structural basis
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2022 ◽  
Vol 177 ◽  
pp. 114391
Raghu Deshpande ◽  
Lars Sundvall ◽  
Hans Grundberg ◽  
Gunnar Henriksson ◽  
Martin Lawoko

2022 ◽  
Vol 68 (68.04) ◽  
pp. 9-12
Tatyana Aleksandrova

The first three papers featured in Issue 4/2021 of Balgarski ezik present results of the work on a project titled Everyday Life in the Middle Ages according to Lexical Data from Bulgarian and Romanian – a bilateral effort between the Bulgarian Academy of Sciences and the Romanian Academy. Mariyana Tsibranska-Kostova’s paper Magic and its Faces (the 61st Canon of Trullo in Slavic Translations) proposes an analysis of several representatives of the lexical-semantic group of performers of magical practices according to three translations of the canon. The author discusses the word-formation structure of the lexical group as well as the semantic adaptation of Greek names for unknown realia. The text of the 61st Canon of Trullo is published as an appendix. Elka Mircheva provides a discussion on the topic of Bad Thoughts are Worse than Illness (to the Analysis of Medieval Texts) by analysing examples of illness in Pope Gregory the Great’s Dialogues which have been interpreted by earlier studies as cases of psychological conditions. The author’s analysis points to the fact that some of these occurrences are evidence of the influence of bad thoughts resulting in unacceptable reprehen-sible behaviour. Vanya Micheva’s paper Names for Living Places in the Bulgarian Language Picture of the World in the Middle Ages deals with the linguistic and semantic realisations of the concept of living places in the Old Bulgarian classical and original works from the 9th – 11th centuries and in the works of Patriarch Euthymius. The author traces the process of enrichment of the names for living places and the changes in the conceptual content of the studied lexemes. Tatyana Braga’s paper A Little-known Damaskin from the Karlovo-Adzhar School of Calligraphy and Art: Odessa Damascus № 36 (62) – Palaeography, Codicology, Dating offers a meticulous palaeographic and codicological description of a Bulgarian written monument, the Odessa Damaskin № 36 (62) from the manuscript collection of V.I. Grigorovich. Nadka Nikolova’s paper Общ язик с виражение народно. The Language Norms in the Translation of A. Granitski’s За Тръговско писмописанїе (On Commercial Letter Writing), 1858 presents the results of a study on Anastas Granitski’s contribution to the establishment of the structural basis and spelling and language norms of the Bulgarian literary language of the Revival period. On the basis of her observations on adjectives, numerals, pronouns and verbs, the author comes to the conclusion that the text reveals significant convergence of written and spoken language. Maria Mitskova addresses some Issues in the Verb Morphology of Bulgarian Dialects in the Studies of Three European Slavicists from the First Half of the 19th Century – Vuk Karadžić, Victor Grigorovich, Stefan Verković. The paper emphasises the contribution of the first Slavicists whose work marks the origination of the scientific interest in one of the most characteristic features of Bulgarian verbs. Elena Kanevska-Nikolova and Simeon Marinov present a study on the Names for Women’s Outerwear in the Rhodope Folk Clothing based on ma-terial excerpted from various ethnographic, regional historical and dialectological studies. The authors examine ambiguous and synonymous terms, main word-formation patterns, as well as the etymology of some of the names under study. They go on to analyse the terminological unity of many names for women’s outerwear characteristic of both confessional groups to which the Bulgarian population in the Rhodopes belong. Georgi Mitrinov’s paper Is there a Pomak Dialect in Bulgaria? is a critical look at a study by Emel Balakchi dealing with the Bulgarian Rhodope dialects. The author addresses Balakchi’s attempt at presenting the Rhodope dialects as Pomak dialects, while ignoring the presence of a native Bulgarian Christian population in the Rhodopes. