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Parui PP, Deshpande MS, Nagao S, Kamikubo H, Komori H, Higuchi Y, Kataoka M, Hirota S. Formation of Oligomeric Cytochrome c during Folding by Intermolecular Hydrophobic Interaction between N- and C-Terminal α-Helices. Biochemistry 2013; 52:8732-44. [DOI: 10.1021/bi400986g] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Partha Pratim Parui
- Graduate
School of Materials Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
- Department
of Chemistry, Jadavpur University, Kolkata 700032, India
| | - Megha Subhash Deshpande
- Graduate
School of Materials Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Satoshi Nagao
- Graduate
School of Materials Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Hironari Kamikubo
- Graduate
School of Materials Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Hirofumi Komori
- Department
of Life Science, Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan
- RIKEN SPring-8 Center, 1-1-1
Koto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Yoshiki Higuchi
- Department
of Life Science, Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan
- RIKEN SPring-8 Center, 1-1-1
Koto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Mikio Kataoka
- Graduate
School of Materials Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Shun Hirota
- Graduate
School of Materials Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
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29
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Anderson JLR, Armstrong CT, Kodali G, Lichtenstein BR, Watkins DW, Mancini JA, Boyle AL, Farid TA, Crump MP, Moser CC, Dutton PL. Constructing a man-made c-type cytochrome maquette in vivo: electron transfer, oxygen transport and conversion to a photoactive light harvesting maquette. Chem Sci 2013; 5:507-514. [PMID: 24634717 DOI: 10.1039/c3sc52019f] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The successful use of man-made proteins to advance synthetic biology requires both the fabrication of functional artificial proteins in a living environment, and the ability of these proteins to interact productively with other proteins and substrates in that environment. Proteins made by the maquette method integrate sophisticated oxidoreductase function into evolutionarily naive, non-computationally designed protein constructs with sequences that are entirely unrelated to any natural protein. Nevertheless, we show here that we can efficiently interface with the natural cellular machinery that covalently incorporates heme into natural cytochromes c to produce in vivo an artificial c-type cytochrome maquette. Furthermore, this c-type cytochrome maquette is designed with a displaceable histidine heme ligand that opens to allow functional oxygen binding, the primary event in more sophisticated functions ranging from oxygen storage and transport to catalytic hydroxylation. To exploit the range of functions that comes from the freedom to bind a variety of redox cofactors within a single maquette framework, this c-type cytochrome maquette is designed with a second, non-heme C, tetrapyrrole binding site, enabling the construction of an elementary electron transport chain, and when the heme C iron is replaced with zinc to create a Zn porphyrin, a light-activatable artificial redox protein. The work we describe here represents a major advance in de novo protein design, offering a robust platform for new c-type heme based oxidoreductase designs and an equally important proof-of-principle that cofactor-equipped man-made proteins can be expressed in living cells, paving the way for constructing functionally useful man-made proteins in vivo.
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Affiliation(s)
- J L Ross Anderson
- School of Biochemistry, University of Bristol, University Walk, Bristol, BS8 1TD, UK.,The Johnson Research Foundation, Dept. of Biochemistry and Biophysics, University of Pennsylvania, PA19104-6059, USA
| | - Craig T Armstrong
- School of Biochemistry, University of Bristol, University Walk, Bristol, BS8 1TD, UK
| | - Goutham Kodali
- The Johnson Research Foundation, Dept. of Biochemistry and Biophysics, University of Pennsylvania, PA19104-6059, USA
| | - Bruce R Lichtenstein
- The Johnson Research Foundation, Dept. of Biochemistry and Biophysics, University of Pennsylvania, PA19104-6059, USA
| | - Daniel W Watkins
- School of Biochemistry, University of Bristol, University Walk, Bristol, BS8 1TD, UK
| | - Joshua A Mancini
- The Johnson Research Foundation, Dept. of Biochemistry and Biophysics, University of Pennsylvania, PA19104-6059, USA
| | - Aimee L Boyle
- School of Chemistry, University of Bristol, Bristol, BS8 1TS, UK
| | - Tammer A Farid
- The Johnson Research Foundation, Dept. of Biochemistry and Biophysics, University of Pennsylvania, PA19104-6059, USA
| | - Matthew P Crump
- School of Chemistry, University of Bristol, Bristol, BS8 1TS, UK
| | - Christopher C Moser
- The Johnson Research Foundation, Dept. of Biochemistry and Biophysics, University of Pennsylvania, PA19104-6059, USA
| | - P Leslie Dutton
- The Johnson Research Foundation, Dept. of Biochemistry and Biophysics, University of Pennsylvania, PA19104-6059, USA
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30
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Mikšovská J, Larsen RW. Ligand Binding Subsequent to NO Photolyses of Partially Unfolded Cytochromec. J CHIN CHEM SOC-TAIP 2013. [DOI: 10.1002/jccs.200400167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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31
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Sun Y, Karunakaran V, Champion PM. Investigations of the low-frequency spectral density of cytochrome c upon equilibrium unfolding. J Phys Chem B 2013; 117:9615-25. [PMID: 23863217 DOI: 10.1021/jp404881k] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The equilibrium unfolding process of ferric horse heart cytochrome c (cyt c), induced by guanidinium hydrochloride (GdHCl), was studied using UV-vis absorption spectroscopy, resonance Raman spectroscopy, and vibrational coherence spectroscopy (VCS). The unfolding process was successfully fit using a three-state model which included the fully folded (N) and unfolded (U) states, along with an intermediate (I) assigned to a Lys bound heme. The VCS spectra revealed for the first time several low-frequency heme modes that are sensitive to cyt c unfolding: γ(a) (~50 cm(-1)), γ(b) (~80 cm(-1)), γ(c) (~100 cm(-1)), and ν(s)(His-Fe-His) at 205 cm(-1). These out-of-plane modes have potential functional relevance and are activated by protein-induced heme distortions. The free energies for the N-I and the I-U transitions at pH 7.0 and 20 °C were found to be 4.6 kcal/M and 11.6 kcal/M, respectively. Imidazole was also introduced to replace the methionine ligand so the unfolding can be modeled as a two-state system. The intensity of the mode γ(b)~80 cm(-1) remains nearly constant during the unfolding process, while the amplitudes of the other low frequency modes track with spectral changes observed at higher frequency. This confirms that the heme deformation changes are coupled to the protein tertiary structural changes that take place upon unfolding. These studies also reveal that damping of the coherent oscillations depends sensitively on the coupling between heme and the surrounding water solvent.
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Affiliation(s)
- Yuhan Sun
- Department of Physics and Center for Interdisciplinary Research on Complex Systems, Northeastern University, Boston, Massachusetts 02115, United States
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32
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Soffer JB, Fradkin E, Pandiscia LA, Schweitzer-Stenner R. The (Not Completely Irreversible) Population of a Misfolded State of Cytochrome c under Folding Conditions. Biochemistry 2013; 52:1397-408. [DOI: 10.1021/bi301586e] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Jonathan B. Soffer
- Departments of Chemistry and
Biology, Drexel University, 3141 Chestnut
Street, Philadelphia, Pennsylvania 19104, United
States
| | - Emma Fradkin
- Departments of Chemistry and
Biology, Drexel University, 3141 Chestnut
Street, Philadelphia, Pennsylvania 19104, United
States
| | - Leah A. Pandiscia
- Departments of Chemistry and
Biology, Drexel University, 3141 Chestnut
Street, Philadelphia, Pennsylvania 19104, United
States
| | - Reinhard Schweitzer-Stenner
- Departments of Chemistry and
Biology, Drexel University, 3141 Chestnut
Street, Philadelphia, Pennsylvania 19104, United
States
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33
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Behera RK, Nakajima H, Rajbongshi J, Watanabe Y, Mazumdar S. Thermodynamic Effects of the Alteration of the Axial Ligand on the Unfolding of Thermostable Cytochrome c. Biochemistry 2013; 52:1373-84. [DOI: 10.1021/bi300982v] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Rabindra Kumar Behera
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha
Road, Colaba, Mumbai 400005, India
| | - Hiroshi Nakajima
- Department of Chemistry, Graduate
School of Science, Nagoya University, Nagoya
464-8602, Japan
| | - Jitumani Rajbongshi
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha
Road, Colaba, Mumbai 400005, India
- Department
of Chemistry, Gauhati University, Guwahati
781014, India
| | - Yoshihito Watanabe
- Department of Chemistry, Graduate
School of Science, Nagoya University, Nagoya
464-8602, Japan
| | - Shyamalava Mazumdar
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha
Road, Colaba, Mumbai 400005, India
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34
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Sun J, Ruchmann J, Pallier A, Jullien L, Desmadril M, Tribet C. Unfolding of Cytochrome c upon Interaction with Azobenzene-Modified Copolymers. Biomacromolecules 2012; 13:3736-46. [DOI: 10.1021/bm301200p] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Jing Sun
- Ecole Normale Supérieure, Département de chimie, UMR8640 CNRS-ENS-UPMC, 24 rue Lhomond, F-75005 Paris, France
| | - Juliette Ruchmann
- Ecole Normale Supérieure, Département de chimie, UMR8640 CNRS-ENS-UPMC, 24 rue Lhomond, F-75005 Paris, France
| | - A. Pallier
- ESPCI, Physico-Chimie
des Polymeres et Milieux Disperses, CNRS UMR7615, 10 rue Vauquelin, 75005 Paris, France
| | - L. Jullien
- Ecole Normale Supérieure, Département de chimie, UMR8640 CNRS-ENS-UPMC, 24 rue Lhomond, F-75005 Paris, France
| | - M. Desmadril
- Laboratoire de Modélisation
et d’Ingénierie des Protéines, UMR8619, Université de Paris-Sud, Bât 430, F-91405
ORSAY CEDEX, France
| | - Christophe Tribet
- Ecole Normale Supérieure, Département de chimie, UMR8640 CNRS-ENS-UPMC, 24 rue Lhomond, F-75005 Paris, France
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35
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Mason JM, Bendall DS, Howe CJ, Worrall JA. The role of a disulfide bridge in the stability and folding kinetics of Arabidopsis thaliana cytochrome c6A. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2012; 1824:311-8. [DOI: 10.1016/j.bbapap.2011.10.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2011] [Revised: 10/11/2011] [Accepted: 10/26/2011] [Indexed: 10/15/2022]
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36
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Abstract
Recent NMR structural and dynamical data on partially folded forms of mono-heme cytochrome c provide a unifying picture of the behavior of the protein far from the native conditions and suggest useful hints to explain the redox dependent stability of the protein. A fragile hinge in the structure of mitochondrial cytochrome c is identified, which may not have correspondents in smaller type-1 cytochromes. Former spectroscopic and kinetic data are here discussed in terms of this new view.
