1
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Xu G, Wang Q, Ma J. OPUS-Mut: Studying the Effect of Protein Mutation through Side-Chain Modeling. J Chem Theory Comput 2023; 19:1629-1640. [PMID: 36813264 PMCID: PMC10018731 DOI: 10.1021/acs.jctc.2c00847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Abstract
Predicting the effect of protein mutation is crucial in many applications such as protein design, protein evolution, and genetic disease analysis. Structurally, mutation is basically the replacement of the side chain of a particular residue. Therefore, accurate side-chain modeling is useful in studying the effect of mutation. Here, we propose a computational method, namely, OPUS-Mut, which significantly outperforms other backbone-dependent side-chain modeling methods including our previous method OPUS-Rota4. We evaluate OPUS-Mut by four case studies on Myoglobin, p53, HIV-1 protease, and T4 lysozyme. The results show that the predicted structures of side chains of different mutants are consistent well with their experimentally determined results. In addition, when the residues with significant structural shifts upon the mutation are considered, it is found that the extent of the predicted structural shift of these affected residues can be correlated reasonably well with the functional changes of the mutant measured by experiments. OPUS-Mut can also help one to identify the harmful and benign mutations and thus may guide the construction of a protein with relatively low sequence homology but with a similar structure.
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Affiliation(s)
- Gang Xu
- Multiscale Research Institute of Complex Systems, Fudan University, Shanghai 200433, China.,Zhangjiang Fudan International Innovation Center, Fudan University, Shanghai 201210, China.,Shanghai AI Laboratory, Shanghai 200030, China
| | - Qinghua Wang
- Center for Biomolecular Innovation, Harcam Biomedicines, Shanghai 200131, China
| | - Jianpeng Ma
- Multiscale Research Institute of Complex Systems, Fudan University, Shanghai 200433, China.,Zhangjiang Fudan International Innovation Center, Fudan University, Shanghai 201210, China.,Shanghai AI Laboratory, Shanghai 200030, China
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2
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Wu G, Sharina I, Martin E. Soluble guanylyl cyclase: Molecular basis for ligand selectivity and action in vitro and in vivo. Front Mol Biosci 2022; 9:1007768. [PMID: 36304925 PMCID: PMC9592903 DOI: 10.3389/fmolb.2022.1007768] [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: 07/30/2022] [Accepted: 09/27/2022] [Indexed: 01/14/2023] Open
Abstract
Nitric oxide (NO), carbon monoxide (CO), oxygen (O2), hydrogen sulfide (H2S) are gaseous molecules that play important roles in the physiology and pathophysiology of eukaryotes. Tissue concentrations of these physiologically relevant gases vary remarkable from nM range for NO to high μM range of O2. Various hemoproteins play a significant role in sensing and transducing cellular signals encoded by gaseous molecules or in transporting them. Soluble guanylyl cyclase (sGC) is a hemoprotein that plays vital roles in a wide range of physiological functions and combines the functions of gaseous sensor and signal transducer. sGC uniquely evolved to sense low non-toxic levels of NO and respond to elevated NO levels by increasing its catalytic ability to generate the secondary signaling messenger cyclic guanosine monophosphate (cGMP). This review discusses sGC's gaseous ligand selectivity and the molecular basis for sGC function as high-affinity and selectivity NO receptor. The effects of other gaseous molecules and small molecules of cellular origin on sGC's function are also discussed.
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Affiliation(s)
- Gang Wu
- Hematology-Oncology Division, Department of Internal Medicine, The University of Texas—McGovern Medical School, Houston, TX, United States,*Correspondence: Gang Wu, ; Emil Martin,
| | - Iraida Sharina
- Cardiology Division, Department of Internal Medicine, The University of Texas—McGovern Medical School, Houston, TX, United States
| | - Emil Martin
- Cardiology Division, Department of Internal Medicine, The University of Texas—McGovern Medical School, Houston, TX, United States,*Correspondence: Gang Wu, ; Emil Martin,
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3
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Van Stappen C, Deng Y, Liu Y, Heidari H, Wang JX, Zhou Y, Ledray AP, Lu Y. Designing Artificial Metalloenzymes by Tuning of the Environment beyond the Primary Coordination Sphere. Chem Rev 2022; 122:11974-12045. [PMID: 35816578 DOI: 10.1021/acs.chemrev.2c00106] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Metalloenzymes catalyze a variety of reactions using a limited number of natural amino acids and metallocofactors. Therefore, the environment beyond the primary coordination sphere must play an important role in both conferring and tuning their phenomenal catalytic properties, enabling active sites with otherwise similar primary coordination environments to perform a diverse array of biological functions. However, since the interactions beyond the primary coordination sphere are numerous and weak, it has been difficult to pinpoint structural features responsible for the tuning of activities of native enzymes. Designing artificial metalloenzymes (ArMs) offers an excellent basis to elucidate the roles of these interactions and to further develop practical biological catalysts. In this review, we highlight how the secondary coordination spheres of ArMs influence metal binding and catalysis, with particular focus on the use of native protein scaffolds as templates for the design of ArMs by either rational design aided by computational modeling, directed evolution, or a combination of both approaches. In describing successes in designing heme, nonheme Fe, and Cu metalloenzymes, heteronuclear metalloenzymes containing heme, and those ArMs containing other metal centers (including those with non-native metal ions and metallocofactors), we have summarized insights gained on how careful controls of the interactions in the secondary coordination sphere, including hydrophobic and hydrogen bonding interactions, allow the generation and tuning of these respective systems to approach, rival, and, in a few cases, exceed those of native enzymes. We have also provided an outlook on the remaining challenges in the field and future directions that will allow for a deeper understanding of the secondary coordination sphere a deeper understanding of the secondary coordintion sphere to be gained, and in turn to guide the design of a broader and more efficient variety of ArMs.
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Affiliation(s)
- Casey Van Stappen
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Yunling Deng
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Yiwei Liu
- Department of Chemistry, University of Illinois, Urbana-Champaign, 505 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Hirbod Heidari
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Jing-Xiang Wang
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Yu Zhou
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Aaron P Ledray
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Yi Lu
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States.,Department of Chemistry, University of Illinois, Urbana-Champaign, 505 South Mathews Avenue, Urbana, Illinois 61801, United States
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4
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Foley EL, Hvitved AN, Eich RF, Olson JS. Mechanisms of nitric oxide reactions with Globins using mammalian myoglobin as a model system. J Inorg Biochem 2022; 233:111839. [DOI: 10.1016/j.jinorgbio.2022.111839] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 04/13/2022] [Accepted: 04/16/2022] [Indexed: 12/15/2022]
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5
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Jelinski J, Cortez M, Terwilliger A, Clark J, Maresso A. Loss of Dihydroxyacid Dehydratase Induces Auxotrophy in Bacillus anthracis. J Bacteriol 2021; 203:e0041521. [PMID: 34570623 PMCID: PMC8604071 DOI: 10.1128/jb.00415-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 09/14/2021] [Indexed: 11/20/2022] Open
Abstract
Anthrax disease is caused by infection with the bacteria Bacillus anthracis which, if left untreated, can result in fatal bacteremia and toxemia. Current treatment for infection requires prolonged administration of antibiotics. Despite this, inhalational and gastrointestinal anthrax still result in lethal disease. By identifying key metabolic steps that B. anthracis uses to grow in host-like environments, new targets for antibacterial strategies can be identified. Here, we report that the ilvD gene, which encodes dihydroxyacid dehydratase in the putative pathway for synthesizing branched chain amino acids, is necessary for B. anthracis to synthesize isoleucine de novo in an otherwise limiting microenvironment. We observed that ΔilvD B. anthracis cannot grow in media lacking isoleucine, but growth is restored when exogenous isoleucine is added. In addition, ΔilvD bacilli are unable to utilize human hemoglobin or serum albumin to overcome isoleucine auxotrophy, but can when provided with the murine forms. This species-specific effect is due to the lack of isoleucine in human hemoglobin. Furthermore, even when supplemented with physiological levels of human serum albumin, apotransferrin, fibrinogen, and IgG, the ilvD knockout strain grew poorly relative to nonsupplemented wild type. In addition, comparisons upon infecting humanized mice suggest that murine hemoglobin is a key source of isoleucine for both WT and ΔilvD bacilli. Further growth comparisons in murine and human blood show that the auxotrophy is detrimental for growth in human blood, not murine. This report identifies ilvD as necessary for isoleucine production in B. anthracis, and that it plays a key role in allowing the bacilli to effectively grow in isoleucine poor hosts. IMPORTANCE Anthrax disease, caused by B. anthracis, can cause lethal bacteremia and toxemia, even following treatment with antibiotics. This report identifies the ilvD gene, which encodes a dihydroxyacid dehydratase, as necessary for B. anthracis to synthesize the amino acid isoleucine in a nutrient-limiting environment, such as its mammalian host. The use of this strain further demonstrated a unique species-dependent utilization of hemoglobin as an exogenous source of extracellular isoleucine. By identifying mechanisms that B. anthracis uses to grow in host-like environments, new targets for therapeutic intervention are revealed.
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Affiliation(s)
- Joseph Jelinski
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Madeline Cortez
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Austen Terwilliger
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Justin Clark
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Anthony Maresso
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
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6
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Olson JS. Kinetic mechanisms for O 2 binding to myoglobins and hemoglobins. Mol Aspects Med 2021; 84:101024. [PMID: 34544605 DOI: 10.1016/j.mam.2021.101024] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 09/06/2021] [Accepted: 09/12/2021] [Indexed: 11/29/2022]
Abstract
Antonini and Brunori's 1971 book "Hemoglobin and Myoglobin in Their Reactions with Ligands" was a truly remarkable publication that summarized almost 100 years of research on O2 binding to these globins. Over the ensuing 50 years, ultra-fast laser photolysis techniques, high-resolution and time resolved X-ray crystallography, molecular dynamics simulations, and libraries of recombinant myoglobin (Mb) and hemoglobin (Hb) variants have provided structural interpretations of O2 binding to these proteins. The resultant mechanisms provide quantitative descriptions of the stereochemical factors that govern overall affinity, including proximal and distal steric restrictions that affect iron reactivity and favorable positive electrostatic interactions that preferentially stabilize bound O2. The pathway for O2 uptake and release by Mb and subunits of Hb has been mapped by screening libraries of site-directed mutants in laser photolysis experiments. O2 enters mammalian Mb and the α and β subunits of human HbA through a channel created by upward and outward rotation of the distal His at the E7 helical position, is non-covalently captured in the interior of the distal cavity, and then internally forms a bond with the heme Fe(II) atom. O2 dissociation is governed by disruption of hydrogen bonding interactions with His (E7), breakage of the Fe(II)-O2 bond, and then competition between rebinding and escape through the E7-gate. The structural features that govern the rates of both the individual steps and overall reactions have been determined and provide the framework for: (1) defining the physiological functions of specific globins and their evolution; (2) understanding the clinical features of hemoglobinopathies; and (3) designing safer and more efficient acellular hemoglobin-based oxygen carriers (HBOCs) for transfusion therapy, organ preservation, and other commercially relevant O2 transport and storage processes.
