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Lui TY, Chen X, Hu D, Chan TWD. Probing High-order Protein Complexes Using Native Mass Spectrometry and Hydrogen/Deuterium Exchange Mass Spectrometry: A Case Study Using Fresh and Commercial Hemoglobin Samples. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:1921-1929. [PMID: 38957002 DOI: 10.1021/jasms.4c00201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2024]
Abstract
Native mass spectrometry (MS) analysis of protein complexes is highly susceptible to matrix effect, and addressing this predicament using buffer exchange is a common approach. Nevertheless, optimization of the buffer exchange protocol is not trivial. With the use of hemoglobin (Hb) as the model entity, it was discovered that the native mass spectrum of protein assembly is highly dependent on the buffer-exchange protocol. Given the dependence of native MS on the purification protocol, this work attempts to use hydrogen/deuterium exchange mass spectrometry (HDX-MS) for comparative studies of hemoglobin complexes in untreated fresh and commercial samples. The information obtained from the HDX study was found to correlate well with the native mass spectrometry analysis of the properly buffer-exchanged Hb samples. Both native MS and HDX-MS showed that the fresh Hb sample has retained the expected tetrameric structure, whereas the commercial Hb has largely been denatured to the dimeric form. These findings prove the complementarity of native MS and HDX-MS in the analysis of high-order protein complexes and stress the necessity to validate the integrity of the high-order structures of the proteins prior to the use of the protein samples for other biomedical studies.
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Affiliation(s)
- T-Y Lui
- Department of Chemistry, The Chinese University of Hong Kong, Hong Kong SAR 999077, P. R. China
| | - Xiangfeng Chen
- Department of Chemistry, The Chinese University of Hong Kong, Hong Kong SAR 999077, P. R. China
- School of Pharmaceutical Sciences, Qilu University of Technology (Shandong Academy of Sciences), Jinan, Shandong 250000, P. R. China
| | - Danna Hu
- Department of Chemistry, The Chinese University of Hong Kong, Hong Kong SAR 999077, P. R. China
| | - T-W Dominic Chan
- Department of Chemistry, The Chinese University of Hong Kong, Hong Kong SAR 999077, P. R. China
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2
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McCullagh M, Zeczycki TN, Kariyawasam CS, Durie CL, Halkidis K, Fitzkee NC, Holt JM, Fenton AW. What is allosteric regulation? Exploring the exceptions that prove the rule! J Biol Chem 2024; 300:105672. [PMID: 38272229 PMCID: PMC10897898 DOI: 10.1016/j.jbc.2024.105672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 01/09/2024] [Accepted: 01/12/2024] [Indexed: 01/27/2024] Open
Abstract
"Allosteric" was first introduced to mean the other site (i.e., a site distinct from the active or orthosteric site), an adjective for "regulation" to imply a regulatory outcome resulting from ligand binding at another site. That original idea outlines a system with two ligand-binding events at two distinct locations on a macromolecule (originally a protein system), which defines a four-state energy cycle. An allosteric energy cycle provides a quantifiable allosteric coupling constant and focuses our attention on the unique properties of the four equilibrated protein complexes that constitute the energy cycle. Because many observed phenomena have been referenced as "allosteric regulation" in the literature, the goal of this work is to use literature examples to explore which systems are and are not consistent with the two-ligand thermodynamic energy cycle-based definition of allosteric regulation. We emphasize the need for consistent language so comparisons can be made among the ever-increasing number of allosteric systems. Building on the mutually exclusive natures of an energy cycle definition of allosteric regulation versus classic two-state models, we conclude our discussion by outlining how the often-proposed Rube-Goldberg-like mechanisms are likely inconsistent with an energy cycle definition of allosteric regulation.
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Affiliation(s)
- Martin McCullagh
- Department of Chemistry, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Tonya N Zeczycki
- Department of Biochemistry and Molecular Biology, Brody School of Medicine at East Carolina University, Greenville, North Carolina, USA
| | - Chathuri S Kariyawasam
- Department of Chemistry, Mississippi State University, Mississippi State, Mississippi, USA
| | - Clarissa L Durie
- Department of Biochemistry, University of Missouri, Columbia, Missouri, USA
| | - Konstantine Halkidis
- Department of Hematologic Malignancies and Cellular Therapeutics, The University of Kansas Medical Center, Kansas City, Kansas, USA; Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Nicholas C Fitzkee
- Department of Chemistry, Mississippi State University, Mississippi State, Mississippi, USA
| | - Jo M Holt
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Aron W Fenton
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, Kansas, USA.
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3
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Schay G, Fidy J, Herenyi L. Slow dynamics measured by phosphorescence lifetime reveals global conformational changes in human adult hemoglobin induced by allosteric effectors. PLoS One 2022; 17:e0278417. [PMID: 36454779 PMCID: PMC9714750 DOI: 10.1371/journal.pone.0278417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 11/16/2022] [Indexed: 12/03/2022] Open
Abstract
The mechanism underlying allostery in hemoglobin (Hb) is still not completely understood. Various models describing the action of allosteric effectors on Hb function have been published in the literature. It has also been reported that some allosteric effectors-such as chloride ions, inositol hexaphosphate, 2,3-diphospho-glycerate and bezafibrate-considerably lower the oxygen affinity of Hb. In this context, an important question is the extent to which these changes influence the conformational dynamics of the protein. Earlier, we elaborated a challenging method based on phosphorescence quenching, which makes characterizing protein-internal dynamics possible in the ms time range. The experimental technique involves phosphorescence lifetime measurements in thermal equilibrium at varied temperatures from 10 K up to 273 K, based on the signal of Zn-protoporphyrin substituted for the heme in the β-subunits of Hb. The thermal activation of protein dynamics was observed by the enhancement of phosphorescence quenching attributed to O2 diffusion. It was shown that the thermal activation of protein matrix dynamics was clearly distinguishable from the dynamic activation of the aqueous solvent, and was therefore highly specific for the protein. In the present work, the same method was used to study the changes in the parameters of the dynamic activation of human HbA induced by binding allosteric effectors. We interpreted the phenomenon as phase transition between two states. The fitting of this model to lifetime data yielded the change of energy and entropy in the activation process and the quenching rate in the dynamically activated state. The fitted parameters were particularly sensitive to the presence of allosteric effectors and could be interpreted in line with results from earlier experimental studies. The results suggest that allosteric effectors are tightly coupled to the dynamics of the whole protein, and thus underline the importance of global dynamics in the regulation of Hb function.
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Affiliation(s)
- Gusztáv Schay
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary
| | - Judit Fidy
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary
| | - Levente Herenyi
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary
- * E-mail:
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4
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Cipriano LA, Di Liberto G, Pacchioni G. Superoxo and Peroxo Complexes on Single-Atom Catalysts: Impact on the Oxygen Evolution Reaction. ACS Catal 2022. [DOI: 10.1021/acscatal.2c03020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Luis A. Cipriano
- Dipartimento di Scienza dei Materiali, Università di Milano─Bicocca, Via Roberto Cozzi 55, 20125 Milano, Italy
| | - Giovanni Di Liberto
- Dipartimento di Scienza dei Materiali, Università di Milano─Bicocca, Via Roberto Cozzi 55, 20125 Milano, Italy
| | - Gianfranco Pacchioni
- Dipartimento di Scienza dei Materiali, Università di Milano─Bicocca, Via Roberto Cozzi 55, 20125 Milano, Italy
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5
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Structure and function of H +/K + pump mutants reveal Na +/K + pump mechanisms. Nat Commun 2022; 13:5270. [PMID: 36085139 PMCID: PMC9463140 DOI: 10.1038/s41467-022-32793-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 08/17/2022] [Indexed: 11/09/2022] Open
Abstract
Ion-transport mechanisms evolve by changing ion-selectivity, such as switching from Na+ to H+ selectivity in secondary-active transporters or P-type-ATPases. Here we study primary-active transport via P-type ATPases using functional and structural analyses to demonstrate that four simultaneous residue substitutions transform the non-gastric H+/K+ pump, a strict H+-dependent electroneutral P-type ATPase, into a bona fide Na+-dependent electrogenic Na+/K+ pump. Conversion of a H+-dependent primary-active transporter into a Na+-dependent one provides a prototype for similar studies of ion-transport proteins. Moreover, we solve the structures of the wild-type non-gastric H+/K+ pump, a suitable drug target to treat cystic fibrosis, and of its Na+/K+ pump-mimicking mutant in two major conformations, providing insight on how Na+ binding drives a concerted mechanism leading to Na+/K+ pump phosphorylation.
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6
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Nagatomo S, Nagai M, Kitagawa T. Structural origin of cooperativity in human hemoglobin: a view from different roles of α and β subunits in the α2β2 tetramer. Biophys Rev 2022; 14:483-498. [PMID: 35528033 PMCID: PMC9043147 DOI: 10.1007/s12551-022-00945-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 03/14/2022] [Indexed: 11/26/2022] Open
Abstract
This mini-review, mainly based on our resonance Raman studies on the structural origin of cooperative O2 binding in human adult hemoglobin (HbA), aims to answering why HbA is a tetramer consisting of two α and two β subunits. Here, we focus on the Fe-His bond, the sole coordination bond connecting heme to a globin. The Fe-His stretching frequencies reflect the O2 affinity and also the magnitude of strain imposed through globin by inter-subunit interactions, which is the origin of cooperativity. Cooperativity was first explained by Monod, Wyman, and Changeux, referred to as the MWC theory, but later explained by the two tertiary states (TTS) theory. Here, we related the higher-order structures of globin observed mainly by vibrational spectroscopy to the MWC theory. It became clear from the recent spectroscopic studies, X-ray crystallographic analysis, and mutagenesis experiments that the Fe-His bonds exhibit different roles between the α and β subunits. The absence of the Fe-His bond in the α subunit in some mutant and artificial Hbs inhibits T to R quaternary structural change upon O2 binding. However, its absence from the β subunit in mutant and artificial Hbs simply enhances the O2 affinity of the α subunit. Accordingly, the inter-subunit interactions between α and β subunits are nonsymmetric but substantial for HbA to perform cooperative O2 binding.
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Affiliation(s)
- Shigenori Nagatomo
- Department of Chemistry, Faculty of Pure and Applied Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8571 Japan
| | - Masako Nagai
- Research Center for Micro-Nano Technology, Hosei University, Koganei, Tokyo, 184-0003 Japan
- School of Health Sciences, College of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa, Ishikawa 920-0942 Japan
| | - Teizo Kitagawa
- Graduate School of Life Science, Picobiology Institute, University of Hyogo, Kouto, Kamigori, Ako-gun Hyogo, 678-1297 Japan
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7
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Lavrinenko IA, Vashanov GA, Sulin VY, Nechipurenko YD. An Analysis of Models of Cooperative Oxygen Binding by Hemoglobin. Biophysics (Nagoya-shi) 2021. [DOI: 10.1134/s0006350921060105] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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8
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Abe K, Yamamoto K, Irie K, Nishizawa T, Oshima A. Gastric proton pump with two occluded K + engineered with sodium pump-mimetic mutations. Nat Commun 2021; 12:5709. [PMID: 34588453 PMCID: PMC8481561 DOI: 10.1038/s41467-021-26024-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 09/10/2021] [Indexed: 12/13/2022] Open
Abstract
The gastric H+,K+-ATPase mediates electroneutral exchange of 1H+/1K+ per ATP hydrolysed across the membrane. Previous structural analysis of the K+-occluded E2-P transition state of H+,K+-ATPase showed a single bound K+ at cation-binding site II, in marked contrast to the two K+ ions occluded at sites I and II of the closely-related Na+,K+-ATPase which mediates electrogenic 3Na+/2K+ translocation across the membrane. The molecular basis of the different K+ stoichiometry between these K+-counter-transporting pumps is elusive. We show a series of crystal structures and a cryo-EM structure of H+,K+-ATPase mutants with changes in the vicinity of site I, based on the structure of the sodium pump. Our step-wise and tailored construction of the mutants finally gave a two-K+ bound H+,K+-ATPase, achieved by five mutations, including amino acids directly coordinating K+ (Lys791Ser, Glu820Asp), indirectly contributing to cation-binding site formation (Tyr340Asn, Glu936Val), and allosterically stabilizing K+-occluded conformation (Tyr799Trp). This quintuple mutant in the K+-occluded E2-P state unambiguously shows two separate densities at the cation-binding site in its 2.6 Å resolution cryo-EM structure. These results offer new insights into how two closely-related cation pumps specify the number of K+ accommodated at their cation-binding site. The gastric H+,K+-ATPase is a proton pump that creates the acidic environment of the stomach lumen, maintaining high proton gradient across the gastric mucosa cell membrane. Here, structural analysis of rationally designed H+,K+-ATPase mutants provides insight into this and other P-type ATPases cation binding stoichiometry and mechanisms.
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Affiliation(s)
- Kazuhiro Abe
- Cellular and Structural Physiology Institute, Nagoya University, Nagoya, 464-8601, Japan. .,Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, 464-8601, Japan.
