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1.
Adv Protein Chem Struct Biol ; 141: 123-176, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-38960472

RESUMO

Metalloproteins represents more than one third of human proteome, with huge variation in physiological functions and pathological implications, depending on the metal/metals involved and tissue context. Their functions range from catalysis, bioenergetics, redox, to DNA repair, cell proliferation, signaling, transport of vital elements, and immunity. The human metalloproteomic studies revealed that many families of metalloproteins along with individual metalloproteins are dysregulated under several clinical conditions. Also, several sorts of interaction between redox- active or redox- inert metalloproteins are observed in health and disease. Metalloproteins profiling shows distinct alterations in neurodegenerative diseases, cancer, inflammation, infection, diabetes mellitus, among other diseases. This makes metalloproteins -either individually or as families- a promising target for several therapeutic approaches. Inhibitors and activators of metalloenzymes, metal chelators, along with artificial metalloproteins could be versatile in diagnosis and treatment of several diseases, in addition to other biomedical and industrial applications.


Assuntos
Metaloproteínas , Proteômica , Humanos , Metaloproteínas/metabolismo , Neoplasias/metabolismo , Doenças Neurodegenerativas/metabolismo , Doenças Neurodegenerativas/patologia
2.
Adv Protein Chem Struct Biol ; 141: 23-66, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-38960476

RESUMO

Enzymes are nature's ultimate machinery to catalyze complex reactions. Though enzymes are evolved to catalyze specific reactions, they also show significant promiscuity in reactions and substrate selection. Metalloenzymes contain a metal ion or metal cofactor in their active site, which is crucial in their catalytic activity. Depending on the metal and its coordination environment, the metal ion or cofactor may function as a Lewis acid or base and a redox center and thus can catalyze a plethora of natural reactions. In fact, the versatility in the oxidation state of the metal ions provides metalloenzymes with a high level of catalytic adaptability and promiscuity. In this chapter, we discuss different aspects of promiscuity in metalloenzymes by using several recent experimental and theoretical works as case studies. We start our discussion by introducing the concept of promiscuity and then we delve into the mechanistic insight into promiscuity at the molecular level.


Assuntos
Metaloproteínas , Metaloproteínas/química , Metaloproteínas/metabolismo , Enzimas/metabolismo , Enzimas/química , Especificidade por Substrato , Metais/química , Metais/metabolismo , Domínio Catalítico , Oxirredução
3.
Adv Protein Chem Struct Biol ; 141: 299-329, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-38960478

RESUMO

TMEM230 promotes antigen processing, trafficking, and presentation by regulating the endomembrane system of membrane bound organelles (lysosomes, proteosomes and mitochondria) and phagosomes. Activation of the immune system requires trafficking of various cargos between the endomembrane system and cell plasma membrane. The Golgi apparatus is the hub of the endomembrane system and essential for the generation, maintenance, recycling, and trafficking of the components of the endomembrane system itself and immune system. Intracellular trafficking and secretion of immune system components depend on mitochondrial metalloproteins for ATP synthesis that powers motor protein transport of endomembrane cargo. Glycan modifying enzyme genes and motor proteins are essential for the activation of the immune system and trafficking of antigens between the endomembrane system and the plasma membrane. Recently, TMEM230 was identified as co-regulated with RNASET2 in lysosomes and with metalloproteins in various cell types and organelles, including mitochondria in autoimmune diseases. Aberrant metalloproteinase secretion by motor proteins is a major contributor to tissue remodeling of synovial membrane and joint tissue destruction in rheumatoid arthritis (RA) by promoting infiltration of blood vessels, bone erosion, and loss of cartilage by phagocytes. In this study, we identified that specific glycan processing enzymes are upregulated in certain cell types (fibroblast or endothelial cells) that function in destructive tissue remodeling in rheumatoid arthritis compared to osteoarthritis (OA). TMEM230 was identified as a regulator in the secretion of metaloproteinases and heparanase necessary tissue remodeling in OA and RA. In dendritic (DC), natural killer and T cells, TMEM230 was expressed at low or no levels in RA compared to OA. TMEM230 expression in DC likely is necessary for regulatory or helper T cells to maintain tolerance to self-antigens and prevent susceptibility to autoimmune disease. To identify how TMEM230 and the endomembrane system contribute to autoimmunity we investigated, glycan modifying enzymes, metalloproteinases and motor protein genes co-regulated with or regulated by TMEM230 in synovial tissue by analyzing published single cell transcriptomic datasets from RA patient derived synovial tissue.


