Structure, function, and evolution of respiratory proteins

2019 ◽  
pp. 23-40
Author(s):  
Steven F. Perry ◽  
Markus Lambertz ◽  
Anke Schmitz
Keyword(s):  
Metal Ions ◽  
Structure Function ◽  
Molecular Mechanisms ◽  
Molecular Complexes ◽  
Respiratory Protein ◽  
Life Itself ◽  
Respiratory Proteins

Respiratory proteins are complexes of proteins and metal ions. In haemoglobin the metal is iron, in haemocyanin—the most common invertebrate respiratory protein—it is copper. Globins such as haemoglobin and myoglobin and related molecular complexes have probably been around as long as life itself, whereas others such as the most common respiratory protein of molluscs and arthropods, haemocyanin, appear to be younger and are not chemically related to globins. Nevertheless, astounding functional similarities between haemoglobin and haemocyanin are seen. The present chapter takes a look at the molecular mechanisms behind their function, their fundamental integration in the respiratory process, and also traces the evolution of these respiratory proteins.

scholarly journals Tracing the origins of SARS-COV-2 in coronavirus phylogenies: a review

2021 ◽  
Vol 19 (2) ◽  
pp. 769-785 ◽  
Author(s):  
Erwan Sallard ◽  
José Halloy ◽  
Didier Casane ◽  
Etienne Decroly ◽  
Jacques van Helden
Keyword(s):  
Sequence Analysis ◽  
Structure Function ◽  
Molecular Mechanisms ◽  
Laboratory Strain ◽  
Domestic Animals ◽  
Scientific Policy ◽  
Human Coronavirus ◽  
Viral Dissemination ◽  
Link Type ◽  
Intensive Breeding

AbstractSARS-CoV-2 is a new human coronavirus (CoV), which emerged in China in late 2019 and is responsible for the global COVID-19 pandemic that caused more than 97 million infections and 2 million deaths in 12 months. Understanding the origin of this virus is an important issue, and it is necessary to determine the mechanisms of viral dissemination in order to contain future epidemics. Based on phylogenetic inferences, sequence analysis and structure–function relationships of coronavirus proteins, informed by the knowledge currently available on the virus, we discuss the different scenarios on the origin—natural or synthetic—of the virus. The data currently available are not sufficient to firmly assert whether SARS-CoV2 results from a zoonotic emergence or from an accidental escape of a laboratory strain. This question needs to be solved because it has important consequences on the risk/benefit balance of our interactions with ecosystems, on intensive breeding of wild and domestic animals, on some laboratory practices and on scientific policy and biosafety regulations. Regardless of COVID-19 origin, studying the evolution of the molecular mechanisms involved in the emergence of pandemic viruses is essential to develop therapeutic and vaccine strategies and to prevent future zoonoses. This article is a translation and update of a French article published in Médecine/Sciences, August/September 2020 (10.1051/medsci/2020123).

scholarly journals Diversity of molecular mechanisms used by anti-CRISPR proteins: the tip of an iceberg?

2020 ◽  
Vol 48 (2) ◽  
pp. 507-516 ◽  
Author(s):  
Pierre Hardouin ◽  
Adeline Goulet
Keyword(s):  
Immune System ◽  
Structure Function ◽  
Defense Mechanisms ◽  
Molecular Mechanisms ◽  
Current Knowledge ◽  
Arms Race ◽  
Allosteric Inhibitors ◽  
Fundamental Knowledge ◽  
Attack And Defense ◽  
Fine Tune