| | - Kenta Yamamoto
- Cellular and Structural Physiology Institute, Nagoya University, Nagoya, 464-8601, Japan.,Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, 464-8601, Japan
| | - Katsumasa Irie
- Department of Biophysical Chemistry, Faculty of Pharmaceutical Sciences, Wakayama Medical University, 25-1 Shichibancho, Wakayama, 640-8156, Japan
| | - Tomohiro Nishizawa
- Graduate School of Medical Life Science, Yokohama City University, Tsurumi, Yokohama, 230-0045, Japan
| | - Atsunori Oshima
- Cellular and Structural Physiology Institute, Nagoya University, Nagoya, 464-8601, Japan.,Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, 464-8601, Japan
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9
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Sever AIM, Yin V, Konermann L. Interrogating the Quaternary Structure of Noncanonical Hemoglobin Complexes by Electrospray Mass Spectrometry and Collision-Induced Dissociation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:270-280. [PMID: 33124417 DOI: 10.1021/jasms.0c00320] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Various activation methods are available for the fragmentation of gaseous protein complexes produced by electrospray ionization (ESI). Such experiments can potentially yield insights into quaternary structure. Collision-induced dissociation (CID) is the most widely used fragmentation technique. Unfortunately, CID of protein complexes is dominated by the ejection of highly charged monomers, a process that does not yield any structural insights. Using hemoglobin (Hb) as a model system, this work examines under what conditions CID generates structurally informative subcomplexes. Native ESI mainly produced tetrameric Hb ions. In addition, "noncanonical" hexameric and octameric complexes were observed. CID of all these species [(αβ)2, (αβ)3, and (αβ)4] predominantly generated highly charged monomers. In addition, we observed hexamer → tetramer + dimer dissociation, implying that hexamers have a tetramer··dimer architecture. Similarly, the observation of octamer → two tetramer dissociation revealed that octamers have a tetramer··tetramer composition. Gas-phase candidate structures of Hb assemblies were produced by molecular dynamics (MD) simulations. Ion mobility spectrometry was used to identify the most likely candidates. Our data reveal that the capability of CID to produce structurally informative subcomplexes depends on the fate of protein-protein interfaces after transfer into the gas phase. Collapse of low affinity interfaces conjoins the corresponding subunits and favors CID via monomer ejection. Structurally informative subcomplexes are formed only if low affinity interfaces do not undergo a major collapse. However, even in these favorable cases CID is still dominated by monomer ejection, requiring careful analysis of the experimental data for the identification of structurally informative subcomplexes.
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Affiliation(s)
- Alexander I M Sever
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Victor Yin
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Lars Konermann
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
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10
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Chkheidze R, Evangelista W, White MA, Yin YW, Lee JC. Structural Energy Landscapes and Plasticity of the Microstates of Apo Escherichia coli cAMP Receptor Protein. Biochemistry 2020; 59:460-470. [PMID: 31885251 DOI: 10.1021/acs.biochem.9b00895] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The theory for allostery has evolved to a modern energy landscape ensemble theory, the major feature of which is the existence of multiple microstates in equilibrium. The properties of microstates are not well defined due to their transient nature. Characterization of apo protein microstates is important because the specific complex of the ligand-bound microstate defines the biological function. The information needed to link biological function and structure is a quantitative correlation of the energy landscapes between the apo and holo protein states. We employed the Escherichia coli cAMP receptor protein (CRP) system to test the features embedded in the ensemble theory because multiple crystalline apo and holo structures are available. Small angle X-ray scattering data eliminated one of the three apo states but not the other two. We defined the underlying energy landscape differences among the apo microstates by employing the computation algorithm COREX/BEST. The same connectivity patterns among residues in apo CRP are retained upon binding of cAMP. The microstates of apo CRP differ from one another by minor structural perturbations, resulting in changes in the energy landscapes of the various domains of CRP. Using the differences in energy landscapes among these apo states, we computed the cAMP binding energetics that were compared with solution biophysical results. Only one of the three apo microstates yielded data consistent with the solution data. The relative magnitude of changes in energy landscapes embedded in various apo microstates apparently defines the ultimate outcome of the cooperativity of binding.
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Affiliation(s)
| | - Wilfredo Evangelista
- Centro de Espectroscopia de Resonancia Magnética Nuclear (CERMN), Departamento de Ciencias-Química , Pontificia Universidad Católica del Perú , Lima 32 , Peru
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11
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Lee L. Bohr equation and the lost allosteric Bohr effects in symmetry. Biophys Physicobiol 2019; 16:490-503. [PMID: 31984201 PMCID: PMC6975899 DOI: 10.2142/biophysico.16.0_490] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 11/15/2019] [Indexed: 12/02/2022] Open
Abstract
Bohr, Hasselbalch and Krogh demonstrated a group of sigmoid curves under various carbon dioxide contents in 1904. Hill fitted these curves in 1910 with Hill equation without the physical meanings of Hill coefficient and dissociation constant. In 1965, Monod-Wyman-Changeux model (MWC) popularized the word “allostery” with 81 words of symmetry to define an orthosteric nature of cooperativity in a single and symmetric sigmoid curve. Paradoxically the MWC model didn’t quantify the homotropic Hill coefficient and confusingly described the symmetry of sigmoid shapes with three allosteric variables. A heterotropic Bohr equation, by clarifying the biophysical symmetry in allostery, suggests the solution of allosteric coefficients with only one Bohr variable. We reveal that the mathematical need of a fictional monomer by MWC model justify a symmetric logistic curve with a parabolic kernel of dissociation constant to model the 1904 sigmoid curves. The logistic-derived Bohr equation and its half-saturated P50 equation successfully used the embedded P50 values in the 1904 sigmoidal curves to quantify their hyperbolic conformational shifts and Hill coefficients (n) pending for a century. Both are the logarithmic functions of carbon dioxide. This truly quantitative Bohr equation digitizes the allosteric regulation of the orthosteric affinity by precisely cloning the original group of dissociation/association curves published in 1904. The Bohr equation honestly suggests that nature should have chosen the allosteric Bohr effects to modify hemoglobin to cope with the swift dynamic of gas exchange. The discovery of the Bohr function in Bohr equation challenges the feasibility of the orthosteric cooperativity of hemoglobin.
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Affiliation(s)
- Lihsin Lee
- Independent Physician of Anesthesia Former Director, Anesthesiology, Taiwan Adventist Hospital, Taipei City 10556, Taiwan
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12
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Baeza-Centurion P, Miñana B, Schmiedel JM, Valcárcel J, Lehner B. Combinatorial Genetics Reveals a Scaling Law for the Effects of Mutations on Splicing. Cell 2019; 176:549-563.e23. [PMID: 30661752 DOI: 10.1016/j.cell.2018.12.010] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 08/29/2018] [Accepted: 12/07/2018] [Indexed: 02/08/2023]
Abstract
Despite a wealth of molecular knowledge, quantitative laws for accurate prediction of biological phenomena remain rare. Alternative pre-mRNA splicing is an important regulated step in gene expression frequently perturbed in human disease. To understand the combined effects of mutations during evolution, we quantified the effects of all possible combinations of exonic mutations accumulated during the emergence of an alternatively spliced human exon. This revealed that mutation effects scale non-monotonically with the inclusion level of an exon, with each mutation having maximum effect at a predictable intermediate inclusion level. This scaling is observed genome-wide for cis and trans perturbations of splicing, including for natural and disease-associated variants. Mathematical modeling suggests that competition between alternative splice sites is sufficient to cause this non-linearity in the genotype-phenotype map. Combining the global scaling law with specific pairwise interactions between neighboring mutations allows accurate prediction of the effects of complex genotype changes involving >10 mutations.
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Affiliation(s)
- Pablo Baeza-Centurion
- Systems Biology Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, 08003 Barcelona, Spain
| | - Belén Miñana
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, 08003 Barcelona, Spain
| | - Jörn M Schmiedel
- Systems Biology Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, 08003 Barcelona, Spain
| | - Juan Valcárcel
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys 23, 08010 Barcelona, Spain.
| | - Ben Lehner
- Systems Biology Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, 08003 Barcelona, Spain; Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, 08003 Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys 23, 08010 Barcelona, Spain.