Assuntos
Metaloproteínas , Humanos , Metaloproteínas/metabolismo , Metaloproteínas/genética , Análise de Célula Única , Autoimunidade , Proteínas de Membrana/metabolismo , Proteínas de Membrana/genética , Animais , Perfilação da Expressão Gênica
4.
Adv Protein Chem Struct Biol ; 141: 495-538, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-38960484

RESUMO

The gut microbial metalloenzymes play an important role in maintaining the balance between gut microbial ecosystem, human physiologically processes and immune system. The metals coordinated into active site contribute in various detoxification and defense strategies to avoid unfavourable environment and ensure bacterial survival in human gut. Metallo-ß-lactamase is a potent degrader of antibiotics present in periplasmic space of both commensals and pathogenic bacteria. The resistance to anti-microbial agents developed in this enzyme is one of the global threats for human health. The organophosphorus eliminator, organophosphorus hydrolases have evolved over a course of time to hydrolyze toxic organophosphorus compounds and decrease its effect on human health. Further, the redox stress responders namely superoxide dismutase and catalase are key metalloenzymes in reducing both endogenous and exogenous oxidative stress. They hold a great importance for pathogens as they contribute in pathogenesis in human gut along with reduction of oxidative stress. The in-silico study on these enzymes reveals the importance of point mutation for the evolution of these enzymes in order to enhance their enzyme activity and stability. Various mutation studies were conducted to investigate the catalytic activity of these enzymes. By using the "directed evolution" method, the enzymes involved in detoxification and defense system can be engineered to produce new variants with enhance catalytic features, which may be used to predict the severity due to multi-drug resistance and degradation pattern of organophosphorus compounds in human gut.


Assuntos
Microbioma Gastrointestinal , Metaloproteínas , Espécies Reativas de Oxigênio , Xenobióticos , Xenobióticos/metabolismo , Humanos , Metaloproteínas/metabolismo , Metaloproteínas/química , Metaloproteínas/genética , Espécies Reativas de Oxigênio/metabolismo
5.
Adv Protein Chem Struct Biol ; 141: 539-562, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-38960485

RESUMO

Several species during evolution suffered random mutations in response to various environmental factors, which resulted in the formation of venom in phylogenetically distant species. The composition of the venom of most species is poorly known. Snake venom is well characterized while most species have poorly known composition. In contrast, snake venoms are well characterized which proteins and peptides are the main active and most abundant constituents. 42 protein families have been identified, including metalloproteins known as metalloproteinases. These macromolecules are enzymes with zinc in their active site derived from the disintegrin A and metalloproteinase (ADAM) cellular family and are categorized into three classes (PI, PII and PIII) according to their domain organization. The snake venom metalloproteinases (SVMP) are cytotoxic, neurotoxic, myotoxic and/or hematotoxic with a crucial role in the defense and restraint of prey. In this scenario envenoming represents a danger to human health and has been considered a neglected disease worldwide, particularly in tropical and subtropical countries. Nevertheless, recently advances in "omics" technologies have demonstrated interesting biological activities of SVMPs such as antimicrobial, anticancer, against cardiovascular diseases and nervous system disorders. Metalloproteins have the therapeutic potential to be converted into drugs as other components of the venom have undergone this process (e.g., captopril, tirefiban and eptifibatide). So, this chapter is focused on the metalloproteins found in the secretions of venomous species, highlight some aspects such as structure, biological activity, pharmacological therapeutic potential and on.