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Affiliation(s)
- Ivano Bertini
- Department of Chemistry and CERM, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy
| | - Antonio Rosato
- Department of Chemistry and CERM, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy
| | - Paola Turano
- Department of Chemistry and CERM, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy
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37
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Han Z, Chang YY, Au SWN, Zheng B. Measuring rapid kinetics by a potentiometric method in droplet-based microfluidic devices. Chem Commun (Camb) 2012; 48:1601-3. [DOI: 10.1039/c1cc12383a] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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38
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Lan W, Wang Z, Yang Z, Zhu J, Ying T, Jiang X, Zhang X, Wu H, Liu M, Tan X, Cao C, Huang ZX. Conformational toggling of yeast iso-1-cytochrome C in the oxidized and reduced states. PLoS One 2011; 6:e27219. [PMID: 22087268 PMCID: PMC3210782 DOI: 10.1371/journal.pone.0027219] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2011] [Accepted: 10/12/2011] [Indexed: 11/18/2022] Open
Abstract
To convert cyt c into a peroxidase-like metalloenzyme, the P71H mutant was designed to introduce a distal histidine. Unexpectedly, its peroxidase activity was found even lower than that of the native, and that the axial ligation of heme iron was changed to His71/His18 in the oxidized state, while to Met80/His18 in the reduced state, characterized by UV-visible, circular dichroism, and resonance Raman spectroscopy. To further probe the functional importance of Pro71 in oxidation state dependent conformational changes occurred in cyt c, the solution structures of P71H mutant in both oxidation states were determined. The structures indicate that the half molecule of cyt c (aa 50-102) presents a kind of "zigzag riveting ruler" structure, residues at certain positions of this region such as Pro71, Lys73 can move a big distance by altering the tertiary structure while maintaining the secondary structures. This finding provides a molecular insight into conformational toggling in different oxidation states of cyt c that is principle significance to its biological functions in electron transfer and apoptosis. Structural analysis also reveals that Pro71 functions as a key hydrophobic patch in the folding of the polypeptide of the region (aa 50-102), to prevent heme pocket from the solvent.
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Affiliation(s)
- Wenxian Lan
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China
| | - Zhonghua Wang
- Chemical Biology Laboratory, Department of Chemistry, Fudan University, Shanghai, China
| | - Zhongzheng Yang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China
| | - Jing Zhu
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China
| | - Tianlei Ying
- Chemical Biology Laboratory, Department of Chemistry, Fudan University, Shanghai, China
| | - Xianwang Jiang
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, China
| | - Xu Zhang
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, China
| | - Houming Wu
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China
| | - Maili Liu
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, China
| | - Xiangshi Tan
- Chemical Biology Laboratory, Department of Chemistry, Fudan University, Shanghai, China
| | - Chunyang Cao
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China
- * E-mail: (CC); (Z-XH)
| | - Zhong-Xian Huang
- Chemical Biology Laboratory, Department of Chemistry, Fudan University, Shanghai, China
- * E-mail: (CC); (Z-XH)
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39
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Chung JK, Thielges MC, Bowman SEJ, Bren KL, Fayer MD. Temperature dependent equilibrium native to unfolded protein dynamics and properties observed with IR absorption and 2D IR vibrational echo experiments. J Am Chem Soc 2011; 133:6681-91. [PMID: 21469666 PMCID: PMC3088310 DOI: 10.1021/ja111009s] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Dynamic and structural properties of carbonmonoxy (CO)-coordinated cytochrome c(552) from Hydrogenobacter thermophilus (Ht-M61A) at different temperatures under thermal equilibrium conditions were studied with infrared absorption spectroscopy and ultrafast two-dimensional infrared (2D IR) vibrational echo experiments using the heme-bound CO as the vibrational probe. Depending on the temperature, the stretching mode of CO shows two distinct bands corresponding to the native and unfolded proteins. As the temperature is increased from low temperature, a new absorption band for the unfolded protein grows in and the native band decreases in amplitude. Both the temperature-dependent circular dichroism and the IR absorption area ratio R(A)(T), defined as the ratio of the area under the unfolded band to the sum of the areas of the native and unfolded bands, suggest a two-state transition from the native to the unfolded protein. However, it is found that the absorption spectrum of the unfolded protein increases its inhomogeneous line width and the center frequency shifts as the temperature is increased. The changes in line width and center frequency demonstrate that the unfolding does not follow simple two-state behavior. The temperature-dependent 2D IR vibrational echo experiments show that the fast dynamics of the native protein are virtually temperature independent. In contrast, the fast dynamics of the unfolded protein are slower than those of the native protein, and the unfolded protein fast dynamics and at least a portion of the slower dynamics of the unfolded protein change significantly, becoming faster as the temperature is raised. The temperature dependence of the absorption spectrum and the changes in dynamics measured with the 2D IR experiments confirm that the unfolded ensemble of conformers continuously changes its nature as unfolding proceeds, in contrast to the native state, which displays a temperature-independent distribution of structures.
