Authors: Sagar Bhattacharya, Eleonora G Margheritis, Katsuya Takahashi...

Directed evolution is a powerful tool for improving existing properties and imparting completely new functionalities to proteins. Nonetheless, its potential in even small proteins is inherently limited by the astronomical number of possible amino acid sequences. Sampling the complete sequence space of a 100-residue protein would require testing of 20 combinations, which is beyond any existing experimental approach. In practice, selective modification of relatively few residues is sufficient for efficient improvement, functional enhancement and repurposing of existing proteins. Moreover, computational methods have been developed to predict the locations and, in certain cases, identities of potentially productive mutations. Importantly, all current approaches for prediction of hot spots and productive mutations rely heavily on structural information and/or bioinformatics, which is not always available for proteins of interest. Moreover, they offer a limited ability to identify beneficial mutations far from the active site, even though such changes may markedly improve the catalytic properties of an enzyme. Machine learning methods have recently showed promise in predicting productive mutations, but they frequently require large, high-quality training datasets, which are difficult to obtain in directed evolution experiments. Here we show that mutagenic hot spots in enzymes can be identified using NMR spectroscopy. In a proof-of-concept study, we converted myoglobin, a non-enzymatic oxygen storage protein, into a highly efficient Kemp eliminase using only three mutations. The observed levels of catalytic efficiency exceed those of proteins designed using current approaches and are similar with those of natural enzymes for the reactions that they are evolved to catalyse. Given the simplicity of this experimental approach, which requires no a priori structural or bioinformatic knowledge, we expect it to be widely applicable and to enable the full potential of directed enzyme evolution.

Topics: Biocatalysis; Catalytic Domain; Directed Molecular Evolution; Magnetic Resonance Spectroscopy; Mutation; Myoglobin; Oxygen

PubMed: 36198791
DOI: 10.1038/s41586-022-05278-9

Review

Authors: T Suzuki, K Imai

The distribution, physiological function, amino acid sequence and gene structure of myoglobin and myoglobin-like proteins from various taxa are summarized, and their evolution is discussed. Although it has long been thought that all haemoglobins and myoglobins have evolved from a common ancestral gene, the knowledge presently accumulated about the structures of these proteins suggests that there may be three distinct origins: a 'universal globin', a 'compact globin' and an 'IDO-like globin'.

Topics: Amino Acid Sequence; Animals; Eukaryotic Cells; Evolution, Molecular; Hemoglobins; Humans; Invertebrates; Models, Molecular; Molecular Sequence Data; Myoglobin; Oxygen; Phylogeny; Prokaryotic Cells; Protein Conformation; Sequence Homology, Amino Acid; Vertebrates

PubMed: 9791540
DOI: 10.1007/s000180050227

Review

Authors: D J Garry, A Meeson, Z Yan...

Hemoproteins are widely distributed among prokaryotes, unicellular eukaryotes, plants and animals [1]. Myoglobin, a cytoplasmic hemoprotein that is restricted to cardiomyocytes and oxidative skeletal myofibers in vertebrates, has been proposed to facilitate oxygen transport to the mitochondria [1-3]. This cytoplasmic hemoprotein was the first protein to be subjected to definitive structural analysis and has been a subject of long-standing and ongoing interest to biologists [1-3]. Recently, we utilized gene disruption technology to generate mice that are viable and fertile despite a complete absence of myoglobin [4]. This unexpected result led us to reexamine existing paradigms regarding the function of myoglobin in striated muscle.

Topics: Animals; Biological Transport; Gene Expression Regulation; Mice; Mice, Knockout; Muscle, Skeletal; Myocardium; Myoglobin; Oxygen

PubMed: 10950305
DOI: 10.1007/PL00000732

Review

Authors: Maurizio Brunori

Over the last half century, myoglobin (Mb) has been an excellent model system to test a number of concepts, theories, and new experimental methods that proved valuable to investigate protein structure, function, evolution, and dynamics. Mb's function, most often considered just an oxygen repository, has considerably diversified over the last 15 years, especially because it was shown to have a role in the biochemistry of quenching and synthesizing nitric oxide in the red muscle, thereby protecting the cell. To tackle protein's structural dynamics by innovative biophysical methods, Mb has been the best prototype; laser flash technology made it possible to obtain molecular movies by time-resolved Laue crystallography (with ps resolution). This approach unveiled the complexity of the energy landscape and the structural basis of the stretched interconversion between conformational substates of a protein.