Assuntos
Metaloproteínas , Venenos de Serpentes , Animais , Humanos , Venenos de Serpentes/metabolismo , Venenos de Serpentes/química , Venenos de Serpentes/enzimologia , Metaloproteínas/metabolismo , Metaloproteínas/química , Metaloproteínas/antagonistas & inibidores
6.
Adv Protein Chem Struct Biol ; 141: 67-86, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-38960487

RESUMO

Metalloproteins play a crucial role in regulating different aspects of the immune system in humans. They have various functions in immunity, including recognizing and presenting antigens, aiding in the movement and effectiveness of immune cells, and facilitating interactions between the host and pathogens. Understanding how these proteins work can help us develop new methods to control the immune response in different diseases. Metalloproteins contain metal ions in their structure, which allows them to perform these diverse functions. They encompass a wide range of enzymes, signaling molecules, and structural proteins that utilize metal ions as cofactors for their activities. Examples of metalloproteins include superoxide dismutase, catalase, and metalloproteases, which regulate oxidative stress, inflammation, and tissue remodelling processes associated with immune activation. By studying their functions and the effects of their dysfunction, researchers can develop strategies to improve immune function and combat various diseases. This review explores the diverse functions of metalloproteins in immune processes, highlighting their significance in both health and disease.


Assuntos
Metaloproteínas , Humanos , Metaloproteínas/química , Metaloproteínas/imunologia , Metaloproteínas/metabolismo , Animais
7.
J Inorg Biochem ; 258: 112621, 2024 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-38852295

RESUMO

CH functionalization, a promising frontier in modern organic chemistry, facilitates the direct conversion of inert CH bonds into many valuable functional groups. Despite its merits, traditional homogeneous catalysis, often faces challenges in efficiency, selectivity, and sustainability towards this transformation. In this context, artificial metalloenzymes (ArMs), resulting from the incorporation of a catalytically-competent metal cofactor within an evolvable protein scaffold, bridges the gap between the efficiency of enzymatic transformations and the versatility of transition metal catalysis. Accordingly, ArMs have emerged as attractive tools for various challenging catalytic transformations. Additionally, the coming of age of directed evolution has unlocked unprecedented avenues for optimizing enzymatic catalysis. Taking advantage of their genetically-encoded protein scaffold, ArMs have been evolved to catalyze various CH functionalization reactions. This review delves into the recent developments of ArM-catalyzed CH functionalization reactions, highlighting the benefits of engineering the second coordination sphere around a metal cofactor within a host protein.


Assuntos
Metaloproteínas , Metaloproteínas/química , Metaloproteínas/metabolismo , Catálise , Engenharia de Proteínas/métodos , Hidrogênio/química
8.
Chem Commun (Camb) ; 60(42): 5490-5493, 2024 May 21.
Artigo em Inglês | MEDLINE | ID: mdl-38699837

RESUMO

The immobilisation of artificial metalloenzymes (ArMs) holds promise for the implementation of new biocatalytic reactions. We present the synthesis of cross-linked artificial metalloenzyme aggregates (CLArMAs) with excellent recyclability, as an alternative to carrier-based immobilisation strategies. Furthermore, iron-siderophore supramolecular anchoring facilitates redox-triggered cofactor release, enabling CLArMAs to be recharged with alternative cofactors for diverse selectivity.


Assuntos
Oxirredução , Sideróforos , Sideróforos/química , Estereoisomerismo , Metaloproteínas/química , Metaloproteínas/metabolismo , Catálise , Biocatálise , Reagentes de Ligações Cruzadas/química , Ferro/química
9.
J Inorg Biochem ; 257: 112595, 2024 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-38759262

RESUMO

Globins, such as myoglobin (Mb) and neuroglobin (Ngb), are ideal protein scaffolds for the design of functional metalloenzymes. To date, numerous approaches have been developed for enzyme design. This review presents a summary of the progress made in the design of functional metalloenzymes based on Mb and Ngb, with a focus on the exploitation of covalent interactions, including coordination bonds and covalent modifications. These include the construction of a metal-binding site, the incorporation of a non-native metal cofactor, the formation of Cys/Tyr-heme covalent links, and the design of disulfide bonds, as well as other Cys-covalent modifications. As exemplified by recent studies from our group and others, the designed metalloenzymes have potential applications in biocatalysis and bioconversions. Furthermore, we discuss the current trends in the design of functional metalloenzymes and highlight the importance of covalent interactions in the design of functional metalloenzymes.


Assuntos
Globinas , Mioglobina , Proteínas do Tecido Nervoso , Neuroglobina , Neuroglobina/metabolismo , Neuroglobina/química , Mioglobina/química , Mioglobina/metabolismo , Globinas/química , Globinas/metabolismo , Proteínas do Tecido Nervoso/metabolismo , Proteínas do Tecido Nervoso/química , Humanos , Animais , Heme/química , Heme/metabolismo , Sítios de Ligação , Metaloproteínas/química , Metaloproteínas/metabolismo , Engenharia de Proteínas/métodos
10.
Nucleic Acids Res ; 52(11): 6459-6471, 2024 Jun 24.
Artigo em Inglês | MEDLINE | ID: mdl-38726868

RESUMO

CRISPR-Cas systems serve as adaptive immune systems in bacteria and archaea, protecting against phages and other mobile genetic elements. However, phages and archaeal viruses have developed countermeasures, employing anti-CRISPR (Acr) proteins to counteract CRISPR-Cas systems. Despite the revolutionary impact of CRISPR-Cas systems on genome editing, concerns persist regarding potential off-target effects. Therefore, understanding the structural and molecular intricacies of diverse Acrs is crucial for elucidating the fundamental mechanisms governing CRISPR-Cas regulation. In this study, we present the structure of AcrIIA28 from Streptococcus phage Javan 128 and analyze its structural and functional features to comprehend the mechanisms involved in its inhibition of Cas9. Our current study reveals that AcrIIA28 is a metalloprotein that contains Zn2+ and abolishes the cleavage activity of Cas9 only from Streptococcus pyrogen (SpyCas9) by directly interacting with the REC3 domain of SpyCas9. Furthermore, we demonstrate that the AcrIIA28 interaction prevents the target DNA from being loaded onto Cas9. These findings indicate the molecular mechanisms underlying AcrIIA28-mediated Cas9 inhibition and provide valuable insights into the ongoing evolutionary battle between bacteria and phages.


Assuntos
Proteína 9 Associada à CRISPR , Sistemas CRISPR-Cas , Fagos de Streptococcus , Streptococcus , Proteína 9 Associada à CRISPR/metabolismo , Proteína 9 Associada à CRISPR/genética , Proteína 9 Associada à CRISPR/química , DNA/metabolismo , DNA/genética , Edição de Genes , Metaloproteínas/metabolismo , Metaloproteínas/genética , Metaloproteínas/química , Modelos Moleculares , Ligação Proteica , Domínios Proteicos , Streptococcus/genética , Streptococcus/virologia , Fagos de Streptococcus/genética , Fagos de Streptococcus/metabolismo , Proteínas Virais/metabolismo , Proteínas Virais/genética , Proteínas Virais/química , Zinco/metabolismo
11.
Clin Immunol ; 263: 110205, 2024 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-38575044

RESUMO

Increasing clinical data show that the imbalance of host metallome is closely associated with different kinds of disease, however, the intrinsic mechanisms of action of metals in immunity and pathogenesis of disease remain largely undefined. There is lack of multiplexed profiling system to integrate the metalloproteome-immunoproteome information at systemic level for exploring the roles of metals in immunity and disease pathogenesis. In this study, we build up a metal-coding assisted multiplexed proteome assay platform for serum metalloproteomic and immunoproteomic profiling. By taking COVID-19 as a showcase, we unbiasedly uncovered the most evident modulation of iron-related proteins, i.e., Ft and Tf, in serum of severe COVID-19 patients, and the value of Ft/Tf could work as a robust biomarker for COVID-19 severity stratification, which overtakes the well-established clinical risk factors (cytokines). We further uncovered a tight association of transferrin with inflammation mediator IL-10 in COVID-19 patients, which was proved to be mainly governed by the monocyte/macrophage of liver, shedding light on new pathophysiological and immune regulatory mechanisms of COVID-19 disease. We finally validated the beneficial effects of iron chelators as anti-viral agents in SARS-CoV-2-infected K18-hACE2 mice through modulation of iron dyshomeostasis and alleviating inflammation response. Our findings highlight the critical role of liver-mediated iron dysregulation in COVID-19 disease severity, providing solid evidence on the involvement of iron-related proteins in COVID-19 pathophysiology and immunity.