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Affiliation(s)
- Jean K. Chung
- Department of Chemistry, Stanford University, Stanford, California 94305
| | - Megan C. Thielges
- Department of Chemistry, Stanford University, Stanford, California 94305
| | - Sarah E. J. Bowman
- Department of Chemistry, University of Rochester, Rochester, New York 14627
| | - Kara L. Bren
- Department of Chemistry, University of Rochester, Rochester, New York 14627
| | - M. D. Fayer
- Department of Chemistry, Stanford University, Stanford, California 94305
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40
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Structural and kinetic studies of imidazole binding to two members of the cytochrome c 6 family reveal an important role for a conserved heme pocket residue. J Biol Inorg Chem 2011; 16:577-88. [DOI: 10.1007/s00775-011-0758-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2010] [Accepted: 01/01/2011] [Indexed: 10/18/2022]
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41
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Bhuyan AK. The Off-Pathway Status of the Alkali Molten Globule Is Unrelated to Heme Misligation and Trans-pH Effects: Experiments with Ferrocytochrome c. Biochemistry 2010; 49:7774-82. [DOI: 10.1021/bi100881n] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Abani K. Bhuyan
- School of Chemistry, University of Hyderabad, Hyderabad 500046, India
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42
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Haldar S, Mitra S, Chattopadhyay K. Role of protein stabilizers on the conformation of the unfolded state of cytochrome c and its early folding kinetics: investigation at single molecular resolution. J Biol Chem 2010; 285:25314-23. [PMID: 20538585 PMCID: PMC2919094 DOI: 10.1074/jbc.m110.116673] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2010] [Revised: 05/31/2010] [Indexed: 11/06/2022] Open
Abstract
An insight into the conformation and dynamics of unfolded and early intermediate states of a protein is essential to understand the mechanism of its aggregation and to design potent inhibitor molecules. Fluorescence correlation spectroscopy has been used to study the effects of several model protein stabilizers on the conformation of the unfolded state and early folding dynamics of tetramethyl rhodamine-labeled cytochrome c from Saccharomyces cerevisiae at single molecular resolution. Special attention has been given to arginine, which is a widely used stabilizer for improving refolding yield of different proteins. The value of the hydrodynamic radius (r(H)) obtained by analyzing the intensity fluctuations of the diffusing molecules has been found to increase in a two-state manner as the protein is unfolded by urea. The results further show that the presence of arginine and other protein stabilizers favors a relatively structured conformation of the unfolded states (r(H) of 29 A) over an extended one (r(H) of 40 A), which forms in their absence. Also, the time constant of a kinetic component (tau(R)) of about 30 micros has been observed by analyzing the correlation functions, which represents formation of a collapsed state. This time constant varies with urea concentration representing an inverted Chevron plot that shows a roll-over and behavior in the absence of arginine. To the best of our knowledge, this is one of the first applications of fluorescence correlation spectroscopy to study direct folding kinetics of a protein.