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13
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Gutheil WG. Derivation and numerical profile analysis of a hierarchically formulated microscopic model of hemoglobin oxygen binding. Biophys Chem 2018; 241:38-49. [PMID: 30099247 DOI: 10.1016/j.bpc.2018.07.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 07/25/2018] [Accepted: 07/28/2018] [Indexed: 10/28/2022]
Abstract
To address complex thermodynamic systems with multiple interacting events, we have developed the concept of hierarchical thermodynamic interactions. In this study, this concept is extended to protein-ligand systems with similar but not identical protein subunits, and applied to the analysis of previously published NMR and UV-vis monitored hemoglobin oxygen binding data. Non-linear regression provided estimated errors for statistically significant parameters, but not for null (zero) valued parameters. A numerical/graphical profiling approach was therefore used to assess confidence intervals and correlations for both the statistically significant and nulled valued parameters in this model. Individual parameters were set to fixed values around their best-fit value, and the subset of statistically significant parameters re-minimized against hemoglobin oxygen binding data. Plots provide a graphical representation of parameter confidence intervals and correlations, and demonstrate how the two different data types - UV-vis and NMR - constrain the range of values for each parameter. This analysis further illustrates the value of hierarchically formulated models for the analysis of complex state systems, and illuminates the complexity of parameter space around the derived minimum microscopic model of hemoglobin oxygen binding.
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Affiliation(s)
- William G Gutheil
- School of Pharmacy, Division of Pharmaceutical Sciences, University of Missouri Kansas City, 2464 Charlotte Street, Kansas City, MO 64108, USA.
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14
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Schay G, Kaposi AD, Smeller L, Szigeti K, Fidy J, Herenyi L. Dissimilar flexibility of α and β subunits of human adult hemoglobin influences the protein dynamics and its alteration induced by allosteric effectors. PLoS One 2018; 13:e0194994. [PMID: 29584765 PMCID: PMC5871000 DOI: 10.1371/journal.pone.0194994] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 03/14/2018] [Indexed: 12/19/2022] Open
Abstract
The general question by what mechanism an "effector" molecule and the hemes of hemoglobin interact over widely separated intramolecular distances to change the oxygen affinity has been extensively investigated, and still has remained of central interest. In the present work we were interested in clarifying the general role of the protein matrix and its dynamics in the regulation of human adult hemoglobin (HbA). We used a spectroscopy approach that yields the compressibility (κ) of the protein matrix around the hemes of the subunits in HbA and studied how the binding of heterotropic allosteric effectors modify this parameter. κ is directly related to the variance of volume fluctuation, therefore it characterizes the molecular dynamics of the protein structure. For the experiments the heme groups either in the α or in the β subunits of HbA were replaced by fluorescent Zn-protoporphyrinIX, and series of fluorescence line narrowed spectra were measured at varied pressures. The evaluation of the spectra yielded the compressibility that showed significant dynamic asymmetry between the subunits: κ of the α subunit was 0.17±0.05/GPa, while for the β subunit it was much higher, 0.36±0.07/GPa. The heterotropic effectors, chloride ions, inositol hexaphosphate and bezafibrate did not cause significant changes in κ of the α subunits, while in the β subunits the effectors lead to a significant reduction down to 0.15±0.04/GPa. We relate our results to structural data, to results of recent functional studies and to those of molecular dynamics simulations, and find good agreements. The observed asymmetry in the flexibility suggests a distinct role of the subunits in the regulation of Hb that results in the observed changes of the oxygen binding capability.
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Affiliation(s)
- Gusztáv Schay
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary
| | - András D. Kaposi
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary
| | - László Smeller
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary
| | - Krisztián Szigeti
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary
| | - Judit Fidy
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary
| | - Levente Herenyi
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary
- * E-mail:
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Khasnis MD, Halkidis K, Bhardwaj A, Root MJ. Receptor Activation of HIV-1 Env Leads to Asymmetric Exposure of the gp41 Trimer. PLoS Pathog 2016; 12:e1006098. [PMID: 27992602 PMCID: PMC5222517 DOI: 10.1371/journal.ppat.1006098] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Revised: 01/09/2017] [Accepted: 11/29/2016] [Indexed: 11/18/2022] Open
Abstract
Structural rearrangements of HIV-1 glycoprotein Env promote viral entry through membrane fusion. Env is a symmetric homotrimer with each protomer composed of surface subunit gp120 and transmembrane subunit gp41. Cellular CD4- and chemokine receptor-binding to gp120 coordinate conformational changes in gp41, first to an extended prehairpin intermediate (PHI) and, ultimately, into a fusogenic trimer-of-hairpins (TOH). HIV-1 fusion inhibitors target gp41 in the PHI and block TOH formation. To characterize structural transformations into and through the PHI, we employed asymmetric Env trimers containing both high and low affinity binding sites for individual fusion inhibitors. Asymmetry was achieved using engineered Env heterotrimers composed of protomers deficient in either CD4- or chemokine receptor-binding. Linking receptor engagement to inhibitor affinity allowed us to assess conformational changes of individual Env protomers in the context of a functioning trimer. We found that the transition into the PHI could occur symmetrically or asymmetrically depending on the stoichiometry of CD4 binding. Sequential engagement of multiple CD4s promoted progressive exposure of individual fusion inhibitor binding sites in a CD4-dependent fashion. By contrast, engagement of only a single CD4 molecule led to a delayed, but symmetric, exposure of the gp41 trimer. This complex coupling between Env-CD4 interaction and gp41 exposure explained the multiphasic fusion-inhibitor titration observed for a mutant Env homotrimer with a naturally asymmetric gp41. Our results suggest that the spatial and temporal exposure of gp41 can proceed in a nonconcerted, asymmetric manner depending on the number of CD4s that engage the Env trimer. The findings have important implications for the mechanism of viral membrane fusion and the development of vaccine candidates designed to elicit neutralizing antibodies targeting gp41 in the PHI. For HIV, cellular invasion requires merging viral and cellular membranes, an event achieved through the activity of the viral fusion protein Env. Env consists of three gp120 and three gp41 subunits symmetrically arranged on the viral surface. The gp120 subunits bind cellular receptors, which, in turn, coordinate gp41 conformational changes that promote membrane fusion. Understanding these structural rearrangements illuminates the mechanism of viral membrane fusion, and also spurs development of targeted inhibitors of viral entry and vaccine candidates that elicit antiviral immune responses. In this study, we employed a novel strategy to investigate individual subunits in the context of functioning Env complexes. The strategy links distinct gp120-receptor interactions to conformational changes that expose specific gp41 subunits. We found that, despite the initial symmetric arrangement of its subunits, Env conformational changes most often proceed quite asymmetrically, leading to exposure of only one-third of the gp41 trimer for much of the fusion event. This finding might explain why attempts to elicit potent anti-HIV antibodies to a fully exposed gp41 trimer have been largely unsuccessful. The study gives us a glimpse of the early structural transitions leading to Env-mediated membrane fusion and provides a framework for interrogating the fusion proteins of other membrane-encapsulated viruses.