Assuntos
COVID-19 , Ferro , Proteoma , SARS-CoV-2 , COVID-19/imunologia , Humanos , Animais , SARS-CoV-2/imunologia , Camundongos , Ferro/metabolismo , Proteômica/métodos , Transferrina/metabolismo , Metaloproteínas/imunologia , Metaloproteínas/metabolismo , Masculino , Feminino , Biomarcadores/sangue , Biomarcadores/metabolismo , Quelantes de Ferro/uso terapêutico , Quelantes de Ferro/farmacologia , Interleucina-10/imunologia , Interleucina-10/metabolismo , Pessoa de Meia-Idade
12.
Biochim Biophys Acta Mol Cell Res ; 1871(5): 119731, 2024 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-38631442

RESUMO

Molybdenum cofactor (Moco) biosynthesis is a complex process that involves the coordinated function of several proteins. In the recent years it has become evident that the availability of Fe-S clusters play an important role for the biosynthesis of Moco. First, the MoaA protein binds two [4Fe-4S] clusters per monomer. Second, the expression of the moaABCDE and moeAB operons is regulated by FNR, which senses the availability of oxygen via a functional [4Fe-4S] cluster. Finally, the conversion of cyclic pyranopterin monophosphate to molybdopterin requires the availability of the L-cysteine desulfurase IscS, which is an enzyme involved in the transfer of sulfur to various acceptor proteins with a main role in the assembly of Fe-S clusters. In this review, we dissect the dependence of the production of active molybdoenzymes in detail, starting from the regulation of gene expression and further explaining sulfur delivery and Fe-S cluster insertion into target enzymes. Further, Fe-S cluster assembly is also linked to iron availability. While the abundance of selected molybdoenzymes is largely decreased under iron-limiting conditions, we explain that the expression of the genes is dependent on an active FNR protein. FNR is a very important transcription factor that represents the master-switch for the expression of target genes in response to anaerobiosis. Moco biosynthesis is further directly dependent on the presence of ArcA and also on an active Fur protein.


Assuntos
Coenzimas , Proteínas Ferro-Enxofre , Metaloproteínas , Cofatores de Molibdênio , Pteridinas , Metaloproteínas/metabolismo , Metaloproteínas/genética , Metaloproteínas/biossíntese , Proteínas Ferro-Enxofre/metabolismo , Proteínas Ferro-Enxofre/genética , Coenzimas/metabolismo , Coenzimas/biossíntese , Coenzimas/genética , Pteridinas/metabolismo , Proteínas de Escherichia coli/metabolismo , Proteínas de Escherichia coli/genética , Ferro/metabolismo , Enxofre/metabolismo , Escherichia coli/genética , Escherichia coli/metabolismo , Liases de Carbono-Enxofre/metabolismo , Liases de Carbono-Enxofre/genética , Regulação Bacteriana da Expressão Gênica , Óperon , Isomerases
13.
Insect Mol Biol ; 33(3): 246-258, 2024 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-38323672

RESUMO

Molybdenum cofactor sulfurase (MoCoS) is a key gene involved in the uric acid metabolic pathway that activates xanthine dehydrogenase to synthesise uric acid. Uric acid is harmful to mammals but plays crucial roles in insects, one of which is the immune responses. However, the function of Bombyx mori MoCoS in response to BmNPV remains unclear. In this study, BmMoCoS was found to be relatively highly expressed in embryonic development, gonads and the Malpighian tubules. In addition, the expression levels of BmMoCoS were significantly upregulated in three silkworm strains with different levels of resistance after virus infection, suggesting a close link between them. Furthermore, RNAi and overexpression studies showed that BmMoCoS was involved in resistance to BmNPV infection, and its antivirus effects were found to be related to the regulation of uric acid metabolism, which was uncovered by inosine- and febuxostat-coupled RNAi and overexpression. Finally, the BmMoCoS-mediated uric acid pathway was preliminarily confirmed to be a potential target to protect silkworms from BmNPV infection. Overall, this study provides new evidence for elucidating the molecular mechanism of silkworms in response to BmNPV infection and new strategies for the prevention of viral infections in sericulture.