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Affiliation(s)
- John S Olson
- Department of Biosciences, Rice University, Houston, TX, 77005, USA.
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7
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Thompson MK, Shay MR, de Serrano V, Dumarieh R, Ghiladi RA, Franzen S. A new inhibition mechanism in the multifunctional catalytic hemoglobin dehaloperoxidase as revealed by the DHP A(V59W) mutant: A spectroscopic and crystallographic study. J PORPHYR PHTHALOCYA 2021. [DOI: 10.1142/s1088424621500826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
As multifunctional catalytic hemoglobins, dehaloperoxidase isoenzymes A and B (DHP A and B) are among the most versatile hemoproteins in terms of activities displayed. The ability of DHP to bind over twenty different substrates in the distal pocket might appear to resemble the promiscuousness of monooxygenase enzymes, yet there are identifiable substrate-specific interactions that can steer the type of oxidation (O-atom vs. electron transfer) that occurs inside the DHP distal pocket. Here, we have investigated the DHP A(V59W) mutant in order to probe the limits of conformational flexibility in the distal pocket as it relates to the genesis of this substrate-dependent activity differentiation. The X-ray crystal structure of the metaquo DHP A(V59W) mutant (PDB 3K3U) and the V59W mutant in complex with fluoride [denoted as DHP A(V59W-F)] (PDB 7MNH) show significant mobility of the tryptophan in the distal pocket, with two parallel conformations having W59-N[Formula: see text] H-bonded to a heme-bound ligand (H2O or F[Formula: see text], and another conformation [observed only in DHP A(V59W-F)] that brings W59 sufficiently close to the heme as to preclude axial ligand binding. UV-vis and resonance Raman spectroscopic studies show that DHP A(V59W) is 5-coordinate high spin (5cHS) at pH 5 and 6-coordinate high spin (6cHS) at pH 7, whereas DHP A(V59W-F) is 6cHS from pH 5 to 7. Enzyme assays confirm robust peroxidase activity at pH 5, but complete loss of activity at pH 7. We find no evidence that tryptophan plays a role in the oxidation mechanism ([Formula: see text]. radical formation). Instead, the data reveal a new mechanism of DHP inhibition, namely a shift towards a non-reactive form by OH[Formula: see text] ligation to the heme-Fe that is strongly stabilized (presumably through H-bonding interactions) by the presence of W59 in the distal cavity.
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Affiliation(s)
- Matthew K. Thompson
- Department of Chemistry & Biochemistry, University of Alabama, 250 Hackberry Lane, Tuscaloosa, AL 35487, USA
| | - Madeline R. Shay
- Department of Chemistry & Biochemistry, University of Alabama, 250 Hackberry Lane, Tuscaloosa, AL 35487, USA
| | - Vesna de Serrano
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695, USA
| | - Rania Dumarieh
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695, USA
| | - Reza A. Ghiladi
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695, USA
| | - Stefan Franzen
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695, USA
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8
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A new paradigm for gaseous ligand selectivity of hemoproteins highlighted by soluble guanylate cyclase. J Inorg Biochem 2020; 214:111267. [PMID: 33099233 DOI: 10.1016/j.jinorgbio.2020.111267] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 09/23/2020] [Accepted: 09/27/2020] [Indexed: 02/06/2023]
Abstract
Nitric oxide (NO), carbon monoxide (CO), and oxygen (O2) are important physiological messengers whose concentrations vary in a remarkable range, [NO] typically from nM to several μM while [O2] reaching to hundreds of μM. One of the machineries evolved in living organisms for gas sensing is sensor hemoproteins whose conformational change upon gas binding triggers downstream response cascades. The recently proposed "sliding scale rule" hypothesis provides a general interpretation for gaseous ligand selectivity of hemoproteins, identifying five factors that govern gaseous ligand selectivity. Hemoproteins have intrinsic selectivity for the three gases due to a neutral proximal histidine ligand while proximal strain of heme and distal steric hindrance indiscriminately adjust the affinity of these three gases for heme. On the other hand, multiple-step NO binding and distal hydrogen bond donor(s) specifically enhance affinity for NO and O2, respectively. The "sliding scale rule" hypothesis provides clear interpretation for dramatic selectivity for NO over O2 in soluble guanylate cyclase (sGC) which is an important example of sensor hemoproteins and plays vital roles in a wide range of physiological functions. The "sliding scale rule" hypothesis has so far been validated by all experimental data and it may guide future designs for heme-based gas sensors.
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9
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Tahara S, Mizuno M, Mizutani Y. Nonbonded Atomic Contacts Drive Ultrafast Helix Motions in Myoglobin. J Phys Chem B 2020; 124:5407-5414. [DOI: 10.1021/acs.jpcb.0c04772] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Shinya Tahara
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Misao Mizuno
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Yasuhisa Mizutani
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
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10
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Sacquin-Mora S. Coarse-grain simulations on NMR conformational ensembles highlight functional residues in proteins. J R Soc Interface 2019; 16:20190075. [PMID: 31288649 DOI: 10.1098/rsif.2019.0075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Dynamics are a key feature of protein function, and this is especially true of gating residues, which occupy cavity or tunnel lining positions in the protein structure, and will reversibly switch between open and closed conformations in order to control the diffusion of small molecules within a protein's internal matrix. Earlier work on globins and hydrogenases have shown that these gating residues can be detected using a multiscale scheme combining all-atom classic molecular dynamics simulations and coarse-grain calculations of the resulting conformational ensemble mechanical properties. Here, we show that the structural variations observed in the conformational ensembles produced by NMR spectroscopy experiments are sufficient to induce noticeable mechanical changes in a protein, which in turn can be used to identify residues important for function and forming a mechanical nucleus in the protein core. This new approach, which combines experimental data and rapid coarse-grain calculations and no longer needs to resort to time-consuming all-atom simulations, was successfully applied to five different protein families.
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Affiliation(s)
- Sophie Sacquin-Mora
- Laboratoire de Biochimie Théorique, CNRS UPR9080, Institut de Biologie Physico-Chimique , 13 rue Pierre et Marie Curie, 75005 Paris , France
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11
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Diamantis P, Hage KE, Meuwly M. Effect of Single-Point Mutations on Nitric Oxide Rebinding and the Thermodynamic Stability of Myoglobin. J Phys Chem B 2019; 123:1961-1972. [PMID: 30724565 DOI: 10.1021/acs.jpcb.8b11454] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The effect of single amino acid mutations on the rebinding dynamics of nitrogen monoxide (NO) to myoglobin is investigated using reactive molecular dynamics simulations. In particular, mutations of residues surrounding the heme-active site (Leu29, His64, Val68) were considered. Consistent with experiments, all mutations studied here have a significant effect on the kinetics of the NO-rebinding process, which consists of a rapid (several 10 ps) and a slow (100s of ps) time scale. For all modifications considered, the time scales and rebinding fractions agree to within a few percents with results from experiments by adjusting one single, physically meaningful, conformationally averaged quantity: the asymptotic energy separation between the NO-bound (2A) and photodissociated (4A) states. It is furthermore shown that the thermodynamic stability of wild-type versus mutant Mb for the ligand-free and ligand-bound variants of the protein can be described by the same computational model. Therefore, ligand kinetics and thermodynamics are related in a direct fashion akin to Φ-value analysis, which establishes a relationship between protein folding rates and thermal stability of proteins.
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Affiliation(s)
- Polydefkis Diamantis
- Department of Chemistry , University of Basel , Klingelbergstrasse 80 , 4056 Basel , Switzerland
| | - Krystel El Hage
- Department of Chemistry , University of Basel , Klingelbergstrasse 80 , 4056 Basel , Switzerland
| | - Markus Meuwly
- Department of Chemistry , University of Basel , Klingelbergstrasse 80 , 4056 Basel , Switzerland.,Department of Chemistry , Brown University , Providence , Rhode Island 02912 , United States
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12
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Mahinthichaichan P, Gennis RB, Tajkhorshid E. Bacterial denitrifying nitric oxide reductases and aerobic respiratory terminal oxidases use similar delivery pathways for their molecular substrates. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2018; 1859:712-724. [PMID: 29883591 DOI: 10.1016/j.bbabio.2018.06.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 05/05/2018] [Accepted: 06/04/2018] [Indexed: 10/14/2022]
Abstract
The superfamily of heme‑copper oxidoreductases (HCOs) include both NO and O2 reductases. Nitric oxide reductases (NORs) are bacterial membrane enzymes that catalyze an intermediate step of denitrification by reducing nitric oxide (NO) to nitrous oxide (N2O). They are structurally similar to heme‑copper oxygen reductases (HCOs), which reduce O2 to water. The experimentally observed apparent bimolecular rate constant of NO delivery to the deeply buried catalytic site of NORs was previously reported to approach the diffusion-controlled limit (108-109 M-1 s-1). Using the crystal structure of cytochrome-c dependent NOR (cNOR) from Pseudomonas aeruginosa, we employed several protocols of molecular dynamics (MD) simulation, which include flooding simulations of NO molecules, implicit ligand sampling and umbrella sampling simulations, to elucidate how NO in solution accesses the catalytic site of this cNOR. The results show that NO partitions into the membrane, enters the enzyme from the lipid bilayer and diffuses to the catalytic site via a hydrophobic tunnel that is resolved in the crystal structures. This is similar to what has been found for O2 diffusion through the closely related O2 reductases. The apparent second order rate constant approximated using the simulation data is ~5 × 108 M-1 s-1, which is optimized by the dynamics of the amino acid side chains lining in the tunnel. It is concluded that both NO and O2 reductases utilize well defined hydrophobic tunnels to assure that substrate diffusion to the buried catalytic sites is not rate limiting under physiological conditions.