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Affiliation(s)
- Mukta D. Khasnis
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, United States of America
| | - Konstantine Halkidis
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, United States of America
| | - Anshul Bhardwaj
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, United States of America
| | - Michael J. Root
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, United States of America
- * E-mail:
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16
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Howe EN, Ball GE, Thordarson P. Step-by-step DFT analysis of the cooperativity in the binding of cations and anions to a tetratopic ion-pairing host. Supramol Chem 2015. [DOI: 10.1080/10610278.2015.1088946] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Ethan N.W. Howe
- School of Chemistry, The University of New South Wales, Sydney, Australia
- Australian Centre for Nanomedicine and the ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, The University of New South Wales, Sydney, Australia
| | - Graham E. Ball
- School of Chemistry, The University of New South Wales, Sydney, Australia
| | - Pall Thordarson
- School of Chemistry, The University of New South Wales, Sydney, Australia
- Australian Centre for Nanomedicine and the ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, The University of New South Wales, Sydney, Australia
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17
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Nagatomo S, Nagai Y, Aki Y, Sakurai H, Imai K, Mizusawa N, Ogura T, Kitagawa T, Nagai M. An Origin of Cooperative Oxygen Binding of Human Adult Hemoglobin: Different Roles of the α and β Subunits in the α2β2 Tetramer. PLoS One 2015; 10:e0135080. [PMID: 26244770 PMCID: PMC4526547 DOI: 10.1371/journal.pone.0135080] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Accepted: 07/17/2015] [Indexed: 02/02/2023] Open
Abstract
Human hemoglobin (Hb), which is an α2β2 tetramer and binds four O2 molecules, changes its O2-affinity from low to high as an increase of bound O2, that is characterized by 'cooperativity'. This property is indispensable for its function of O2 transfer from a lung to tissues and is accounted for in terms of T/R quaternary structure change, assuming the presence of a strain on the Fe-histidine (His) bond in the T state caused by the formation of hydrogen bonds at the subunit interfaces. However, the difference between the α and β subunits has been neglected. To investigate the different roles of the Fe-His(F8) bonds in the α and β subunits, we investigated cavity mutant Hbs in which the Fe-His(F8) in either α or β subunits was replaced by Fe-imidazole and F8-glycine. Thus, in cavity mutant Hbs, the movement of Fe upon O2-binding is detached from the movement of the F-helix, which is supposed to play a role of communication. Recombinant Hb (rHb)(αH87G), in which only the Fe-His in the α subunits is replaced by Fe-imidazole, showed a biphasic O2-binding with no cooperativity, indicating the coexistence of two independent hemes with different O2-affinities. In contrast, rHb(βH92G), in which only the Fe-His in the β subunits is replaced by Fe-imidazole, gave a simple high-affinity O2-binding curve with no cooperativity. Resonance Raman, 1H NMR, and near-UV circular dichroism measurements revealed that the quaternary structure change did not occur upon O2-binding to rHb(αH87G), but it did partially occur with O2-binding to rHb(βH92G). The quaternary structure of rHb(αH87G) appears to be frozen in T while its tertiary structure is changeable. Thus, the absence of the Fe-His bond in the α subunit inhibits the T to R quaternary structure change upon O2-binding, but its absence in the β subunit simply enhances the O2-affinity of α subunit.
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Affiliation(s)
- Shigenori Nagatomo
- Department of Chemistry, University of Tsukuba, Tsukuba, Ibaraki, Japan
- * E-mail: (SN); (TK); (MN)
| | - Yukifumi Nagai
- Research Center for Micro-Nano Technology, Hosei University, Koganei, Tokyo, Japan,3 School of Health Sciences, College of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa, Ishikawa, Japan,4 Department of Frontier Biosciences, Hosei University, Koganei, Tokyo, Japan,5 Picobiology Institute, Graduate School of Life Science, University of Hyogo, RSC-UH Leading Program Center, Sayo, Sayo-gun, Hyogo, Japan
| | - Yayoi Aki
- Research Center for Micro-Nano Technology, Hosei University, Koganei, Tokyo, Japan,3 School of Health Sciences, College of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa, Ishikawa, Japan,4 Department of Frontier Biosciences, Hosei University, Koganei, Tokyo, Japan,5 Picobiology Institute, Graduate School of Life Science, University of Hyogo, RSC-UH Leading Program Center, Sayo, Sayo-gun, Hyogo, Japan
| | - Hiroshi Sakurai
- Research Center for Micro-Nano Technology, Hosei University, Koganei, Tokyo, Japan,3 School of Health Sciences, College of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa, Ishikawa, Japan,4 Department of Frontier Biosciences, Hosei University, Koganei, Tokyo, Japan,5 Picobiology Institute, Graduate School of Life Science, University of Hyogo, RSC-UH Leading Program Center, Sayo, Sayo-gun, Hyogo, Japan
| | - Kiyohiro Imai
- Research Center for Micro-Nano Technology, Hosei University, Koganei, Tokyo, Japan,3 School of Health Sciences, College of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa, Ishikawa, Japan,4 Department of Frontier Biosciences, Hosei University, Koganei, Tokyo, Japan,5 Picobiology Institute, Graduate School of Life Science, University of Hyogo, RSC-UH Leading Program Center, Sayo, Sayo-gun, Hyogo, Japan
| | - Naoki Mizusawa
- Research Center for Micro-Nano Technology, Hosei University, Koganei, Tokyo, Japan,3 School of Health Sciences, College of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa, Ishikawa, Japan,4 Department of Frontier Biosciences, Hosei University, Koganei, Tokyo, Japan,5 Picobiology Institute, Graduate School of Life Science, University of Hyogo, RSC-UH Leading Program Center, Sayo, Sayo-gun, Hyogo, Japan
| | - Takashi Ogura
- Research Center for Micro-Nano Technology, Hosei University, Koganei, Tokyo, Japan,3 School of Health Sciences, College of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa, Ishikawa, Japan,4 Department of Frontier Biosciences, Hosei University, Koganei, Tokyo, Japan,5 Picobiology Institute, Graduate School of Life Science, University of Hyogo, RSC-UH Leading Program Center, Sayo, Sayo-gun, Hyogo, Japan
| | - Teizo Kitagawa
- Research Center for Micro-Nano Technology, Hosei University, Koganei, Tokyo, Japan,3 School of Health Sciences, College of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa, Ishikawa, Japan,4 Department of Frontier Biosciences, Hosei University, Koganei, Tokyo, Japan,5 Picobiology Institute, Graduate School of Life Science, University of Hyogo, RSC-UH Leading Program Center, Sayo, Sayo-gun, Hyogo, Japan
- * E-mail: (SN); (TK); (MN)
| | - Masako Nagai
- Research Center for Micro-Nano Technology, Hosei University, Koganei, Tokyo, Japan,3 School of Health Sciences, College of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa, Ishikawa, Japan,4 Department of Frontier Biosciences, Hosei University, Koganei, Tokyo, Japan,5 Picobiology Institute, Graduate School of Life Science, University of Hyogo, RSC-UH Leading Program Center, Sayo, Sayo-gun, Hyogo, Japan
- * E-mail: (SN); (TK); (MN)
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18
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Oh J, Yoon H, Sung YM, Kang P, Choi MG, Jang WD, Kim D. Modulation of Axial-Ligand Binding and Releasing Processes onto the Triazole-Bearing Nickel(II) Picket-Fence Porphyrins: Steric Repulsion versus Hydrogen-Bonding Effects. J Phys Chem B 2015; 119:7053-61. [DOI: 10.1021/acs.jpcb.5b03033] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Juwon Oh