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Affiliation(s)
- Shubhasis Haldar
- From the Structural Biology and Bioinformatics Division, Indian Institute of Chemical Biology, Council of Scientific and Industrial Research, 4, Raja S. C. Mullick Road, Kolkata 700032, India
| | - Samaresh Mitra
- From the Structural Biology and Bioinformatics Division, Indian Institute of Chemical Biology, Council of Scientific and Industrial Research, 4, Raja S. C. Mullick Road, Kolkata 700032, India
| | - Krishnananda Chattopadhyay
- From the Structural Biology and Bioinformatics Division, Indian Institute of Chemical Biology, Council of Scientific and Industrial Research, 4, Raja S. C. Mullick Road, Kolkata 700032, India
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43
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Stocks BB, Konermann L. Time-dependent changes in side-chain solvent accessibility during cytochrome c folding probed by pulsed oxidative labeling and mass spectrometry. J Mol Biol 2010; 398:362-73. [PMID: 20230834 DOI: 10.1016/j.jmb.2010.03.015] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2010] [Revised: 03/08/2010] [Accepted: 03/08/2010] [Indexed: 11/28/2022]
Abstract
The current work employs a novel approach for characterizing structural changes during the refolding of acid-denatured cytochrome c (cyt c). At various time points (ranging from 10 ms to 5 min) after a pH jump from 2 to 7, the protein is exposed to a microsecond hydroxyl radical (.OH) pulse that induces oxidative labeling of solvent-exposed side chains. Most of the covalent modifications appear as +16-Da adducts that are readily detectable by mass spectrometry. The overall extent of labeling decreases as folding proceeds, reflecting dramatic changes in the accessibility of numerous residues. Peptide mapping and tandem mass spectrometry reveal that the side chains of C14, C17, H33, F46, Y48, W59, M65, Y67, Y74, M80, I81, and Y97 are among the dominant sites of oxidation. Temporal changes in the accessibility of these residues are consistent with docking of the N- and C-terminal helices as early as 10 ms. However, structural reorganization at the helix interface takes place up to at least 1 s. Initial misligation of the heme iron by H33 leads to distal crowding, giving rise to low solvent accessibility of the displaced (native) M80 ligand and the adjacent I81. W59 retains a surprisingly high level of accessibility long into the folding process, indicating the presence of packing defects in the hydrophobically collapsed core. Overall, the results of this work are consistent with previous hydrogen/deuterium exchange studies that proposed a foldon-mediated mechanism. The structural data obtained by .OH labeling monitor the packing and burial of side chains, whereas hydrogen/deuterium exchange primarily monitors the formation of secondary structure elements. Hence, the two approaches yield complementary information. Considering the very short time scale of pulsed oxidative labeling, an extension of the approach used here to sub-millisecond folding studies should be feasible.
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Affiliation(s)
- Bradley B Stocks
- Department of Biochemistry, The University of Western Ontario, London, Ontario, Canada
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44
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Singh SR, Prakash S, Vasu V, Karunakaran C. Conformational flexibility decreased due to Y67F and F82H mutations in cytochrome c: Molecular dynamics simulation studies. J Mol Graph Model 2009; 28:270-7. [DOI: 10.1016/j.jmgm.2009.08.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2009] [Revised: 07/17/2009] [Accepted: 08/03/2009] [Indexed: 10/20/2022]
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45
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Geremia S, Garau G, Vaccari L, Sgarra R, Viezzoli MS, Calligaris M, Randaccio L. Cleavage of the iron-methionine bond in c-type cytochromes: Crystal structure of oxidized and reduced cytochrome c2 from Rhodopseudomonas palustris and its ammonia complex. Protein Sci 2009. [DOI: 10.1110/ps.13102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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46
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Shang W, Nuffer JH, Muñiz-Papandrea VA, Colón W, Siegel RW, Dordick JS. Cytochrome C on silica nanoparticles: influence of nanoparticle size on protein structure, stability, and activity. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2009; 5:470-6. [PMID: 19189325 DOI: 10.1002/smll.200800995] [Citation(s) in RCA: 124] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The structure, thermodynamic and kinetic stability, and activity of cytochrome c (cyt c) on silica nanoparticles (SNPs) of different sizes have been studied. Adsorption of cyt c onto larger SNPs results in both greater disruption of the cyt c global structure and more significant changes of the local heme microenvironment than upon adsorption onto smaller SNPs. The disruption of the heme microenvironment leads to a more solvent-accessible protein active site, as suggested by Soret circular dichroism spectroscopy and through an increase in peroxidase activity as a function of increased SNP size. Similarly, the stability of cyt c decreases more dramatically upon adsorption onto larger SNPs. These results are consistent with changes in protein-nanoparticle interactions that depend on the size or surface curvature of the supporting nanostructure. This study provides further fundamental insights into the effects of nanoscale surfaces on adsorbed protein structure and function.