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Affiliation(s)
- Paween Mahinthichaichan
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Street, Urbana, IL 61801, USA; NIH Center for Macromolecular Modeling and Bioinformatics, 405 North Mathews Avenue, Urbana, IL 61801, USA; Beckman Institute for Advanced Science and Technology, 405 N. Mathews Avenue, Urbana, IL 61801, USA
| | - Robert B Gennis
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Street, Urbana, IL 61801, USA; Center for Biophysics and Quantitative Biology, 179 Looomis, MC-704, 1110 Green Street, Urbana, IL 61801, USA.
| | - Emad Tajkhorshid
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Street, Urbana, IL 61801, USA; NIH Center for Macromolecular Modeling and Bioinformatics, 405 North Mathews Avenue, Urbana, IL 61801, USA; Beckman Institute for Advanced Science and Technology, 405 N. Mathews Avenue, Urbana, IL 61801, USA; Center for Biophysics and Quantitative Biology, 179 Looomis, MC-704, 1110 Green Street, Urbana, IL 61801, USA.
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13
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Molecular basis of hemoglobin adaptation in the high-flying bar-headed goose. PLoS Genet 2018; 14:e1007331. [PMID: 29608560 PMCID: PMC5903655 DOI: 10.1371/journal.pgen.1007331] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 04/17/2018] [Accepted: 03/23/2018] [Indexed: 01/14/2023] Open
Abstract
During the adaptive evolution of a particular trait, some selectively fixed mutations may be directly causative and others may be purely compensatory. The relative contribution of these two classes of mutation to adaptive phenotypic evolution depends on the form and prevalence of mutational pleiotropy. To investigate the nature of adaptive substitutions and their pleiotropic effects, we used a protein engineering approach to characterize the molecular basis of hemoglobin (Hb) adaptation in the high-flying bar-headed goose (Anser indicus), a hypoxia-tolerant species renowned for its trans-Himalayan migratory flights. To test the effects of observed substitutions on evolutionarily relevant genetic backgrounds, we synthesized all possible genotypic intermediates in the line of descent connecting the wildtype bar-headed goose genotype with the most recent common ancestor of bar-headed goose and its lowland relatives. Site-directed mutagenesis experiments revealed one major-effect mutation that significantly increased Hb-O2 affinity on all possible genetic backgrounds. Two other mutations exhibited smaller average effect sizes and less additivity across backgrounds. One of the latter mutations produced a concomitant increase in the autoxidation rate, a deleterious side-effect that was fully compensated by a second-site mutation at a spatially proximal residue. The experiments revealed three key insights: (i) subtle, localized structural changes can produce large functional effects; (ii) relative effect sizes of function-altering mutations may depend on the sequential order in which they occur; and (iii) compensation of deleterious pleiotropic effects may play an important role in the adaptive evolution of protein function.
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14
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Solvent Composition Drives the Rebinding Kinetics of Nitric Oxide to Microperoxidase. Sci Rep 2018; 8:5281. [PMID: 29588445 PMCID: PMC5869715 DOI: 10.1038/s41598-018-22944-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 02/27/2018] [Indexed: 12/25/2022] Open
Abstract
The rebinding kinetics of NO after photodissociation from microperoxidase (Mp-9) is studied in different solvent environments. In mixed glycerol/water (G/W) mixtures the dissociating ligand rebinds with a yield close to 1 due to the cavities formed by the solvent whereas in pure water the ligand can diffuse into the solvent after photodissociation. In the G/W mixture, only geminate rebinding on the sub-picosecond and 5 ps time scales was found and the rebinding fraction is unity which compares well with available experiments. Contrary to that, simulations in pure water find two time scales – ~10 ps and ~200 ps - indicating that both, geminate rebinding and rebinding after diffusion of NO in the surrounding water contribute. The rebinding fraction is around 0.63 within 1 ns which is in stark contrast with experiment. Including ions (Na and Cl) at 0.15 M concentration in water leads to rebinding kinetics tending to that in the glycerol/water mixture and yields agreement with experiments. The effect of temperature is also probed and found to be non-negligible. The present simulations suggest that NO rebinding in Mp is primarily driven by thermal fluctuations which is consistent with recent resonance Raman spectroscopy experiments and simulations on MbNO.
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15
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Gell DA. Structure and function of haemoglobins. Blood Cells Mol Dis 2017; 70:13-42. [PMID: 29126700 DOI: 10.1016/j.bcmd.2017.10.006] [Citation(s) in RCA: 108] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2017] [Revised: 10/29/2017] [Accepted: 10/30/2017] [Indexed: 12/18/2022]
Abstract
Haemoglobin (Hb) is widely known as the iron-containing protein in blood that is essential for O2 transport in mammals. Less widely recognised is that erythrocyte Hb belongs to a large family of Hb proteins with members distributed across all three domains of life-bacteria, archaea and eukaryotes. This review, aimed chiefly at researchers new to the field, attempts a broad overview of the diversity, and common features, in Hb structure and function. Topics include structural and functional classification of Hbs; principles of O2 binding affinity and selectivity between O2/NO/CO and other small ligands; hexacoordinate (containing bis-imidazole coordinated haem) Hbs; bacterial truncated Hbs; flavohaemoglobins; enzymatic reactions of Hbs with bioactive gases, particularly NO, and protection from nitrosative stress; and, sensor Hbs. A final section sketches the evolution of work on the structural basis for allosteric O2 binding by mammalian RBC Hb, including the development of newer kinetic models. Where possible, reference to historical works is included, in order to provide context for current advances in Hb research.
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Affiliation(s)
- David A Gell
- School of Medicine, University of Tasmania, TAS 7000, Australia.
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16
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Bindings of NO, CO, and O 2 to multifunctional globin type dehaloperoxidase follow the 'sliding scale rule'. Biochem J 2017; 474:3485-3498. [PMID: 28899945 DOI: 10.1042/bcj20170515] [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: 06/28/2017] [Revised: 09/06/2017] [Accepted: 09/12/2017] [Indexed: 01/09/2023]
Abstract
Dehaloperoxidase-hemoglobin (DHP), a multifunctional globin protein, not only functions as an oxygen carrier as typical globins such as myoglobin and hemoglobin, but also as a peroxidase, a mono- and dioxygenase, peroxygenase, and an oxidase. Kinetics of DHP binding to NO, CO, and O2 were characterized for wild-type DHP A and B and the H55D and H55V DHP A mutants using stopped-flow methods. All three gaseous ligands bind to DHP significantly more weakly than sperm whale myoglobin (SWMb). Both CO and NO bind to DHP in a one-step process to form a stable six-coordinate complex. Multiple-step NO binding is not observed in DHP, which is similar to observations in SWMb, but in contrast with many heme sensor proteins. The weak affinity of DHP for O2 is mainly due to a fast O2 dissociation rate, in accordance with a longer εN-Fe distance between the heme iron and distal histidine in DHP than that in Mb, and an open-distal pocket that permits ligand escape. Binding affinities in DHP show the same 3-4 orders separation between the pairs NO/CO and CO/O2, consistent with the 'sliding scale rule' hypothesis. Strong gaseous ligand discrimination by DHP is very different from that observed in typical peroxidases, which show poor gaseous ligand selectivity, correlating with a neutral proximal imidazole ligand rather than an imidazolate. The present study provides useful insights into the rationale for DHP to function both as mono-oxygenase and oxidase, and is the first example of a globin peroxidase shown to follow the 'sliding scale rule' hypothesis in gaseous ligand discrimination.
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17
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Andrew CR, Petrova ON, Lamarre I, Lambry JC, Rappaport F, Negrerie M. The Dynamics Behind the Affinity: Controlling Heme-Gas Affinity via Geminate Recombination and Heme Propionate Conformation in the NO Carrier Cytochrome c'. ACS Chem Biol 2016; 11:3191-3201. [PMID: 27709886 DOI: 10.1021/acschembio.6b00599] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Nitric oxide (NO) sensors are heme proteins which may also bind CO and O2. Control of heme-gas affinity and their discrimination are achieved by the structural properties and reactivity of the heme and its distal and proximal environments, leading to several energy barriers. In the bacterial NO sensor cytochrome c' from Alcaligenes xylosoxidans (AXCP), the single Leu16Ala distal mutation boosts the affinity for gas ligands by a remarkable 106-108-fold, transforming AXCP from one of the lowest affinity gas binding proteins to one of the highest. Here, we report the dynamics of diatomics after photodissociation from wild type and L16A-AXCP over 12 orders of magnitude in time. For the L16A variant, the picosecond geminate rebinding of both CO and NO appears with an unprecedented 100% yield, and no exit of these ligands from protein to solvent could be observed. Molecular dynamic simulations saliently demonstrate that dissociated CO stays within 4 Å from Fe2+, in contrast to wild-type AXCP. The L16A mutation confers a heme propionate conformation and docking site which traps the diatomics, maximizing the probability of recombination and directly explaining the ultrahigh affinities for CO, NO, and O2. Overall, our results point to a novel mechanism for modulating heme-gas affinities in proteins.