- Spectroscopy
Laboratory for Functional π-Electronic Systems
and Department of Chemistry, ‡Biopolymer Laboratory and Department of Chemistry, and §Molecular Structure
Laboratory and Department of Chemistry, Yonsei University, Seoul 120-749, Korea
| | - Hongsik Yoon
- Spectroscopy
Laboratory for Functional π-Electronic Systems
and Department of Chemistry, ‡Biopolymer Laboratory and Department of Chemistry, and §Molecular Structure
Laboratory and Department of Chemistry, Yonsei University, Seoul 120-749, Korea
| | - Young Mo Sung
- Spectroscopy
Laboratory for Functional π-Electronic Systems
and Department of Chemistry, ‡Biopolymer Laboratory and Department of Chemistry, and §Molecular Structure
Laboratory and Department of Chemistry, Yonsei University, Seoul 120-749, Korea
| | - Philjae Kang
- Spectroscopy
Laboratory for Functional π-Electronic Systems
and Department of Chemistry, ‡Biopolymer Laboratory and Department of Chemistry, and §Molecular Structure
Laboratory and Department of Chemistry, Yonsei University, Seoul 120-749, Korea
| | - Moon-Gun Choi
- Spectroscopy
Laboratory for Functional π-Electronic Systems
and Department of Chemistry, ‡Biopolymer Laboratory and Department of Chemistry, and §Molecular Structure
Laboratory and Department of Chemistry, Yonsei University, Seoul 120-749, Korea
| | - Woo-Dong Jang
- Spectroscopy
Laboratory for Functional π-Electronic Systems
and Department of Chemistry, ‡Biopolymer Laboratory and Department of Chemistry, and §Molecular Structure
Laboratory and Department of Chemistry, Yonsei University, Seoul 120-749, Korea
| | - Dongho Kim
- Spectroscopy
Laboratory for Functional π-Electronic Systems
and Department of Chemistry, ‡Biopolymer Laboratory and Department of Chemistry, and §Molecular Structure
Laboratory and Department of Chemistry, Yonsei University, Seoul 120-749, Korea
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19
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Experiments on Hemoglobin in Single Crystals and Silica Gels Distinguish among Allosteric Models. Biophys J 2015; 109:1264-72. [PMID: 26038112 DOI: 10.1016/j.bpj.2015.04.037] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Accepted: 04/24/2015] [Indexed: 01/14/2023] Open
Abstract
Trapping quaternary structures of hemoglobin in single crystals or by encapsulation in silica gels has provided a demanding set of data to test statistical mechanical models of allostery. In this work, we compare the results of those experiments with predictions of the four major allosteric models for hemoglobin: the quaternary two-state model of Monod, Wyman, and Changeux; the tertiary two-state model of Henry et al., which is the simplest extension of the Monod-Wyman-Changeux model to include pre-equilibria of tertiary as well as quaternary conformations; the structure-based model of Szabo and Karplus; and the modification of the latter model by Lee and Karplus. We show that only the tertiary two-state model can provide a near quantitative explanation of the single-crystal and gel experimental results.
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20
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Structural basis for cooperative oxygen binding and bracelet-assisted assembly of Lumbricus terrestris hemoglobin. Sci Rep 2015; 5:9494. [PMID: 25897633 PMCID: PMC5383013 DOI: 10.1038/srep09494] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Accepted: 03/04/2015] [Indexed: 11/25/2022] Open
Abstract
The iron-containing hemoglobins (Hbs) are essential proteins to serve as oxygen transporters in the blood. Among various kinds of Hbs, the earthworm Hbs are the champions in carrying oxygen due to not only their large size but also the unusually high cooperativity of ligand binding. However, the cooperative oxygen binding mechanisms are still mostly unknown. Here we report the cryo-electron microscopy structure of Lumbricus terrestris Hb in its native, oxygenated state at 9.1 Å resolution, showing remarkable differences from the carbon monoxide-binding X-ray structure. Our structural analysis first indicates that the cooperative ligand binding of L. terrestris Hb requires tertiary and quaternary transitions in the heme pocket and a global subunit movement facilitated by intra-ring and inter-ring contacts. Moreover, the additional sinusoidal bracelet provides the confirmation for the long-standing debate about the additional electron densities absent in the X-ray crystal structure.
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21
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Caraglio M, Imparato A. Energy transfer in molecular devices. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2014; 90:062712. [PMID: 25615134 DOI: 10.1103/physreve.90.062712] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Indexed: 06/04/2023]
Abstract
Protein machines often exhibit long-range interplay between different sites in order to achieve their biological tasks. We investigate and characterize the nonlinear energy localization and the basic mechanisms of energy transfer in protein devices. By studying two different model protein machines, with different biological functions, we show that genuinely nonlinear phenomena are responsible for energy transport between the different machine sites involved in the biological functions. The energy transfer turns out to be extremely efficient from an energetic point of view: by changing the energy initially provided to the model device, we identify a well defined range of energies where the time for the energy transport to occur is minimal and the amount of transferred energy is a maximum. Furthermore, by introducing an implicit solvent, we show that the energy is localized on the internal residues of the protein structure, thus minimizing the dissipation.
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Affiliation(s)
- M Caraglio
- Dipartimento di Fisica e Astronomia, Sezione INFN, Università di Padova, Via Marzolo 8, I-35131 Padova, Italy
| | - A Imparato
- Department of Physics and Astronomy, University of Aarhus, Ny Munkegade, Building 1520, DK-8000 Aarhus C, Denmark
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22
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You Y, Liu F, Du KJ, Wen GB, Lin YW. Structural and functional alterations of myoglobin by glucose-protein interactions. J Mol Model 2014; 20:2358. [DOI: 10.1007/s00894-014-2358-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2014] [Accepted: 06/15/2014] [Indexed: 11/29/2022]
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23
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Lin YW, Wang J. Structure and function of heme proteins in non-native states: a mini-review. J Inorg Biochem 2013; 129:162-71. [PMID: 23916118 DOI: 10.1016/j.jinorgbio.2013.07.023] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Revised: 07/11/2013] [Accepted: 07/13/2013] [Indexed: 12/12/2022]
Abstract
Heme proteins perform various biological functions ranging from electron transfer, oxygen binding and transport, catalysis, to signaling. Although adopting proper native states is very important for these functions, progresses in representative heme proteins, including cytochrome c (cyt c), cytochrome b5 (cyt b5), myoglobin (Mb), neuroglobin (Ngb), cytochrome P450 (CYP) and heme-based sensor proteins such as CO sensor CooA, showed that various native functions, or new functions evolved, are also closely associated with non-native states. The structure and function relationship of heme proteins in non-native states is thus as important as that in native states for elucidating the precise roles of heme proteins in biological systems.