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Affiliation(s)
- Wen Shang
- Department of Materials Science and Engineering, Rensselaer Nanotechnology Center, Rensselaer Polytechnic Institute, 110 8th Street, Troy, NY 12180, USA
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47
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Tai H, Munegumi T, Yamamoto Y. Stability of the heme Fe-N-terminal amino group coordination bond in denatured cytochrome c. Inorg Chem 2009; 48:331-8. [PMID: 19053349 DOI: 10.1021/ic801202d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In the denatured states of Hydrogenobacter thermophilus cytochrome c(552) (HT) and Pseudomonas aeruginosa cytochrome c(551) (PA), and their mutants, the N-terminal amino group of the polypeptide chain is coordinated to heme Fe in place of the axial Met, the His-N(term) form being formed. The coordination of the N-terminal amino group to heme Fe leads to loop formation by the N-terminal stretch preceding the first Cys residue bound to the heme, and the N-terminal stretches of HT and PA are different from each other in terms of both the sequence and the number of constituent amino acid residues. The His-N(term) form was shown to be rather stable, and hence it can influence the stability of the denatured state. We have investigated the heme Fe coordination structures and stabilities of the His-N(term) forms emerging upon guanidine hydrochloric acid-induced unfolding of the oxidized forms of the proteins. The Fe-N(term) coordination bond in the His-N(term) form with a 9-residue N-terminal stretch of HT proteins was found to be tilted to some extent away from the heme normal, as reflected by the great heme methyl proton shift spread. On the other hand, the small heme methyl proton shift spread of the His-N(term) form with an 11-residue stretch of PA proteins indicated that its Fe-N(term) bond is nearly parallel with the heme normal. The stability of the His-N(term) form was found to be affected by the structural properties of the N-terminal stretch, such as its length and the N-terminal residue. With a given N-terminal residue, the stability of the His-N(term) form is higher for a 9-residue N-terminal stretch than an 11-residue one. In addition, with a given length of the N-terminal stretch, the His-N(term) form with an N-terminal Glu is stabilized by a few kJ mol(-1) relative to that with an N-terminal Asn. These results provide a novel insight into the stabilizing interactions in the denatured cyts c that will facilitate elucidation of the folding/unfolding mechanisms of the proteins.
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Affiliation(s)
- Hulin Tai
- Department of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
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48
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Latypov RF, Maki K, Cheng H, Luck SD, Roder H. Folding mechanism of reduced Cytochrome c: equilibrium and kinetic properties in the presence of carbon monoxide. J Mol Biol 2008; 383:437-53. [PMID: 18761351 DOI: 10.1016/j.jmb.2008.08.025] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2008] [Revised: 08/08/2008] [Accepted: 08/13/2008] [Indexed: 11/26/2022]
Abstract
Despite close structural similarity, the ferric and ferrous forms of cytochrome c differ greatly in terms of their ligand binding properties, stability, folding, and dynamics. The reduced heme iron binds diatomic ligands such as CO only under destabilizing conditions that promote weakening or disruption of native methionine-iron linkage. This makes CO a useful conformational probe for detecting partially structured states that cannot be observed in the absence of endogenous ligands. Heme absorbance, circular dichroism, and NMR were used to characterize the denaturant-induced unfolding equilibrium of ferrocytochrome c in the presence and in the absence of CO. In addition to the native state (N), which does not bind CO, and the unfolded CO complex (U-CO), a structurally distinct CO-bound form (M-CO) accumulates to high levels (approximately 75% of the population) at intermediate guanidine HCl concentrations. Comparison of the unfolding transitions for different conformational probes reveals that M-CO is a compact state containing a native-like helical core and regions of local disorder in the segment containing the native Met80 ligand and adjacent loops. Kinetic measurements of CO binding and dissociation under native, partially denaturing, and fully unfolded conditions indicate that a state M that is structurally analogous to M-CO is populated even in the absence of CO. The binding energy of the CO ligand lowers the free energy of this high-energy state to such an extent that it accumulates even under mildly denaturing equilibrium conditions. The thermodynamic and kinetic parameters obtained in this study provide a fully self-consistent description of the linked unfolding/CO binding equilibria of reduced cytochrome c.
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49
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Kim S, Chung JK, Kwak K, Bowman SEJ, Bren KL, Bagchi B, Fayer MD. Native and unfolded cytochrome c--comparison of dynamics using 2D-IR vibrational echo spectroscopy. J Phys Chem B 2008; 112:10054-63. [PMID: 18646797 PMCID: PMC2671645 DOI: 10.1021/jp802246h] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Unfolded vs native CO-coordinated horse heart cytochrome c (h-cyt c) and a heme axial methionine mutant cyt c552 from Hydrogenobacter thermophilus ( Ht-M61A) are studied by IR absorption spectroscopy and ultrafast 2D-IR vibrational echo spectroscopy of the CO stretching mode. The unfolding is induced by guanidinium hydrochloride (GuHCl). The CO IR absorption spectra for both h-cyt c and Ht-M61A shift to the red as the GuHCl concentration is increased through the concentration region over which unfolding occurs. The spectra for the unfolded state are substantially broader than the spectra for the native proteins. A plot of the CO peak position vs GuHCl concentration produces a sigmoidal curve that overlays the concentration-dependent circular dichroism (CD) data of the CO-coordinated forms of both Ht-M61A and h-cyt c within experimental error. The coincidence of the CO peak shift curve with the CD curves demonstrates that the CO vibrational frequency is sensitive to the structural changes induced by the denaturant. 2D-IR vibrational echo experiments are performed on native Ht-M61A and on the protein in low- and high-concentration GuHCl solutions. The 2D-IR vibrational echo is sensitive to the global protein structural dynamics on time scales from subpicosecond to greater than 100 ps through the change in the shape of the 2D spectrum with time (spectral diffusion). At the high GuHCl concentration (5.1 M), at which Ht-M61A is essentially fully denatured as judged by CD, a very large reduction in dynamics is observed compared to the native protein within the approximately 100 ps time window of the experiment. The results suggest the denatured protein may be in a glassy-like state involving hydrophobic collapse around the heme.
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Affiliation(s)
- Seongheun Kim
- Department of Chemistry, Stanford University, Stanford, CA 94305
| | - Jean K. Chung
- Department of Chemistry, Stanford University, Stanford, CA 94305
| | - Kyungwon Kwak
- Department of Chemistry, Stanford University, Stanford, CA 94305
| | - Sarah E. J. Bowman
- Department of Chemistry, University of Rochester, Rochester, NY 14627-0216
| | - Kara L. Bren
- Department of Chemistry, University of Rochester, Rochester, NY 14627-0216
| | - Biman Bagchi
- Department of Chemistry, Stanford University, Stanford, CA 94305
| | - M. D. Fayer
- Department of Chemistry, Stanford University, Stanford, CA 94305
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50
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Abstract
Experimental studies show that many proteins fold along sequential pathways defined by folding intermediates. An intermediate may not always be a single population of molecules but may consist of subpopulations that differ in their average structure. These subpopulations are likely to fold via independent pathways. Parallel folding and unfolding pathways appear to arise because of structural heterogeneity. For some proteins, the folding pathways can effectively switch either because different subpopulations of an intermediate get populated under different folding conditions, or because intermediates on otherwise hidden pathways get stabilized, leading to their utilization becoming discernible, or because mutations stabilize different substructures. Therefore, the same protein may fold via different pathways in different folding conditions. Multiple folding pathways make folding robust, and evolution is likely to have selected for this robustness to ensure that a protein will fold under the varying conditions prevalent in different cellular contexts.
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Affiliation(s)
- Jayant B Udgaonkar
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India.
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