Assuntos
Bombyx , Proteínas de Insetos , Nucleopoliedrovírus , Animais , Bombyx/enzimologia , Bombyx/genética , Bombyx/virologia , Proteínas de Insetos/metabolismo , Proteínas de Insetos/genética , Larva/metabolismo , Larva/crescimento & desenvolvimento , Larva/virologia , Metaloproteínas/metabolismo , Metaloproteínas/genética , Cofatores de Molibdênio , Nucleopoliedrovírus/fisiologia , Interferência de RNA , Ácido Úrico/metabolismo
14.
J Chem Inf Model ; 64(3): 812-824, 2024 Feb 12.
Artigo em Inglês | MEDLINE | ID: mdl-38198652

RESUMO

Metalloproteins widely exist in biology and play important roles in various processes. To accurately simulate metalloprotein systems, modeling polarization and charge transfer effects is vital. The fluctuating charge (FQ) model can efficiently generate atomic charges and simulate the charge transfer effect; it has been developed for a wide range of applications, but few models have been specifically tailored for metalloproteins. In this study, we present a fluctuating charge model specifically for zinc-containing metalloproteins based on the extended charge equilibration (EQeq) scheme. Our model was parametrized to reproduce CM5 charges instead of RESP/CHELPG charges because the former is less dependent on the conformation or basis set, does not suffer from unphysical charges for buried atoms, and is still being able to well reproduce the molecular dipoles. During our study, we found that adding the Pauling-bond-order-like term (referred to as the "+C term" in a previous study) between the zinc ion and ligating atoms significantly improves the model's performance. Although our model was trained for four-coordinated zinc sites only, our results indicated it can well describe the atomic charges in diverse zinc sites. Morever, our model was used to generate partial charges for the metal sites in three different zinc-containing metalloproteins (with four-, five-, and six-coordinated metal sites, respectively). These charges exhibited performance comparable to that of the RESP charges in molecular dynamics (MD) simulations. Additional tests indicated our model could also well reproduce the CM5 charges when geometric changes were involved. Those results indicate that our model can efficiently calculate the atomic charges for metal sites and well simulate the charge transfer effect, which marks an important step toward developing versatile polarizable force fields for metalloproteins.


Assuntos
Metaloproteínas , Zinco , Metaloproteínas/metabolismo , Metais , Simulação de Dinâmica Molecular , Conformação Molecular
15.
J Phys Chem B ; 128(4): 973-984, 2024 Feb 01.
Artigo em Inglês | MEDLINE | ID: mdl-38236012

RESUMO

Metalloproteins make up a class of proteins that incorporate metal ions into their structures, enabling them to perform essential functions in biological systems, such as catalysis and electron transport. Azurin is one such metalloprotein with copper cofactor, having a ß-barrel structure with exceptional thermal stability. The copper metal ion is coordinated at one end of the ß-barrel structure, and there is a disulfide bond at the opposite end. In this study, we explore the effect of this disulfide bond in the high thermal stability of azurin by analyzing both the native S-S bonded and S-S nonbonded (S-S open) forms using temperature replica exchange molecular dynamics (REMD). Similar to experimental observations, we find a 35 K decrease in denaturation temperature for S-S open azurin compared to that of the native holo form (420 K). As observed in the case of native holo azurin, the unfolding process of the S-S open form also started with disruptions of the α-helix. The free energy surfaces of the unfolding process revealed that the denaturation event of the S-S open form progresses through different sets of conformational ensembles. Subsequently, we compared the stabilities of individual ß-sheet strands of both the S-S bonded and the S-S nonbonded forms of azurin. Further, we examined the contacts between individual residues for the central structures from the free energy surfaces of the S-S nonbonded form. The microscopic origin of the lowering in the denaturation temperature is further supplemented by thermodynamic analysis.