Bacteriophages (phages) and their preys are engaged in an evolutionary arms race driving the co-adaptation of their attack and defense mechanisms. In this context, phages have evolved diverse anti-CRISPR proteins to evade the bacterial CRISPR–Cas immune system, and propagate. Anti-CRISPR proteins do not share much resemblance with each other and with proteins of known function, which raises intriguing questions particularly relating to their modes of action. In recent years, there have been many structure–function studies shedding light on different CRISPR–Cas inhibition strategies. As the anti-CRISPR field of research is rapidly growing, it is opportune to review the current knowledge on these proteins, with particular emphasis on the molecular strategies deployed to inactivate distinct steps of CRISPR–Cas immunity. Anti-CRISPR proteins can be orthosteric or allosteric inhibitors of CRISPR–Cas machineries, as well as enzymes that irreversibly modify CRISPR–Cas components. This repertoire of CRISPR–Cas inhibition mechanisms will likely expand in the future, providing fundamental knowledge on phage–bacteria interactions and offering great perspectives for the development of biotechnological tools to fine-tune CRISPR–Cas-based gene edition.

scholarly journals Metal ions and redox balance regulate distinct amyloid-like aggregation pathways of GAPR-1

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Jie Sheng ◽  
Nick K. Olrichs ◽  
Willie J. Geerts ◽  
Dora V. Kaloyanova ◽  
J. Bernd Helms
Keyword(s):  
Metal Ions ◽  
Metal Binding ◽  
Molecular Mechanisms ◽  
Quaternary Structure ◽  
Copper Ions ◽  
Redox Homeostasis ◽  
Secretory Proteins ◽  
Pathogenesis Related Protein ◽  
Pathogenesis Related ◽  
Induced Aggregation

Abstract Members of the CAP superfamily (Cysteine-rich secretory proteins, Antigen 5, and Pathogenesis-Related 1 proteins) are characterized by the presence of a structurally conserved CAP domain. The common structure-function relationship of this domain is still poorly understood. In this study, we unravel specific molecular mechanisms modulating the quaternary structure of the mammalian CAP protein GAPR-1 (Golgi-Associated plant Pathogenesis-Related protein 1). Copper ions are shown to induce a distinct amyloid-like aggregation pathway of GAPR-1 in the presence of heparin. This involves an immediate shift from native multimers to monomers which are prone to form amyloid-like fibrils. The Cu2+-induced aggregation pathway is independent of a conserved metal-binding site and involves the formation of disulfide bonds during the nucleation process. The elongation process occurs independently of the presence of Cu2+ ions, and amyloid-like aggregation can proceed under oxidative conditions. In contrast, the Zn2+-dependent aggregation pathway was found to be independent of cysteines and was reversible upon removal of Zn2+ ions. Together, our results provide insight into the regulation of the quaternary structure of GAPR-1 by metal ions and redox homeostasis with potential implications for regulatory mechanisms of other CAP proteins.

scholarly journals Anticoagulant proteins from snake venoms: structure, function and mechanism

2006 ◽  
Vol 397 (3) ◽  
pp. 377-387 ◽  
Author(s):  
R. Manjunatha Kini
Keyword(s):  
Structure Function ◽  
Blood Coagulation ◽  
Snake Venom ◽  
Molecular Mechanisms ◽  
Cerebrovascular Diseases ◽  
Clot Formation ◽  
Snake Venoms ◽  
New Anticoagulants ◽  
Physiological Processes ◽  
Made In

Over the last several decades, research on snake venom toxins has provided not only new tools to decipher molecular details of various physiological processes, but also inspiration to design and develop a number of therapeutic agents. Blood circulation, particularly thrombosis and haemostasis, is one of the major targets of several snake venom proteins. Among them, anticoagulant proteins have contributed to our understanding of molecular mechanisms of blood coagulation and have provided potential new leads for the development of drugs to treat or to prevent unwanted clot formation. Some of these anticoagulants exhibit various enzymatic activities whereas others do not. They interfere in normal blood coagulation by different mechanisms. Although significant progress has been made in understanding the structure–function relationships and the mechanisms of some of these anticoagulants, there are still a number of questions to be answered as more new anticoagulants are being discovered. Such studies contribute to our fight against unwanted clot formation, which leads to death and debilitation in cardiac arrest and stroke in patients with cardiovascular and cerebrovascular diseases, arteriosclerosis and hypertension. This review describes the details of the structure, mechanism and structure–function relationships of anticoagulant proteins from snake venoms.

TERT Structure, Function, and Molecular Mechanisms

Telomerases ◽  
2012 ◽  
pp. 53-78 ◽  
Author(s):  
Emmanuel Skordalakes ◽  
Neal F. Lue
Keyword(s):  
Structure Function ◽  
Molecular Mechanisms

scholarly journals The Biochemical Properties of Manganese in Plants

Plants ◽  
2019 ◽  
Vol 8 (10) ◽  
pp. 381 ◽  
Author(s):  
Schmidt ◽  
Husted
Keyword(s):  
Metal Ions ◽  
Oxidation State ◽  
Metal Binding ◽  
Molecular Mechanisms ◽  
Current Knowledge ◽  
Biochemical Properties ◽  
Oxygen Evolving Complex ◽  
Functional Roles ◽  
Catalyzed Reactions ◽  
Enzyme Catalyzed Reactions

Manganese (Mn) is an essential micronutrient with many functional roles in plant metabolism. Manganese acts as an activator and co-factor of hundreds of metalloenzymes in plants. Because of its ability to readily change oxidation state in biological systems, Mn plays and important role in a broad range of enzyme-catalyzed reactions, including redox reactions, phosphorylation, decarboxylation, and hydrolysis. Manganese(II) is the prevalent oxidation state of Mn in plants and exhibits fast ligand exchange kinetics, which means that Mn can often be substituted by other metal ions, such as Mg(II), which has similar ion characteristics and requirements to the ligand environment of the metal binding sites. Knowledge of the molecular mechanisms catalyzed by Mn and regulation of Mn insertion into the active site of Mn-dependent enzymes, in the presence of other metals, is gradually evolving. This review presents an overview of the chemistry and biochemistry of Mn in plants, including an updated list of known Mn-dependent enzymes, together with enzymes where Mn has been shown to exchange with other metal ions. Furthermore, the current knowledge of the structure and functional role of the three most well characterized Mn-containing metalloenzymes in plants; the oxygen evolving complex of photosystem II, Mn superoxide dismutase, and oxalate oxidase is summarized.

The structure-function relationship of activated protein C

2011 ◽  
Vol 106 (12) ◽  
pp. 1034-1045. ◽  
Author(s):  
Karin Wildhagen ◽  
Esther Lutgens ◽  
Sarah Loubele ◽  
Hugo ten Cate ◽  
Gerry Nicolaes
Keyword(s):  
Structure Function ◽  
Protein C ◽  
Molecular Mechanisms ◽  
3D Structure ◽  
Activated Protein C ◽  
Protein S ◽  
Coagulation Factors ◽  
Endothelial Protein C Receptor ◽  
Cytoprotective Activity ◽  
Sphingosine 1 Phosphate

SummaryProtein C is the central enzyme of the natural anticoagulant pathway and its activated form APC (activated protein C) is able to proteolyse non-active as well as active coagulation factors V and VIII. Proteolysis renders these cofactors inactive, resulting in an attenuation of thrombin formation and overall down-regulation of coagulation. Presences of the APC cofactor, protein S, thrombomodulin, endothelial protein C receptor and a phospholipid surface are important for the expression of anticoagulant APC activity. Notably, APC also has direct cytoprotective effects on cells: APC is able to protect the endothelial barrier function and expresses anti-inflammatory and anti-apoptotic activities. Exact molecular mechanisms have thus far not been completely described but it has been shown that both the protease activated receptor 1 and EPCR are essential for the cytoprotective activity of APC. Recently it was shown that also other receptors like sphingosine 1 phosphate receptor 1, Cd11b/CD18 and tyrosine kinase with immunoglobulin-like and EGFlike domains 2 are likewise important for APC signalling. Mutagenesis studies are being performed to map the various APC functions and interactions onto its 3D structure and to dissect anticoagulant and cytoprotective properties. The results of these studies have provided a wealth of structure-function information. With this review we describe the state-of-the-art of the intricate structure-function relationships of APC, a protein that harbours several important functions for the maintenance of both humoral and tissue homeostasis.Lessons from natural and engineered mutations

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