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Affiliation(s)
- Colin R. Andrew
- Department
of Chemistry and Biochemistry, Eastern Oregon University, La Grande, Oregon 97850, United States
| | - Olga N. Petrova
- Laboratoire
d’Optique et Biosciences, INSERM, Ecole Polytechnique, 91128 Palaiseau, France
| | - Isabelle Lamarre
- Laboratoire
d’Optique et Biosciences, INSERM, Ecole Polytechnique, 91128 Palaiseau, France
| | - Jean-Christophe Lambry
- Laboratoire
d’Optique et Biosciences, INSERM, Ecole Polytechnique, 91128 Palaiseau, France
| | - Fabrice Rappaport
- Laboratoire
de Physiologie Membranaire et Moléculaire du Chloroplaste, CNRS, Université Pierre et Marie Curie, 75005 Paris, France
| | - Michel Negrerie
- Laboratoire
d’Optique et Biosciences, INSERM, Ecole Polytechnique, 91128 Palaiseau, France
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18
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Ferreras JM, Ragucci S, Citores L, Iglesias R, Pedone PV, Di Maro A. Insight into the phylogenetic relationship and structural features of vertebrate myoglobin family. Int J Biol Macromol 2016; 93:1041-1050. [PMID: 27659002 DOI: 10.1016/j.ijbiomac.2016.09.065] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Accepted: 09/18/2016] [Indexed: 11/17/2022]
Abstract
Myoglobin (Mb) is studied to clarify the structure-function relationships in protein science. In this work, we report the results of a comparative analysis of amino acid sequences from 298 vertebrate Mbs. Forty-one high conserved residues were identified and seven of them were invariants [E18, G25, F43, V68, L72, H93 (proximal histidine) and H97]. E18 is the only invariant amino acid residue located out of the heme-pocket and Xe-cavities playing a role in interaction between the A and E-helices. A comparative analysis of several parameters related to amino acid composition shows an increase of average mass, accessible surface area and volume per residue from Actinopterygii to Mammalia and Aves. This may be due to an increased number of bulky residues reducing the non-specific cavities volume and thus improving the oxygen flow between the heme site and the outside of the protein. Finally, the phylogenetic analyses of Mb in vertebrates are consistent with an evolution that runs with the diversification of the species, but in which several episodes of gene duplication and lost have occurred, less frequently in the ancestors of great taxons, cartilaginous fishes and non-avian reptiles, most frequently in ray-finned fishes and mammals, and very frequently in birds.
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Affiliation(s)
- José M Ferreras
- Department of Biochemistry and Molecular Biology and Physiology, Faculty of Sciences, University of Valladolid, E-47011 Valladolid, Spain
| | - Sara Ragucci
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Second University of Naples, I-81100 Caserta, Italy
| | - Lucía Citores
- Department of Biochemistry and Molecular Biology and Physiology, Faculty of Sciences, University of Valladolid, E-47011 Valladolid, Spain
| | - Rosario Iglesias
- Department of Biochemistry and Molecular Biology and Physiology, Faculty of Sciences, University of Valladolid, E-47011 Valladolid, Spain
| | - Paolo V Pedone
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Second University of Naples, I-81100 Caserta, Italy
| | - Antimo Di Maro
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Second University of Naples, I-81100 Caserta, Italy.
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19
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Berinyuy E, Soliman MES. Identification of Novel Potential gp120 of HIV-1 Antagonist Using Per-Residue Energy Contribution-Based Pharmacophore modelling. Interdiscip Sci 2016; 9:406-418. [PMID: 27165479 DOI: 10.1007/s12539-016-0174-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2015] [Revised: 04/11/2016] [Accepted: 04/15/2016] [Indexed: 01/01/2023]
Abstract
Inhibition of HIV-1 target cell entry, by targeting gp120, has been identified as a promising approach for the identification and development of prophylactic and salvage HIV infection inhibitors. A small molecule compound 18A is an important chemotype in the development of novel and diverse viral cell entry inhibitors, as it inhibits a wide variety of HIV strains by disrupting allosteric structuring on gp120. This study combines residue energy contribution (REC) pharmacophore mapping of 18A and in silico molecular docking in a virtual screening campaign to identify novel and diverse antagonists of gp120. The binding free energy of a validated docked complex of gp120-18A and the quantitative contribution of interacting residues were obtained with a more accurate molecular mechanics/generalised born surface area (MM/GBSA) method followed by mapping the energetically favourable residue contributions onto atom centres in 18A to obtain a pharmacophore model. The generated pharmacophore hypothesis was used to search the ZINC database for 3D structures that match the pharmacophore. Further, molecular docking, molecular dynamics simulations and binding free energy analysis were performed on retrieved hits in order to rank hits based on their affinity and interactions in the CD4 binding cavity of a gp120. Interestingly, the top scoring compound designated with ZINC database ID as ZINC64700951 (docking score = -8.8 kcal/mol, ∆G = -43.77 kcal/mol) showed higher affinity compared to compound 18A docking score = -7.3 kcal/mol, ∆G = -31.97 kcal/mol) and interaction of ZN64700951 with validated allosteric hot spot residues, Asp368 and Met426, and binding hot spot residues, Asn425, Glu370, Gly473, Trp427 and Met475 in gp120, suggest that ZN64700951 is a promising antagonist of gp120. Thus, ZN64700951 could serve as an additional prototype for further optimisation as an HIV target cell viral entry inhibitor.
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Affiliation(s)
- Emiliene Berinyuy
- Molecular Modelling and Drug Design Research Group, School of Health Sciences, University of KwaZulu-Natal, Westville, Durban, 4000, South Africa
| | - Mahmoud E S Soliman
- Molecular Modelling and Drug Design Research Group, School of Health Sciences, University of KwaZulu-Natal, Westville, Durban, 4000, South Africa.
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20
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Carballal S, Cuevasanta E, Yadav PK, Gherasim C, Ballou DP, Alvarez B, Banerjee R. Kinetics of Nitrite Reduction and Peroxynitrite Formation by Ferrous Heme in Human Cystathionine β-Synthase. J Biol Chem 2016; 291:8004-13. [PMID: 26867575 DOI: 10.1074/jbc.m116.718734] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Indexed: 01/01/2023] Open
Abstract
Cystathionine β-synthase (CBS) is a pyridoxal phosphate-dependent enzyme that catalyzes the condensation of homocysteine with serine or with cysteine to form cystathionine and either water or hydrogen sulfide, respectively. Human CBS possesses a noncatalytic heme cofactor with cysteine and histidine as ligands, which in its oxidized state is relatively unreactive. Ferric CBS (Fe(III)-CBS) can be reduced by strong chemical and biochemical reductants to Fe(II)-CBS, which can bind carbon monoxide (CO) or nitric oxide (NO(•)), leading to inactive enzyme. Alternatively, Fe(II)-CBS can be reoxidized by O2to Fe(III)-CBS, forming superoxide radical anion (O2 (̇̄)). In this study, we describe the kinetics of nitrite (NO2 (-)) reduction by Fe(II)-CBS to form Fe(II)NO(•)-CBS. The second order rate constant for the reaction of Fe(II)-CBS with nitrite was obtained at low dithionite concentrations. Reoxidation of Fe(II)NO(•)-CBS by O2showed complex kinetic behavior and led to peroxynitrite (ONOO(-)) formation, which was detected using the fluorescent probe, coumarin boronic acid. Thus, in addition to being a potential source of superoxide radical, CBS constitutes a previously unrecognized source of NO(•)and peroxynitrite.
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Affiliation(s)
- Sebastián Carballal
- From the Departamento de Bioquímica, Facultad de Medicina, Center for Free Radical and Biomedical Research, and
| | - Ernesto Cuevasanta
- Center for Free Radical and Biomedical Research, and Laboratorio de Enzimología, Facultad de Ciencias, Universidad de la República, Montevideo 11800, Uruguay and
| | - Pramod K Yadav
- the Department of Biological Chemistry, Medical Center, University of Michigan, Ann Arbor, Michigan 48109-0600
| | - Carmen Gherasim
- the Department of Biological Chemistry, Medical Center, University of Michigan, Ann Arbor, Michigan 48109-0600
| | - David P Ballou
- the Department of Biological Chemistry, Medical Center, University of Michigan, Ann Arbor, Michigan 48109-0600
| | - Beatriz Alvarez
- Center for Free Radical and Biomedical Research, and Laboratorio de Enzimología, Facultad de Ciencias, Universidad de la República, Montevideo 11800, Uruguay and
| | - Ruma Banerjee
- the Department of Biological Chemistry, Medical Center, University of Michigan, Ann Arbor, Michigan 48109-0600
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21
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De Sancho D, Kubas A, Wang PH, Blumberger J, Best RB. Identification of Mutational Hot Spots for Substrate Diffusion: Application to Myoglobin. J Chem Theory Comput 2015; 11:1919-27. [PMID: 26574395 PMCID: PMC6132223 DOI: 10.1021/ct5011455] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The pathways by which small molecules (substrates or inhibitors) access active sites are a key aspect of the function of enzymes and other proteins. A key problem in designing or altering such proteins is to identify sites for mutation that will have the desired effect on the substrate transport properties. While specific access channels have been invoked in the past, molecular simulations suggest that multiple routes are possible, complicating the analysis. This complexity, however, can be captured by a Markov State Model (MSM) of the ligand diffusion process. We have developed a sensitivity analysis of the resulting rate matrix, which identifies the locations where mutations should have the largest effect on the diffusive on rate. We apply this method to myoglobin, which is the best characterized example both from experiment and simulation. We validate the approach by translating the sensitivity parameter obtained from this method into the CO binding rates in myoglobin upon mutation, resulting in a semi-quantitative correlation with experiments. The model is further validated against an explicit simulation for one of the experimental mutants.