Assuntos
Azurina , Metaloproteínas , Azurina/química , Cobre/química , Metaloproteínas/metabolismo , Dissulfetos/química , Temperatura , Íons , Dobramento de Proteína
16.
Biochemistry ; 63(3): 339-347, 2024 Feb 06.
Artigo em Inglês | MEDLINE | ID: mdl-38232298

RESUMO

Metalloproteins play fundamental roles in organisms and are utilized as starting points for the directed evolution of artificial enzymes. Knowing the strategies of metalloproteins, by which they exquisitely tune their activities, will not only lead to an understanding of biochemical phenomena but also contribute to various applications. The blue copper protein (BCP) has been a renowned model system to understand the biology, chemistry, and physics of metalloproteins. Pseudoazurin (Paz), a blue copper protein, mediates electron transfer in the bacterial anaerobic respiratory chain. Its redox potential is finely tuned by hydrogen (H) bond networks; however, difficulty in visualizing H atom positions in the protein hinders the detailed understanding of the protein's structure-function relationship. We here used neutron and sub-ångström resolution X-ray crystallography to directly observe H atoms in Paz. The 0.86-Å-resolution X-ray structure shows that the peptide bond between Pro80 and the His81 Cu ligand deviates from the ideal planar structure. The 1.9-Å-resolution neutron structure confirms a long-overlooked H bond formed by the amide of His81 and the S atom of another Cu ligand Cys78. Quantum mechanics/molecular mechanics calculations show that this H bond increases the redox potential of the Cu site and explains the experimental results well. Our study demonstrates the potential of neutron and sub-ångström resolution X-ray crystallography to understand the chemistry of metalloproteins at atomic and quantum levels.


Assuntos
Cobre , Metaloproteínas , Cobre/metabolismo , Cristalografia por Raios X , Ligação de Hidrogênio , Ligantes , Modelos Moleculares , Metaloproteínas/metabolismo , Nêutrons
17.
Arch Pharm (Weinheim) ; 357(4): e2300648, 2024 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-38279543

RESUMO

Metalloenzymes play vital roles in various biological processes, requiring the search for inhibitors to develop treatment options for diverse diseases. While compound library screening is a conventional approach, the exploration of virtual chemical spaces housing trillions of compounds has emerged as an alternative strategy. In this study, we investigated the suitability of selected screening libraries and chemical spaces for discovering inhibitors of metalloenzymes featuring common ions (Mg2+, Mn2+, and Zn2+). First, metal-coordinating groups from ligands interacting with ions in the Protein Data Bank were extracted. Subsequently, the prevalence of these groups in two focused screening libraries (Life Chemicals' chelator library, comprising 6,428 compounds, and Otava's chelator fragment library, with 1,784 fragments) as well as two chemical spaces (GalaXi and REAL space, containing billions of virtual products) was investigated. In total, 1,223 metal-coordinating groups were identified, with about a quarter of these groups found within the examined libraries and spaces. Our results indicate that these can serve as valuable starting points for drug discovery targeting metalloenzymes. In addition, this study suggests ways to improve libraries and spaces for better success in finding potential inhibitors for metalloenzymes.


Assuntos
Metaloproteínas , Relação Estrutura-Atividade , Metaloproteínas/química , Metaloproteínas/metabolismo , Descoberta de Drogas , Metais , Quelantes/farmacologia , Íons
18.
Int J Biol Macromol ; 256(Pt 2): 128209, 2024 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-37992940

RESUMO

Since fish metalloproteins are still not thoroughly characterized, the aim of this study was to investigate the acidic/basic nature of biomolecules involved in the sequestration of twelve selected metals in the soluble hepatic fraction of an important aquatic bioindicator organism, namely the fish species northern pike (Esox lucius). For this purpose, the hyphenated system HPLC-ICP-MS was applied, with chromatographic separation based on anion/cation-exchange principle at physiological pH (7.4). The results indicated predominant acidic nature of metal-binding peptides/proteins in the studied hepatic fraction. More than 90 % of Ag, Cd, Co, Cu, Fe, Mo, and Pb were eluted with negatively charged biomolecules, and >70 % of Bi, Mn, and Zn. Thallium was revealed to bind equally to negatively and positively charged biomolecules, and Cs predominantly to positively charged ones. The majority of acidic (negatively charged) metalloproteins/peptides were coeluted within the elution time range of applied standard proteins, having pIs clustered around 4-6. Furthermore, binding of several metals (Ag, Cd, Cu, Zn) to two MT-isoforms was assumed, with Cd and Zn preferentially bound to MT1 and Ag to MT2, and Cu evenly distributed between the two. The results presented here are the first of their kind for the important bioindicator species, the northern pike, as well as one of the rare comprehensive studies on the acidic/basic nature of metal-binding biomolecules in fish, which can contribute significantly to a better understanding of the behaviour and fate of metals in the fish organism, specifically in liver as main metabolic and detoxification organ.