Topics: Animals; Heme; Humans; Myoglobin; Oxygen; Protein Conformation; Substrate Specificity

PubMed: 19953516
DOI: 10.1002/pro.300

Review

Authors: Michael T Wilson, Brandon J Reeder

Under those pathological conditions in which Myoglobin and Hemoglobin escape their cellular environments and are thus separated from cellular reductive/protective systems, the inherent peroxidase activities of these proteins can be expressed. This activity leads to the formation of the highly oxidizing oxo-ferryl species. Evidence that this happens in vivo is provided by the formation of a covalent bond between the heme group and the protein and this acts as an unambiguous biomarker for the presence of the oxo ferryl form. The peroxidatic activity also leads to the oxidation of lipids, the products of which can be powerful vasoconstrictive agents (e.g. isoprostanes, neuroprostanes). Here we review the evidence that lipid oxidation occurs following rhabdomyolysis and sub-arachnoid hemorrhage and that the products formed from arachidonic acid chains of phospholipids lead, through vasoconstriction, to kidney failure and brain vasospasm. Intervention in these pathological conditions through administration of reducing agents to remove ferryl heme is discussed. Through-protein electron transfer pathways that facilitate ferryl reduction at low reductant concentration have been identified. We conclude with consideration of the therapeutic use of Hemoglobin Based Oxygen carriers and how the toxicity of these may be reduced by engineering such electron transfer pathways into hemoglobin.

Topics: Heme; Hemoglobins; Humans; Myoglobin; Oxidation-Reduction; Oxygen

PubMed: 34654576
DOI: 10.1016/j.mam.2021.101045

Review

Authors: G N Phillips, B M Pettitt

The interplay between simulations at various levels of hydration and experimental observables has led to a picture of the role of solvent in thermodynamics and dynamics of protein systems. One of the most studied protein-solvent systems is myoglobin, which serves as a paradigm for the development of structure-function relationships in many biophysical studies. We review here some aspects of the solvation of myoglobin and the resulting implications. In particular, recent theoretical and simulation studies unify much of the diverse set of experimental results on water near proteins.

Topics: Crystallography, X-Ray; Electron Spin Resonance Spectroscopy; Magnetic Resonance Spectroscopy; Models, Molecular; Myoglobin; Structure-Activity Relationship; Thermodynamics; Water; X-Ray Diffraction

PubMed: 7757005
DOI: 10.1002/pro.5560040202

Authors: Kikumi D Ono-Moore, I Mark Olfert, Jennifer M Rutkowsky...

Myoglobin (Mb) is a regulator of O bioavailability in type I muscle and heart, at least when tissue O levels drop. Mb also plays a role in regulating cellular nitric oxide (NO) pools. Robust binding of long-chain fatty acids and long-chain acylcarnitines to Mb, and enhanced glucose metabolism in hearts of Mb knockout (KO) mice, suggest additional roles in muscle intermediary metabolism and fuel selection. To evaluate this hypothesis, we measured energy expenditure (EE), respiratory exchange ratio (RER), body weight gain and adiposity, glucose tolerance, and insulin sensitivity in Mb knockout (Mb) and wild-type (WT) mice challenged with a high-fat diet (HFD, 45% of calories). In males ( = 10/genotype) and females ( = 9/genotype) tested at 5-6, 11-12, and 17-18 wk, there were no genotype effects on RER, EE, or food intake. RER and EE during cold (10°C, 72 h), and glucose and insulin tolerance, were not different compared with within-sex WT controls. At ∼18 and ∼19 wk of age, female Mb adiposity was ∼42%-48% higher versus WT females ( = 0.1). Transcriptomics analyses (whole gastrocnemius, soleus) revealed few consistent changes, with the notable exception of a 20% drop in soleus transferrin receptor (Tfrc) mRNA. Capillarity indices were significantly increased in Mb, specifically in Mb-rich soleus and deep gastrocnemius. The results indicate that Mb loss does not have a major impact on whole body glucose homeostasis, EE, RER, or response to a cold challenge in mice. However, the greater adiposity in female Mb mice indicates a sex-specific effect of Mb KO on fat storage and feed efficiency. The roles of myoglobin remain to be elaborated. We address sexual dimorphism in terms of outcomes in response to the loss of myoglobin in knockout mice and perform, for the first time, a series of comprehensive metabolic studies under conditions in which fat is mobilized (high-fat diet, cold). The results highlight that myoglobin is not necessary and sufficient for maintaining oxidative metabolism and point to alternative roles for this protein in muscle and heart.