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Affiliation(s)
- David De Sancho
- Department of Chemistry, University of Cambridge , Lensfield Road, Cambridge CB2 1EW, United Kingdom
- CIC nanoGUNE , Tolosa Hiribidea 76, 20018 Donostia-San Sebastian, Spain
- IKERBASQUE, Basque Foundation for Science , Maria Diaz de Haro 3, 48013 Bilbao, Spain
| | - Adam Kubas
- Department of Physics and Astronomy, University College London , Gower Street, London WC1E 6BT, United Kingdom
| | - Po-Hung Wang
- Department of Physics and Astronomy, University College London , Gower Street, London WC1E 6BT, United Kingdom
- Theoretical Molecular Science Laboratory , 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan
| | - Jochen Blumberger
- Department of Physics and Astronomy, University College London , Gower Street, London WC1E 6BT, United Kingdom
| | - Robert B Best
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health , Bethesda, Maryland 20892-0520, United States
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22
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Affiliation(s)
- Yue Yuan
- Department of Biological Sciences Carnegie Mellon University Pittsburgh, PA 15213
| | - Ming F. Tam
- Department of Biological Sciences Carnegie Mellon University Pittsburgh, PA 15213
| | - Virgil Simplaceanu
- Department of Biological Sciences Carnegie Mellon University Pittsburgh, PA 15213
| | - Chien Ho
- Department of Biological Sciences Carnegie Mellon University Pittsburgh, PA 15213
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23
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Hough MA, Andrew CR. Cytochromes c': Structure, Reactivity and Relevance to Haem-Based Gas Sensing. Adv Microb Physiol 2015; 67:1-84. [PMID: 26616515 DOI: 10.1016/bs.ampbs.2015.08.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Cytochromes c' are a group of class IIa cytochromes with pentacoordinate haem centres and are found in photosynthetic, denitrifying and methanotrophic bacteria. Their function remains unclear, although roles in nitric oxide (NO) trafficking during denitrification or in cellular defence against nitrosoative stress have been proposed. Cytochromes c' are typically dimeric with each c-type haem-containing monomer folding as a four-α-helix bundle. Their hydrophobic and crowded distal sites impose severe restrictions on the binding of distal ligands, including diatomic gases. By contrast, NO binds to the proximal haem face in a similar manner to that of the eukaryotic NO sensor, soluble guanylate cyclase and bacterial analogues. In this review, we focus on how structural features of cytochromes c' influence haem spectroscopy and reactivity with NO, CO and O2. We also discuss the relevance of cytochrome c' to understanding the mechanisms of gas binding to haem-based sensor proteins.
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24
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Uppal S, Salhotra S, Mukhi N, Zaidi FK, Seal M, Dey SG, Bhat R, Kundu S. Significantly enhanced heme retention ability of myoglobin engineered to mimic the third covalent linkage by nonaxial histidine to heme (vinyl) in synechocystis hemoglobin. J Biol Chem 2014; 290:1979-93. [PMID: 25451928 DOI: 10.1074/jbc.m114.603225] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Heme proteins, which reversibly bind oxygen and display a particular fold originally identified in myoglobin (Mb), characterize the "hemoglobin (Hb) superfamily." The long known and widely investigated Hb superfamily, however, has been enriched by the discovery and investigation of new classes and members. Truncated Hbs typify such novel classes and exhibit a distinct two-on-two α-helical fold. The truncated Hb from the freshwater cyanobacterium Synechocystis exhibits hexacoordinate heme chemistry and bears an unusual covalent bond between the nonaxial His(117) and a heme porphyrin 2-vinyl atom, which remains tightly associated with the globin unlike any other. It seems to be the most stable Hb known to date, and His(117) is the dominant force holding the heme. Mutations of amino acid residues in the vicinity did not influence this covalent linkage. Introduction of a nonaxial His into sperm whale Mb at the topologically equivalent position and in close proximity to vinyl group significantly increased the heme stability of this prototype globin. Reversed phase chromatography, electrospray ionization-MS, and MALDI-TOF analyses confirmed the presence of covalent linkage in Mb I107H. The Mb mutant with the engineered covalent linkage was stable to denaturants and exhibited ligand binding and auto-oxidation rates similar to the wild type protein. This indeed is a novel finding and provides a new perspective to the evolution of Hbs. The successful attempt at engineering heme stability holds promise for the production of stable Hb-based blood substitute.
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Affiliation(s)
- Sheetal Uppal
- From the Department of Biochemistry, University of Delhi South Campus, New Delhi 110021, India
| | - Shikha Salhotra
- From the Department of Biochemistry, University of Delhi South Campus, New Delhi 110021, India
| | - Nitika Mukhi
- From the Department of Biochemistry, University of Delhi South Campus, New Delhi 110021, India
| | - Fatima Kamal Zaidi
- the School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India, and
| | - Manas Seal
- the Department of Inorganic Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Somdatta Ghosh Dey
- the Department of Inorganic Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Rajiv Bhat
- the School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India, and
| | - Suman Kundu
- From the Department of Biochemistry, University of Delhi South Campus, New Delhi 110021, India,
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25
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Neya S, Yonetani T, Kawaguchi AT. Usefulness of Myoglobin Containing Cobalt Heme Cofactor in Designing a Myoglobin-Based Artificial Oxygen Carrier. Artif Organs 2014; 38:715-9. [DOI: 10.1111/aor.12327] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Saburo Neya
- Department of Physical Chemistry; Graduate School of Pharmaceutical Sciences; Chiba University; Chiba Japan
| | - Takashi Yonetani
- Department of Biochemistry and Biophysics; University of Pennsylvania; Philadelphia PA USA
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26
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Park SY, Undeland I, Sannaveerappa T, Richards MP. Novel interactions of caffeic acid with different hemoglobins: Effects on discoloration and lipid oxidation in different washed muscles. Meat Sci 2013; 95:110-7. [DOI: 10.1016/j.meatsci.2013.04.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2012] [Revised: 01/21/2013] [Accepted: 04/03/2013] [Indexed: 10/27/2022]
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27
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Tam MF, Rice NW, Maillett DH, Simplaceanu V, Ho NT, Tam TCS, Shen TJ, Ho C. Autoxidation and oxygen binding properties of recombinant hemoglobins with substitutions at the αVal-62 or βVal-67 position of the distal heme pocket. J Biol Chem 2013; 288:25512-25521. [PMID: 23867463 DOI: 10.1074/jbc.m113.474841] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
The E11 valine in the distal heme pocket of either the α- or β-subunit of human adult hemoglobin (Hb A) was replaced by leucine, isoleucine, or phenylalanine. Recombinant proteins were expressed in Escherichia coli and purified for structural and functional studies. (1)H NMR spectra were obtained for the CO and deoxy forms of Hb A and the mutants. The mutations did not disturb the α1β2 interface in either form, whereas the H-bond between αHis-103 and βGln-131 in the α1β1 interfaces of the deoxy α-subunit mutants was weakened. Localized structural changes in the mutated heme pocket were detected for the CO form of recombinant Hb (rHb) (αV62F), rHb (βV67I), and rHb (βV67F) compared with Hb A. In the deoxy form the proximal histidyl residue in the β-subunit of rHb (βV67F) has been altered. Furthermore, the interactions between the porphyrin ring and heme pocket residues have been perturbed in rHb (αV62I), rHb (αV62F), and rHb (βV67F). Functionally, the oxygen binding affinity (P50), cooperativity (n50), and the alkaline Bohr Effect of the three α-subunit mutants and rHb (βV67L) are similar to those of Hb A. rHb (βV67I) and rHb (βV67F) exhibit low and high oxygen affinity, respectively. rHb (βV67F) has P50 values lower that those reported for rHb (αL29F), a B10 mutant studied previously in our laboratory (Wiltrout, M. E., Giovannelli, J. L., Simplaceanu, V., Lukin, J. A., Ho, N. T., and Ho, C. (2005) Biochemistry 44, 7207-7217). These E11 mutations do not slow down the autoxidation and azide-induced oxidation rates of the recombinant proteins. Results from this study provide new insights into the roles of E11 mutants in the structure-function relationship in hemoglobin.
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Affiliation(s)
- Ming F Tam
- From the Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213
| | - Natalie W Rice
- From the Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213
| | - David H Maillett
- From the Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213
| | - Virgil Simplaceanu
- From the Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213
| | - Nancy T Ho
- From the Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213
| | - Tsuey Chyi S Tam
- From the Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213
| | - Tong-Jian Shen
- From the Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213
| | - Chien Ho
- From the Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213.
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28
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Astudillo L, Bernad S, Derrien V, Sebban P, Miksovska J. Conformational dynamics in human neuroglobin: effect of His64, Val68, and Cys120 on ligand migration. Biochemistry 2012; 51:9984-94. [PMID: 23176629 DOI: 10.1021/bi301016u] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Neuroglobin belongs to the family of hexacoordinate hemoglobins and has been implicated in the protection of neuronal tissue under hypoxic and ischemic conditions. Here we present transient absorption and photoacoustic calorimetry studies of CO photodissociation and bimolecular rebinding to neuroglobin focusing on the ligand migration process and the role of distal pocket residues (His64 and Val68) and two Cys residues (Cys55 and Cys120). Our results indicate that His64 has a minor impact on the migration of CO between the distal heme pocket and protein exterior, whereas the Val68 side chain regulates the transition of the photodissociated ligand between the distal pocket and internal hydrophobic cavities, which is evident from the increased geminate quantum yield in this mutated protein (Φ(gem) = 0.32 for WT and His64Gln, and Φ(gem) = 0.85 for Val68Phe). The interface between helix G and the A-B loop provides an escape pathway for the photodissociated ligand, which is evident from a decrease in the reaction enthalpy for the transition between the CO-bound hNgb and five-coordinate hNgb in the Cys120Ser mutant (ΔH = -3 ± 4 kcal mol(-1)) compared to that of the WT protein (ΔH = 20 ± 4 kcal mol(-1)). The extensive electrostatic/hydrogen binding network that includes heme propionate groups, Lys67, His64, and Tyr44 not only restricts the heme binding but also modulates the energetics of binding of CO to the five-coordinate hNgb as substitution of His64 with Gln leads to an endothermic association of CO with the five-coordinate hNgb (ΔH = 6 ± 3 kcal mol(-1)).