Assuntos
Metaloproteínas , Poluentes Químicos da Água , Animais , Esocidae/metabolismo , Cádmio/metabolismo , Poluentes Químicos da Água/análise , Metalotioneína/metabolismo , Metais/metabolismo , Metaloproteínas/metabolismo , Peptídeos/metabolismo , Fígado/metabolismo
19.
Biochim Biophys Acta Bioenerg ; 1865(1): 149015, 2024 01 01.
Artigo em Inglês | MEDLINE | ID: mdl-37742749

RESUMO

The aim of this study was to investigate how acclimation to medium-level, long-term, non-lethal iron limitation changes the electron flux around the Photosystem II of the oceanic diazotroph Trichodesmium erythraeum IMS101. Fe availability of about 5× and 100× lower than a replete level, i.e. conditions common in the natural environment of this cyanobacterium, were applied in chemostats. The response of the cells was studied not only in terms of growth, but also mechanistically, measuring the chlorophyll fluorescence of dark-adapted filaments via imaging fluorescence kinetic microscopy (FKM) with 0.3 ms time resolution. Combining these measurements with those of metal binding to proteins via online coupling of metal-free HPLC (size exclusion chromatography SEC) to sector-field ICP-MS allowed to track the fate of the photosystems, together with other metalloproteins. General increase of fluorescence has been observed, with the consequent decrease in the quantum yields φ of the PSII, while the efficiency ψ of the electron flux between PSII and the PSI remained surprisingly unchanged. This indicates the ability of Trichodesmium to cope with a situation that makes assembling the many iron clusters in Photosystem I a particular challenge, as shown by decreasing ratios of Fe to Mg in these proteins. The negative effect of Fe limitation on PSII may also be due to its fast turnover. A broader view was obtained from metalloproteomics via HPLC-ICP-MS, revealing a differential protein expression pattern under iron limitation with a drastic down-regulation especially of iron-containing proteins and some increase in low MW metal-binding complexes.


Assuntos
Metaloproteínas , Trichodesmium , Trichodesmium/metabolismo , Ferro/metabolismo , Metaloproteínas/metabolismo , Elétrons , Aclimatação
20.
J Phys Chem B ; 127(48): 10326-10337, 2023 Dec 07.
Artigo em Inglês | MEDLINE | ID: mdl-38010277

RESUMO

Although the ion selectivity of metalloproteins has been well established, selective metal antigen recognition by immunoproteins remains elusive. One such case is the recognition of the Be2+ ion against its heavier congeners, Mg2+ and Ca2+, by the human leukocyte antigen immunoprotein (HLA-DP2), leading to immunotoxicity. Integrating with our previous mechanistic study on Be2+ toxicity, herein, we have explored the basis of characteristic nontoxicity of Mg2+ and Ca2+ ions despite their in vivo abundance. The ion binding cleft of the HLA-DP2-peptide complex is composed of four acidic residues, p4D and p7E from the peptide and ß26E and ß69E from the protein. While the tetrahedral coordination site of the smaller Be2+ ion is located deep inside the cavity, hexa- to octa-coordination sites of Mg2+ and Ca2+ ions are located closer to the protein surface. The intrinsic high coordination number of Mg2+/Ca2+ ions induces allosteric modifications on the HLA-DP2_M2 surface, which are atypical for TCR recognition. Furthermore, the lower binding energy of larger Mg2+ and Ca2+ ions with the cavity residues can be correlated to the lower charge density and reduced covalent bonding nature as compared to those of the smaller Be2+ ion. In short, weak binding of Mg2+ and Ca2+ ions and the unfavorable allosteric surface modifications are probably the major determinants for the absence of Mg2+/Ca2+ ion-mediated hypersensitivity in humans.


Assuntos
Metaloproteínas , Metais , Humanos , Sítios de Ligação , Metais/química , Peptídeos/metabolismo , Íons/química , Metaloproteínas/metabolismo
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