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Affiliation(s)
- Ying-Wu Lin
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China.
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24
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Ronda L, Bettati S, Henry ER, Kashav T, Sanders JM, Royer WE, Mozzarelli A. Tertiary and quaternary allostery in tetrameric hemoglobin from Scapharca inaequivalvis. Biochemistry 2013; 52:2108-17. [PMID: 23458680 DOI: 10.1021/bi301620x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The clam Scapharca inaequivalvis possesses two cooperative oxygen binding hemoglobins in its red cells: a homodimeric HbI and a heterotetrameric A2B2 HbII. Each AB dimeric half of HbII is assembled in a manner very similar to that of the well-studied HbI. This study presents crystal structures of HbII along with oxygen binding data both in the crystalline state and in wet nanoporous silica gels. Despite very similar ligand-linked structural transitions observed in HbI and HbII crystals, HbII in the crystal or encapsulated in silica gels apparently exhibits minimal cooperativity in oxygen binding, in contrast with the full cooperativity exhibited by HbI crystals. However, oxygen binding curves in the crystal indicate the presence of a significant functional inequivalence of A and B chains. When this inequivalence is taken into account, both crystal and R state gel functional data are consistent with the conservation of a tertiary contribution to cooperative oxygen binding, quantitatively similar to that measured for HbI, and are in keeping with the structural information. Furthermore, our results indicate that to fully express cooperative ligand binding, HbII requires quaternary transitions hampered by crystal lattice and gel encapsulation, revealing greater complexity in cooperative function than the direct communication across a dimeric interface observed in HbI.
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Affiliation(s)
- Luca Ronda
- Department of Pharmacy, University of Parma , Parco Area delle Scienze, 23/A, 43124 Parma, Italy
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25
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Sahún-Roncero M, Rubio-Ruiz B, Saladino G, Conejo-García A, Espinosa A, Velázquez-Campoy A, Gervasio FL, Entrena A, Hurtado-Guerrero R. The mechanism of allosteric coupling in choline kinase α1 revealed by the action of a rationally designed inhibitor. Angew Chem Int Ed Engl 2013; 52:4582-6. [PMID: 23441033 DOI: 10.1002/anie.201209660] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2012] [Revised: 01/16/2013] [Indexed: 01/21/2023]
Abstract
Applying a CHOK hold: Combined experimental and computational studies of the binding mode of a rationally designed inhibitor of the dimeric choline kinase α1 (CHOKα1) explain the molecular mechanism of negative cooperativity (see scheme) and how the monomers are connected. The results give insight into how the symmetry of the dimer can be partially conserved despite a lack of conservation in the static crystal structures.
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Affiliation(s)
- María Sahún-Roncero
- Institute of Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza, BIFI-IQFR (CSIC) Joint Unit, Mariano Esquillor s/n, Campus Rio Ebro, Edificio I+D; Fundacion ARAID, Edificio Pignatelli 36, Spain
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26
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Sahún-Roncero M, Rubio-Ruiz B, Saladino G, Conejo-García A, Espinosa A, Velázquez-Campoy A, Gervasio FL, Entrena A, Hurtado-Guerrero R. The Mechanism of Allosteric Coupling in Choline Kinase α1 Revealed by the Action of a Rationally Designed Inhibitor. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201209660] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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27
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Selwood T, Jaffe EK. Dynamic dissociating homo-oligomers and the control of protein function. Arch Biochem Biophys 2012; 519:131-43. [PMID: 22182754 PMCID: PMC3298769 DOI: 10.1016/j.abb.2011.11.020] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2011] [Revised: 11/16/2011] [Accepted: 11/28/2011] [Indexed: 11/20/2022]
Abstract
Homo-oligomeric protein assemblies are known to participate in dynamic association/disassociation equilibria under native conditions, thus creating an equilibrium of assembly states. Such quaternary structure equilibria may be influenced in a physiologically significant manner either by covalent modification or by the non-covalent binding of ligands. This review follows the evolution of ideas about homo-oligomeric equilibria through the 20th and into the 21st centuries and the relationship of these equilibria to allosteric regulation by the non-covalent binding of ligands. A dynamic quaternary structure equilibria is described where the dissociated state can have alternate conformations that cannot reassociate to the original multimer; the alternate conformations dictate assembly to functionally distinct alternate multimers of finite stoichiometry. The functional distinction between different assemblies provides a mechanism for allostery. The requirement for dissociation distinguishes this morpheein model of allosteric regulation from the classical MWC concerted and KNF sequential models. These models are described alongside earlier dissociating allosteric models. The identification of proteins that exist as an equilibrium of diverse native quaternary structure assemblies has the potential to define new targets for allosteric modulation with significant consequences for further understanding and/or controlling protein structure and function. Thus, a rationale for identifying proteins that may use the morpheein model of allostery is presented and a selection of proteins for which published data suggests this mechanism may be operative are listed.
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Affiliation(s)
- Trevor Selwood
- Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA, 19111
| | - Eileen K. Jaffe
- Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA, 19111
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28
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Kinetic trapping of a key hemoglobin intermediate. Methods Mol Biol 2012; 796:19-29. [PMID: 22052483 DOI: 10.1007/978-1-61779-334-9_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The complete binding cascade of human hemoglobin consists of a series of partially ligated intermediates. The individual intermediate binding constants cannot be distinguished in O(2) binding curves, however, each constant can be determined from the O(2)-induced change in assembly constant for the α(2)β(2) tetramer from its constituent αβ dimers. The characterization of these O(2) binding constants has shown the Hb cascade to be asymmetric in nature, with binding dependent upon the specific distribution of O(2) among the four hemesites. A stopped-flow approach to measuring the dissociation constant of a key doubly ligated intermediate, that in which one dimer is oxygenated and the other is not, is described. The intermediate is transiently formed in the absence of O(2) and then allowed to dissociate in the presence of O(2). The free dimers thus released are trapped by the plasma protein haptoglobin, the rate limiting step being that of tetramer dissociation. The kinetic constant observed for the dissociation of this intermediate confirms the value for its equilibrium O(2) binding constant, previously determined under equilibrium conditions by subzero isoelectric focusing.
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29
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Kano K, Chimoto S, Tamaki M, Itoh Y, Kitagishi H. Supramolecular dioxygen receptors composed of an anionic water-soluble porphinatoiron(ii) and cyclodextrin dimers. Dalton Trans 2012; 41:453-61. [DOI: 10.1039/c1dt11596k] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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30
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Shibayama N. Symmetry distortion in the human hemoglobin tetramer induced by asymmetric ligation. FEBS Lett 2011; 586:74-8. [DOI: 10.1016/j.febslet.2011.11.027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2011] [Revised: 11/23/2011] [Accepted: 11/23/2011] [Indexed: 10/14/2022]
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31
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Shea MA, Correia JJ, Brenowitz MD. Introduction: twenty five years of the Gibbs Conference on Biothermodynamics. Biophys Chem 2011; 159:1-5. [PMID: 21840113 DOI: 10.1016/j.bpc.2011.07.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2011] [Accepted: 07/05/2011] [Indexed: 11/16/2022]
Abstract
In 2011, the Gibbs Conference on Biothermodynamics will celebrate its 25th anniversary. Since the inaugural meeting in 1987, it has brought together laboratories that lived, breathed and argued about the molecular logic of macromolecular machines. The participants have a deep commitment to understanding the nature of physico-chemical forces that govern regulation of biological systems, and share a passion for applying linkage theory. The collective goal is to understand how ligand binding, subunit assembly and conformational change drive what we observe as physiological processes such as regulated transport, enzyme cascades, gene regulation, membrane permeability, viral infection, intracellular trafficking and folding of macromolecules. In this special issue, articles by former organizers of the Gibbs Conference showcase the current breadth and depth of the field of biothermodynamics, and how thoroughly it is integrated with the study of macromolecular structures, computational modeling and physiological studies of human health and disease.
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Nagatomo S, Nagai M, Kitagawa T. A New Way To Understand Quaternary Structure Changes of Hemoglobin upon Ligand Binding On the Basis of UV-Resonance Raman Evaluation of Intersubunit Interactions. J Am Chem Soc 2011; 133:10101-10. [DOI: 10.1021/ja111370f] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Shigenori Nagatomo
- Department of Chemistry, University of Tsukuba, Tsukuba, Ibaraki 305-8571, Japan
| | - Masako Nagai
- Research Center for Micro-Nano Technology, Hosei University, Koganei, Tokyo 184-0003, Japan
| | - Teizo Kitagawa
- Picobiology Institute, Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigori, Ako-gun, Hyogo 678-1297, Japan
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Schay G, Herényi L, Kellermayer M, Módos K, Yonetani T, Fidy J. Millisecond Time-Scale Protein Dynamics Exists Prior to the Activation of the Bulk Solvent Matrix. J Phys Chem B 2011; 115:5707-15. [DOI: 10.1021/jp106755t] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Gusztáv Schay
- Semmelweis University Budapest, Department of Biophysics and Radiation Biology, P.O. Box 263, H-1444 Budapest, Hungary
| | - Levente Herényi
- Semmelweis University Budapest, Department of Biophysics and Radiation Biology, P.O. Box 263, H-1444 Budapest, Hungary
| | - Miklós Kellermayer
- Semmelweis University Budapest, Department of Biophysics and Radiation Biology, P.O. Box 263, H-1444 Budapest, Hungary
| | - Károly Módos
- Semmelweis University Budapest, Department of Biophysics and Radiation Biology, P.O. Box 263, H-1444 Budapest, Hungary
| | - Takashi Yonetani
- Department of Biochemistry and Biophysics, University of Pennsylvania School of Medicine and the Johnson Research Foundation, Philadelphia, Pennsylvania 19104-6059, United States
| | - Judit Fidy
- Semmelweis University Budapest, Department of Biophysics and Radiation Biology, P.O. Box 263, H-1444 Budapest, Hungary
- Research Group for Membrane Biology, Hungarian Academy of Sciences, Budapest, Hungary
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Peracchi A, Mozzarelli A. Exploring and exploiting allostery: Models, evolution, and drug targeting. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2010; 1814:922-33. [PMID: 21035570 DOI: 10.1016/j.bbapap.2010.10.008] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2010] [Revised: 10/19/2010] [Accepted: 10/20/2010] [Indexed: 12/11/2022]
Abstract
The concept of allostery was elaborated almost 50years ago by Monod and coworkers to provide a framework for interpreting experimental studies on the regulation of protein function. In essence, binding of a ligand at an allosteric site affects the function at a distant site exploiting protein flexibility and reshaping protein energy landscape. Both monomeric and oligomeric proteins can be allosteric. In the past decades, the behavior of allosteric systems has been analyzed in many investigations while general theoretical models and variations thereof have been steadily proposed to interpret the experimental data. Allostery has been established as a fundamental mechanism of regulation in all organisms, governing a variety of processes that range from metabolic control to receptor function and from ligand transport to cell motility. A number of studies have shed light on how evolutionary pressures have favored and molded the development of allosteric features in specific macromolecular systems. The widespread occurrence of allostery has been recently exploited for the development and design of allosteric drugs that bind to either physiological or non-physiological allosteric sites leading to gain of function or loss of function. This article is part of a Special Issue entitled: Protein Dynamics: Experimental and Computational Approaches.
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Affiliation(s)
- Alessio Peracchi
- Department of Biochemistry and Molecular Biology, University of Parma, Parma, Italy.
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Abstract
The Hill coefficient nH is a dimensionless parameter that has long been used as a measure of the extent of cooperativity. Originally derived from the oxygen-binding curve of human hemoglobin (Hb) by A. V. Hill in 1910, and reinvented by J. Wyman several decades later, nH is indexed to the stoichiometry of ligation and is indirectly related to the overall cooperative free energy for binding all four oxygen ligands. However, the overall cooperative free energy of Hb ligation can be measured directly by experimental methods. The microscopic cooperative free energies that relate to energetic coupling between specific subunit pairs can also be experimentally determined, while the Hill coefficient is, by its nature, a macroscopic parameter that cannot detect differences among specific subunit-subunit couplings. Its continued use in studies of the mechanism of cooperativity in Hb is therefore of increasingly limited value.
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Fenton AW. Allostery: an illustrated definition for the 'second secret of life'. Trends Biochem Sci 2008; 33:420-5. [PMID: 18706817 DOI: 10.1016/j.tibs.2008.05.009] [Citation(s) in RCA: 217] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2008] [Revised: 05/15/2008] [Accepted: 05/28/2008] [Indexed: 11/29/2022]
Abstract
Although allosteric regulation is the 'second secret of life', the molecular mechanisms that give rise to allostery currently elude understanding. In my opinion, experimental progress is hampered by a commonly used but misleading definition of allostery as protein structural changes that are elicited by the binding of a single ligand. Allostery is more strictly defined in functional terms as a comparison of how one ligand binds in the absence, versus the presence, of a second ligand. Therefore, as each of the two binding events involves two protein complexes, a study of allostery must consider four complexes and not just two. Such a comparison can distinguish allosteric from non-allosteric protein changes, the importance of which is frequently overlooked. When a study of all four complexes is not feasible, an alternative, albeit limited, strategy can identify subsets of allosteric-specific changes.
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Affiliation(s)
- Aron W Fenton
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, 3901 Rainbow Boulevard, Kansas City, KS 66160, USA.
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Mutagenic Analysis of Membrane Protein Functional Mechanisms: Bacteriorhodopsin as a Model Example. Methods Cell Biol 2008. [DOI: 10.1016/s0091-679x(07)84016-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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Rana MS, Knapp JE, Holland RAB, Riggs AF. Component D of chicken hemoglobin and the hemoglobin of the embryonic Tammar wallaby (Macropus eugenii) self-associate upon deoxygenation: Effect on oxygen binding. Proteins 2007; 70:553-61. [DOI: 10.1002/prot.21793] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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