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Affiliation(s)
- Luisana Astudillo
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA
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29
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Tsai AL, Martin E, Berka V, Olson JS. How do heme-protein sensors exclude oxygen? Lessons learned from cytochrome c', Nostoc puntiforme heme nitric oxide/oxygen-binding domain, and soluble guanylyl cyclase. Antioxid Redox Signal 2012; 17:1246-63. [PMID: 22356101 PMCID: PMC3430480 DOI: 10.1089/ars.2012.4564] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
SIGNIFICANCE Ligand selectivity for dioxygen (O(2)), carbon monoxide (CO), and nitric oxide (NO) is critical for signal transduction and is tailored specifically for each heme-protein sensor. Key NO sensors, such as soluble guanylyl cyclase (sGC), specifically recognized low levels of NO and achieve a total O(2) exclusion. Several mechanisms have been proposed to explain the O(2) insensitivity, including lack of a hydrogen bond donor and negative electrostatic fields to selectively destabilize bound O(2), distal steric hindrance of all bound ligands to the heme iron, and restriction of in-plane movements of the iron atom. RECENT ADVANCES Crystallographic structures of the gas sensors, Thermoanaerobacter tengcongensis heme-nitric oxide/oxygen-binding domain (Tt H-NOX(1)) or Nostoc puntiforme (Ns) H-NOX, and measurements of O(2) binding to site-specific mutants of Tt H-NOX and the truncated β subunit of sGC suggest the need for a H-bonding donor to facilitate O(2) binding. CRITICAL ISSUES However, the O(2) insensitivity of full length sGC with a site-specific replacement of isoleucine by a tyrosine on residue 145 and the very slow autooxidation of Ns H-NOX and cytochrome c' suggest that more complex mechanisms have evolved to exclude O(2) but retain high affinity NO binding. A combined graphical analysis of ligand binding data for libraries of heme sensors, globins, and model heme shows that the NO sensors dramatically inhibit the formation of six-coordinated NO, CO, and O(2) complexes by direct distal steric hindrance (cyt c'), proximal constraints of in-plane iron movement (sGC), or combinations of both following a sliding scale rule. High affinity NO binding in H-NOX proteins is achieved by multiple NO binding steps that produce a high affinity five-coordinate NO complex, a mechanism that also prevents NO dioxygenation. FUTURE DIRECTIONS Knowledge advanced by further extensive test of this "sliding scale rule" hypothesis should be valuable in guiding novel designs for heme based sensors.
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Affiliation(s)
- Ah-Lim Tsai
- Division of Hematology, University of Texas Health Science Center at Houston, Houston, Texas 77225, USA.
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30
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Salter MD, Blouin GC, Soman J, Singleton EW, Dewilde S, Moens L, Pesce A, Nardini M, Bolognesi M, Olson JS. Determination of ligand pathways in globins: apolar tunnels versus polar gates. J Biol Chem 2012; 287:33163-78. [PMID: 22859299 DOI: 10.1074/jbc.m112.392258] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Although molecular dynamics simulations suggest multiple interior pathways for O(2) entry into and exit from globins, most experiments indicate well defined single pathways. In 2001, we highlighted the effects of large-to-small amino acid replacements on rates for ligand entry and exit onto the three-dimensional structure of sperm whale myoglobin. The resultant map argued strongly for ligand movement through a short channel from the heme iron to solvent that is gated by the distal histidine (His-64(E7)) near the solvent edge of the porphyrin ring. In this work, we have applied the same mutagenesis mapping strategy to the neuronal mini-hemoglobin from Cerebratulus lacteus (CerHb), which has a large internal tunnel from the heme iron to the C-terminal ends of the E and H helices, a direction that is 180° opposite to the E7 channel. Detailed comparisons of the new CerHb map with expanded results for Mb show unambiguously that the dominant (>90%) ligand pathway in CerHb is through the internal tunnel, and the major (>75%) ligand pathway in Mb is through the E7 gate. These results demonstrate that: 1) mutagenesis mapping can identify internal pathways when they exist; 2) molecular dynamics simulations need to be refined to address discrepancies with experimental observations; and 3) alternative pathways have evolved in globins to meet specific physiological demands.
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Affiliation(s)
- Mallory D Salter
- Department of Biochemistry and Cell Biology, Rice University, Houston, Texas 77005-1892, USA
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31
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Kim S, Park J, Lee T, Lim M. Direct Observation of Ligand Rebinding Pathways in Hemoglobin Using Femtosecond Mid-IR Spectroscopy. J Phys Chem B 2012; 116:6346-55. [PMID: 22587393 DOI: 10.1021/jp3026495] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Seongheun Kim
- Department of Chemistry and Chemistry
Institute for
Functional Materials, Pusan National University, Busan 609-735, Korea
| | - Jaeheung Park
- Department of Chemistry and Chemistry
Institute for
Functional Materials, Pusan National University, Busan 609-735, Korea
| | - Taegon Lee
- Department of Chemistry and Chemistry
Institute for
Functional Materials, Pusan National University, Busan 609-735, Korea
| | - Manho Lim
- Department of Chemistry and Chemistry
Institute for
Functional Materials, Pusan National University, Busan 609-735, Korea
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32
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Kim S, Lim M. Protein Conformation-Controlled Rebinding Barrier of NO and Its Binding Trajectories in Myoglobin and Hemoglobin at Room Temperature. J Phys Chem B 2012; 116:5819-30. [DOI: 10.1021/jp300176q] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Seongheun Kim
- Department of Chemistry and Chemistry Institute for
Functional Materials, Pusan National University, Busan 609-735, Korea
| | - Manho Lim
- Department of Chemistry and Chemistry Institute for
Functional Materials, Pusan National University, Busan 609-735, Korea
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33
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Zeng W, Barabanschikov A, Wang N, Lu Y, Zhao J, Sturhahn W, Alp EE, Sage JT. Vibrational dynamics of oxygenated heme proteins. Chem Commun (Camb) 2012; 48:6340. [PMID: 22498848 DOI: 10.1039/c2cc31239e] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
Advanced spectroscopic techniques coupled with DFT calculations reveal the vibrational dynamics of the iron in stable dioxygen complexes with myoglobin and with a mutant engineered to model the catalytic site of heme-copper oxidases. The unprecedented level of detail will constrain computational modelling of reactions with oxygen.
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Affiliation(s)
- Weiqiao Zeng
- Department of Physics and Center for Interdisciplinary Research on Complex Systems, Northeastern University, BostonMA 02115, USA.
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34
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Munro OQ, Pearson N. Hydrogen bonding and crystal packing favor a nonplanarCo(III)porphyrin conformation and unusually weak axial ligation in [Co(TPP)(benzylamine)2](SCN): A crystallographic and density functional theory investigation. J PORPHYR PHTHALOCYA 2012. [DOI: 10.1142/s1088424604000441] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The single crystal X-ray structure of [ Co ( TPP )( BzNH2)2]( SCN ), compound 2, where TPP = 5,10,15,20-tetraphenylporphyrin dianion and BzNH2= benzylamine, reveals that the SCN-ion is hydrogen-bonded to one of the coordinated amino group hydrogen atoms via its sulfur atom. Furthermore, the N – H ⋯ SCN interaction is balanced by a stronger N – H ⋯ NCS hydrogen bonding interaction for the trans BzNH2ligand as a result of the multiple hydrogen bond accepting character of the thiocyanate ion. Analysis of the crystal packing shows that these two hydrogen bonds play a major role in fixing unusual orientations for the axial ligands relative to the porphyrin ring in this system. This, in turn, leads to the formation of a nonplanar porphyrin core conformation that is a mixture of ruffle- and saddle-type distortions. The intricate hydrogen bonding between the cations and anions in 2 results in an unusually long mean Co – Naminecoordination distance of 2.033(4) Å, some 0.05 Å longer than previously observed for other bis(primary amine) complexes of Co(III) porphyrins with comparable porphyrin ligands. Density functional theory (DFT) calculations at the B3LYP/LACVP* level of theory have been used to gauge the perturbation of the electronic structure of the [ Co ( TPP )( BzNH2)2]+cation caused by the N – H ⋯ SCN and N – H ⋯ NCS hydrogen-bonded SCN-ions. The calculations show that partial mixing of the anion MOs with those of the porphyrin cation lead to changes in the electron populations of the 3d orbitals of up to 0.42 e as well as more nearly tetragonal electronic symmetry for the Co(III) ion as a result of adjustments of the relative energies of the MOs with predominantly 3d character.
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Affiliation(s)
- Orde Q. Munro
- School of Chemistry, University of KwaZulu-Natal, Private Bag X01, Scottsville, Pietermaritzburg 3209, South Africa
| | - Nicole Pearson
- School of Chemistry, University of KwaZulu-Natal, Private Bag X01, Scottsville, Pietermaritzburg 3209, South Africa
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35
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Tsai AL, Berka V, Martin E, Olson JS. A "sliding scale rule" for selectivity among NO, CO, and O₂ by heme protein sensors. Biochemistry 2011; 51:172-86. [PMID: 22111978 DOI: 10.1021/bi2015629] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Selectivity among NO, CO, and O₂ is crucial for the physiological function of most heme proteins. Although there is a million-fold variation in equilibrium dissociation constants (K(D)), the ratios for NO:CO:O₂ binding stay roughly the same, 1:~10(3):~10(6), when the proximal ligand is a histidine and the distal site is apolar. For these proteins, there is a "sliding scale rule" for plots of log(K(D)) versus ligand type that allows predictions of K(D) values if one or two are missing. The predicted K(D) for binding of O₂to Ns H-NOX coincides with the value determined experimentally at high pressures. Active site hydrogen bond donors break the rule and selectively increase O₂ affinity with little effect on CO and NO binding. Strong field proximal ligands such as thiolate, tyrosinate, and imidazolate exert a "leveling" effect on ligand binding affinity. The reported picomolar K(D) for binding of NO to sGC deviates even more dramatically from the sliding scale rule, showing a NO:CO K(D) ratio of 1:~10(8). This deviation is explained by a complex, multistep process, in which an initial low-affinity hexacoordinate NO complex with a measured K(D) of ≈54 nM, matching that predicted from the sliding scale rule, is formed initially and then is converted to a high-affinity pentacoordinate complex. This multistep six-coordinate to five-coordinate mechanism appears to be common to all NO sensors that exclude O₂ binding to capture a lower level of cellular NO and prevent its consumption by dioxygenation.
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Affiliation(s)
- Ah-Lim Tsai
- Division of Hematology, Internal Medicine, University of Texas Medical School at Houston, Houston, Texas 77030, United States.