Topics: Adiposity; Animals; Body Weight; Diet, High-Fat; Energy Metabolism; Fatty Acids; Female; Glucose Tolerance Test; Lipid Metabolism; Male; Mice; Mice, Inbred C57BL; Mice, Knockout; Muscle, Skeletal; Myocardium; Myoglobin; Oxidation-Reduction; Phenotype; Sex Characteristics

PubMed: 33969704
DOI: 10.1152/ajpendo.00624.2020

Authors: Tang-Qing Yu, Mauro Lapelosa, Eric Vanden-Eijnden...

We use Markovian milestoning molecular dynamics (MD) simulations on a tessellation of the collective variable space for CO localization in myoglobin to estimate the kinetics of entry, exit, and internal site-hopping. The tessellation is determined by analysis of the free-energy surface in that space using transition-path theory (TPT), which provides criteria for defining optimal milestones, allowing short, independent, cell-constrained MD simulations to provide properly weighted kinetic data. We coarse grain the resulting kinetic model at two levels: first, using crystallographically relevant internal cavities and their predicted interconnections and solvent portals; and second, as a three-state side-path scheme inspired by similar models developed from geminate recombination experiments. We show semiquantitative agreement with experiment on entry and exit rates and in the identification of the so-called "histidine gate" at position 64 through which ≈90% of flux between solvent and the distal pocket passes. We also show with six-dimensional calculations that the minimum free-energy pathway of escape through the histidine gate is a "knock-on" mechanism in which motion of the ligand and the gate are sequential and interdependent. In total, these results suggest that such TPT simulations are indeed a promising approach to overcome the practical time-scale limitations of MD to allow reliable estimation of transition mechanisms and rates among metastable states.

Topics: Binding Sites; Carbon Monoxide; Diffusion; Kinetics; Ligands; Models, Molecular; Myoglobin; Protein Conformation

PubMed: 25664858
DOI: 10.1021/ja512484q

Review

Authors: John S Olson

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 O 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 O 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 O. The pathway for O uptake and release by Mb and subunits of Hb has been mapped by screening libraries of site-directed mutants in laser photolysis experiments. O 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. O dissociation is governed by disruption of hydrogen bonding interactions with His (E7), breakage of the Fe(II)-O 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 O transport and storage processes.

Topics: Animals; Carbon Monoxide; Hemoglobins; Humans; Kinetics; Ligands; Mammals; Myoglobin; Oxygen

PubMed: 34544605
DOI: 10.1016/j.mam.2021.101024

Review

Authors: Gerolf Gros, Beatrice A Wittenberg, Thomas Jue...

Myoglobin, a mobile carrier of oxygen, is without a doubt an important player central to the physiological function of heart and skeletal muscle. Recently, researchers have surmounted technical challenges to measure Mb diffusion in the living cell. Their observations have stimulated a discussion about the relative contribution made by Mb-facilitated diffusion to the total oxygen flux. The calculation of the relative contribution, however, depends upon assumptions, the cell model and cell architecture, cell bioenergetics, oxygen supply and demand. The analysis suggests that important differences can be observed whether steady-state or transient conditions are considered. This article reviews the current evidence underlying the evaluation of the biophysical parameters of myoglobin-facilitated oxygen diffusion in cells, specifically the intracellular concentration of myoglobin, the intracellular diffusion coefficient of myoglobin and the intracellular myoglobin oxygen saturation. The review considers the role of myoglobin in oxygen transport in vertebrate heart and skeletal muscle, in the diving seal during apnea as well as the role of the analogous leghemoglobin of plants. The possible role of myoglobin in intracellular fatty acid transport is addressed. Finally, the recent measurements of myoglobin diffusion inside muscle cells are discussed in terms of their implications for cytoarchitecture and microviscosity in these cells and the identification of intracellular impediments to the diffusion of proteins inside cells. The recent experimental data then help to refine our understanding of Mb function and establish a basis for future investigation.

Topics: Animals; Diffusion; Diving; Fatty Acids; Humans; Muscle, Skeletal; Myocardium; Myoglobin; Nuclear Magnetic Resonance, Biomolecular; Oxygen; Oxygen Consumption

PubMed: 20675540
DOI: 10.1242/jeb.043075