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36
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Nicoletti FP, Droghetti E, Boechi L, Bonamore A, Sciamanna N, Estrin DA, Feis A, Boffi A, Smulevich G. Fluoride as a Probe for H-Bonding Interactions in the Active Site of Heme Proteins: The Case of Thermobifida fusca Hemoglobin. J Am Chem Soc 2011; 133:20970-80. [DOI: 10.1021/ja209312k] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Francesco P. Nicoletti
- Dipartimento di Chimica “Ugo Schiff”, Università di Firenze, Via della Lastruccia 3-13, I-50019 Sesto Fiorentino (FI), Italy
| | - Enrica Droghetti
- Dipartimento di Chimica “Ugo Schiff”, Università di Firenze, Via della Lastruccia 3-13, I-50019 Sesto Fiorentino (FI), Italy
| | - Leonardo Boechi
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón II, Buenos Aires (C1428EHA), Argentina
| | - Alessandra Bonamore
- Institute Pasteur, Fondazione Cenci Bolognetti, Department of Biochemical Sciences and CNR, Institute of Molecular Biology and Pathology, University of Rome “La Sapienza”, Piazzale Aldo Moro 5, I-00185 Rome, Italy
| | - Natascia Sciamanna
- Institute Pasteur, Fondazione Cenci Bolognetti, Department of Biochemical Sciences and CNR, Institute of Molecular Biology and Pathology, University of Rome “La Sapienza”, Piazzale Aldo Moro 5, I-00185 Rome, Italy
| | - Darío A. Estrin
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón II, Buenos Aires (C1428EHA), Argentina
| | - Alessandro Feis
- Dipartimento di Chimica “Ugo Schiff”, Università di Firenze, Via della Lastruccia 3-13, I-50019 Sesto Fiorentino (FI), Italy
| | - Alberto Boffi
- Institute Pasteur, Fondazione Cenci Bolognetti, Department of Biochemical Sciences and CNR, Institute of Molecular Biology and Pathology, University of Rome “La Sapienza”, Piazzale Aldo Moro 5, I-00185 Rome, Italy
| | - Giulietta Smulevich
- Dipartimento di Chimica “Ugo Schiff”, Università di Firenze, Via della Lastruccia 3-13, I-50019 Sesto Fiorentino (FI), Italy
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37
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Birukou I, Maillett DH, Birukova A, Olson JS. Modulating distal cavities in the α and β subunits of human HbA reveals the primary ligand migration pathway. Biochemistry 2011; 50:7361-74. [PMID: 21793487 DOI: 10.1021/bi200923k] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The free volume in the active site of human HbA plays a crucial role in governing the bimolecular rates of O(2), CO, and NO binding, the fraction of geminate ligand recombination, and the rate of NO dioxygenation by the oxygenated complex. We have decreased the size of the distal pocket by mutating Leu(B10), Val(E11), and Leu(G8) to Phe and Trp and that of other more internal cavities by filling them with Xe at high gas pressures. Increasing the size of the B10 side chain reduces bimolecular rates of ligand binding nearly 5000-fold and inhibits CO geminate recombination due to both reduction of the capture volume in the distal pocket and direct steric hindrance of Fe-ligand bond formation. Phe and Trp(E11) mutations also cause a decrease in distal pocket volume but, at the same time, increase access to the Fe atom because of the loss of the γ2 CH(3) group of the native Val(E11) side chain. The net result of these E11 substitutions is a dramatic increase in the rate of geminate recombination because dissociated CO is sequestered close to the Fe atom and can rapidly rebind without steric resistance. However, the bimolecular rate constants for binding of ligand to the Phe and Trp(E11) mutants are decreased 5-30-fold, because of a smaller capture volume. Geminate and bimolecular kinetic parameters for Phe and Trp(G8) mutants are similar to those for the native HbA subunits because the aromatic rings at this position cause little change in distal pocket volume and because ligands do not move past this position into the globin interior of wild-type HbA subunits. The latter conclusion is verified by the observation that Xe binding to the α and β Hb subunits has little effect on either geminate or bimolecular ligand rebinding. All of these experimental results argue strongly against alternative ligand migration pathways that involve movements through the protein interior in HbA. Instead, ligands appear to enter through the His(E7) gate and are captured directly in the distal cavity.
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Affiliation(s)
- Ivan Birukou
- Department of Biochemistry and Cell Biology and WM Keck Center for Computational Biology, Rice University, Houston, Texas 77005, United States
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38
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Bocahut A, Bernad S, Sebban P, Sacquin-Mora S. Frontier Residues Lining Globin Internal Cavities Present Specific Mechanical Properties. J Am Chem Soc 2011; 133:8753-61. [DOI: 10.1021/ja202587a] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Anthony Bocahut
- Laboratoire de Biochimie Théorique, UMR 9080 CNRS, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Sophie Bernad
- Laboratoire de Chimie Physique, CNRS UMR8000, Bât. 350, Université Paris-sud, 91405 Orsay, France
| | - Pierre Sebban
- Laboratoire de Chimie Physique, CNRS UMR8000, Bât. 350, Université Paris-sud, 91405 Orsay, France
- Université des Sciences et des Technologies de Hanoi, 18 Hoang Quoc Viet, Cau Giay, Hanoi, Vietnam
| | - Sophie Sacquin-Mora
- Laboratoire de Biochimie Théorique, UMR 9080 CNRS, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France
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39
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Crowley MA, Mollan TL, Abdulmalik OY, Butler AD, Goodwin EF, Sarkar A, Stolle CA, Gow AJ, Olson JS, Weiss MJ. A hemoglobin variant associated with neonatal cyanosis and anemia. N Engl J Med 2011; 364:1837-43. [PMID: 21561349 PMCID: PMC3632254 DOI: 10.1056/nejmoa1013579] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Globin-gene mutations are a rare but important cause of cyanosis. We identified a missense mutation in the fetal Gγ-globin gene (HBG2) in a father and daughter with transient neonatal cyanosis and anemia. This new mutation modifies the ligand-binding pocket of fetal hemoglobin by means of two mechanisms. First, the relatively large side chain of methionine decreases both the affinity of oxygen for binding to the mutant hemoglobin subunit and the rate at which it does so. Second, the mutant methionine is converted to aspartic acid post-translationally, probably through oxidative mechanisms. The presence of this polar amino acid in the heme pocket is predicted to enhance hemoglobin denaturation, causing anemia.
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Affiliation(s)
- Moira A Crowley
- Division of Neonatology, Case Western Reserve University, Cleveland, USA
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40
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Birukou I, Soman J, Olson JS. Blocking the gate to ligand entry in human hemoglobin. J Biol Chem 2010; 286:10515-29. [PMID: 21193395 DOI: 10.1074/jbc.m110.176271] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
His(E7) to Trp replacements in HbA lead to markedly biphasic bimolecular CO rebinding after laser photolysis. For isolated mutant subunits, the fraction of fast phase increases with increasing [CO], suggesting a competition between binding to an open conformation with an empty E7 channel and relaxation to blocked or closed, slowly reacting states. The rate of conformational relaxation of the open state is ∼18,000 s(-1) in α subunits and ∼10-fold faster in β subunits, ∼175,000 s(-1). Crystal structures were determined for tetrameric α(WT)β(Trp-63) HbCO, α(Trp-58)β(WT) deoxyHb, and Trp-64 deoxy- and CO-Mb as controls. In Trp-63(E7) βCO, the indole side chain is located in the solvent interface, blocking entry into the E7 channel. Similar blocked Trp-64(E7) conformations are observed in the mutant Mb crystal structures. In Trp-58(E7) deoxy-α subunits, the indole side chain fills both the channel and the distal pocket, forming a completely closed state. The bimolecular rate constant for CO binding, k'(CO), to the open conformations of both mutant Hb subunits is ∼80-90 μm(-1) s(-1), whereas k'(CO) for the completely closed states is 1000-fold slower, ∼0.08 μm(-1) s(-1). A transient intermediate with k'(CO) ≈ 0.7 μm(-1) s(-1) is observed after photolysis of Trp-63(E7) βCO subunits and indicates that the indole ring blocks the entrance to the E7 channel, as observed in the crystal structures of Trp(E7) deoxyMb and βCO subunits. Thus, either blocking or completely filling the E7 channel dramatically slows bimolecular binding, providing strong evidence that the E7 channel is the major pathway (≥90%) for ligand entry in human hemoglobin.
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Affiliation(s)
- Ivan Birukou
- Department of Biochemistry and Cell Biology and the W. M. Keck Center for Computational Biology, Rice University, Houston, Texas 77005, USA
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41
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Kim KH, Oang KY, Kim J, Lee JH, Kim Y, Ihee H. Direct observation of myoglobin structural dynamics from 100 picoseconds to 1 microsecond with picosecond X-ray solution scattering. Chem Commun (Camb) 2010; 47:289-91. [PMID: 20733999 DOI: 10.1039/c0cc01817a] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Here we report structural dynamics of equine myoglobin (Mb) in response to the CO photodissociation visualized by picosecond time-resolved X-ray solution scattering. The data clearly reveal new structural dynamics that occur in the timescale of ∼360 picoseconds (ps) and ∼9 nanoseconds (ns), which have not been clearly detected in previous studies.
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Affiliation(s)
- Kyung Hwan Kim
- Center for Time-Resolved Diffraction, Department of Chemistry, Graduate School of Nanoscience & Technology (WCU), KAIST, Daejeon 305-701, Korea
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42
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Esquerra RM, López-Peña I, Tipgunlakant P, Birukou I, Nguyen RL, Soman J, Olson JS, Kliger DS, Goldbeck RA. Kinetic spectroscopy of heme hydration and ligand binding in myoglobin and isolated hemoglobin chains: an optical window into heme pocket water dynamics. Phys Chem Chem Phys 2010; 12:10270-8. [PMID: 20668762 DOI: 10.1039/c003606b] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The entry of a water molecule into the distal heme pocket of pentacoordinate heme proteins such as myoglobin and the alpha,beta chains of hemoglobin can be detected by time-resolved spectroscopy in the heme visible bands after photolysis of the CO complex. Reviewing the evidence from spectrokinetic studies of Mb variants, we find that this optical method measures the occupancy of non(heme)coordinated water in the distal pocket, n(w), with high fidelity. This evidence further suggests that perturbation of the kinetic barrier presented by distal pocket water is often the dominant mechanism by which active site mutations affect the bimolecular rate constant for CO binding. Water entry into the heme pockets of isolated hemoglobin subunits was detected by optical methods. Internal hydration is higher in the native alpha chains than in the beta chains, in agreement with previous crystallographic results for the subunits within Hb tetramers. The kinetic parameters obtained from modeling of the water entry and ligand rebinding in Mb mutants and native Hb chains are consistent with an inverse dependence of the bimolecular association rate constant on the water occupancy factor. This correlation suggests that water and ligand mutually exclude one another from the distal pockets of both types of hemoglobin chains and myoglobin.
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Affiliation(s)
- Raymond M Esquerra
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, California 94132, USA
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43
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Munk MB, Huvaere K, Van Bocxlaer J, Skibsted LH. Mechanism of light-induced oxidation of nitrosylmyoglobin. Food Chem 2010. [DOI: 10.1016/j.foodchem.2009.12.067] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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44
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Ihee H, Wulff M, Kim J, Adachi SI. Ultrafast X-ray scattering: structural dynamics from diatomic to protein molecules. INT REV PHYS CHEM 2010. [DOI: 10.1080/0144235x.2010.498938] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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45
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Blouin GC, Schweers RL, Olson JS. Alkyl isocyanides serve as transition state analogues for ligand entry and exit in myoglobin. Biochemistry 2010; 49:4987-97. [PMID: 20476741 DOI: 10.1021/bi1001745] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Alkyl isocyanides (CNRs) identify pathways for diatomic ligand movement into and out of Mb, with their side chains acting as transition state analogues. The bound alkyl groups point either into the back of the distal pocket (in conformation, nu(CN) approximately 2070-2090 cm(-1)), which allows hydrogen bond donation from His64(E7) to the isocyano group, or toward solvent through an open His(E7) channel (out conformation, nu(CN) approximately 2110-2130 cm(-1)), which prevents polar interactions with the isocyano atoms. Fractions of the in conformer (F(in)) were measured by FTIR spectroscopy for methyl through n-pentyl isocyanide bound to a series of 20 different distal pocket mutants of sperm whale myoglobin and found to be governed by the ease of rotation of the His(E7) side chain, distal pocket volume and steric interactions, and, for the longer isocyanides, the unfavorable hydrophobic effect of placing their terminal carbon atoms into the solvent phase in the out conformation. There are strong correlations between the fraction of in conformer, F(in), for long-chain MbCNR complexes measured by FTIR spectroscopy, the fraction of geminate recombination of photodissociated O(2), and the bimolecular rates of O(2) entry into the distal pocket. These correlations indicate that alkyl isocyanides serve as transition state analogues for the movement of O(2) into and out of the binding pocket of Mb.
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Affiliation(s)
- George C Blouin
- Department of Biochemistry and Cell Biology and W. M. Keck Center for Computational Biology, Rice University, Houston, Texas 77005, USA
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46
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Smith RD, Blouin GC, Johnson KA, Phillips GN, Olson JS. Straight-chain alkyl isocyanides open the distal histidine gate in crystal structures of myoglobin . Biochemistry 2010; 49:4977-86. [PMID: 20481504 PMCID: PMC4074459 DOI: 10.1021/bi1001739] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Crystal structures of methyl, ethyl, propyl, and butyl isocyanide bound to sperm whale myoglobin (Mb) reveal two major conformations. In the in conformer, His(E7) is in a "closed" position, forcing the ligand alkyl chain to point inward. In the out conformer, His(E7) is in an "open" position, allowing the ligand side chain to point outward. A progressive increase in the population of the out conformer is observed with increasing ligand length in P2(1) crystals of native Mb at pH 7.0. This switch from in to out with increasing ligand size also occurs in solution as measured by the decrease in the relative intensity of the low-frequency ( approximately 2075 cm(-1)) versus high-frequency ( approximately 2125 cm(-1)) isocyano bands. In contrast, all four isocyanides in P6 crystals of wild-type recombinant Mb occupy the in conformation. However, mutating either His64 to Ala, creating a "hole" to solvent, or Phe46 to Val, freeing rotation of His64, causes bound butyl isocyanide to point completely outward in P6 crystals. Thus, the unfavorable hindrance caused with crowding a large alkyl side chain into the distal pocket appears to be roughly equal to that for pushing open the His(E7) gate and is easily affected by crystal packing. This structural conclusion supports the "side path" kinetic mechanism for O(2) release, in which the dissociated ligand first moves toward the protein interior and then encounters steric resistance, which is roughly equal to that for escaping to solvent through the His(E7) channel.
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Affiliation(s)
| | | | | | | | - John S. Olson
- CORRESPONDING AUTHOR FOOTNOTE. Author to whom correspondence should be addressed. Telephone 713-348-4762; Fax 713-348-5154;
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47
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Scorciapino MA, Robertazzi A, Casu M, Ruggerone P, Ceccarelli M. Breathing motions of a respiratory protein revealed by molecular dynamics simulations. J Am Chem Soc 2009; 131:11825-32. [PMID: 19653680 DOI: 10.1021/ja9028473] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Internal cavities, which are central to the biological functions of myoglobin, are exploited by gaseous ligands (e.g., O(2), NO, CO, etc.) to migrate inside the protein matrix. At present, it is not clear whether the ligand makes its own way inside the protein or instead the internal cavities are an intrinsic feature of myoglobin. To address this issue, standard molecular dynamics simulations were performed on horse-heart met-myoglobin with no ligand migrating inside the protein matrix. To reveal intrinsic internal pathways, the use of a statistical approach was applied to the cavity calculation, with special emphasis on the major pathway from the distal pocket to Xe1. Our study points out the remarkable dynamical behavior of Xe4, whose "breathing motions" may facilitate migration of ligands through the distal region. Additionally, our results highlight a two-way path for a ligand to diffuse through the proximal region, possibly allowing an alternative route in case Xe1 is occupied. Finally, our approach has led us to the identification of key residues, such as leucines, that may work as switches between cavities.
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Affiliation(s)
- Mariano Andrea Scorciapino
- Department of Chemical Sciences, University of Cagliari, Cittadella Universitaria, I-09042 Monserrato (Ca), Italy
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48
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Ahn S, Kim KH, Kim Y, Kim J, Ihee H. Protein tertiary structural changes visualized by time-resolved X-ray solution scattering. J Phys Chem B 2009; 113:13131-3. [PMID: 19757799 DOI: 10.1021/jp906983v] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
We obtained a solution structural model of myoglobin (Mb) formed upon the CO photolysis of MbCO by analyzing time-resolved X-ray solution scattering data. An experiment-restrained rigid-body molecular dynamics simulation was used to find the best model whose theoretical difference scattering curve gives a satisfactory agreement with the experimental data at the time delay of 10 ns. The obtained solution model shows structural changes similar to crystallographic models for MbCO --> Mb but also displays a noticeable difference in that the N-terminus and F helix show larger structural changes.
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49
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Goldbeck RA, Pillsbury ML, Jensen RA, Mendoza JL, Nguyen RL, Olson JS, Soman J, Kliger DS, Esquerra RM. Optical detection of disordered water within a protein cavity. J Am Chem Soc 2009; 131:12265-72. [PMID: 19655795 DOI: 10.1021/ja903409j] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Internal water molecules are important to protein structure and function, but positional disorder and low occupancies can obscure their detection by X-ray crystallography. Here, we show that water can be detected within the distal cavities of myoglobin mutants by subtle changes in the absorbance spectrum of pentacoordinate heme, even when the presence of solvent is not readily observed in the corresponding crystal structures. A well-defined, noncoordinated water molecule hydrogen bonded to the distal histidine (His64) is seen within the distal heme pocket in the crystal structure of wild type (wt) deoxymyoglobin. Displacement of this water decreases the rate of ligand entry into wt Mb, and we have shown previously that the entry of this water is readily detected optically after laser photolysis of MbCO complexes. However, for L29F and V68L Mb no discrete positions for solvent molecules are seen in the electron density maps of the crystal structures even though His64 is still present and slow rates of ligand binding indicative of internal water are observed. In contrast, time-resolved perturbations of the visible absorption bands of L29F and V68L deoxyMb generated after laser photolysis detect the entry and significant occupancy of water within the distal pockets of these variants. Thus, the spectral perturbation of pentacoordinate heme offers a potentially robust system for measuring nonspecific hydration of the active sites of heme proteins.
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Affiliation(s)
- Robert A Goldbeck
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, USA.
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Porrini M, Daskalakis V, Farantos SC, Varotsis C. Heme Cavity Dynamics of Photodissociated CO from ba3-Cytochrome c Oxidase: The Role of Ring-D Propionate. J Phys Chem B 2009; 113:12129-35. [DOI: 10.1021/jp904466n] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Massimiliano Porrini
- Institute of Electronic Structure and Laser, Foundation for Research and Technology-Hellas (FORTH), P.O. Box 1527, Vasilika Vouton, Heraklion 71110, Crete, Greece, and Department of Chemistry, University of Crete, P.O. Box 2208, Vasilika Vouton, Heraklion 71305, Crete, Greece
| | - Vangelis Daskalakis
- Institute of Electronic Structure and Laser, Foundation for Research and Technology-Hellas (FORTH), P.O. Box 1527, Vasilika Vouton, Heraklion 71110, Crete, Greece, and Department of Chemistry, University of Crete, P.O. Box 2208, Vasilika Vouton, Heraklion 71305, Crete, Greece
| | - Stavros C. Farantos
- Institute of Electronic Structure and Laser, Foundation for Research and Technology-Hellas (FORTH), P.O. Box 1527, Vasilika Vouton, Heraklion 71110, Crete, Greece, and Department of Chemistry, University of Crete, P.O. Box 2208, Vasilika Vouton, Heraklion 71305, Crete, Greece
| | - Constantinos Varotsis
- Institute of Electronic Structure and Laser, Foundation for Research and Technology-Hellas (FORTH), P.O. Box 1527, Vasilika Vouton, Heraklion 71110, Crete, Greece, and Department of Chemistry, University of Crete, P.O. Box 2208, Vasilika Vouton, Heraklion 71305, Crete, Greece
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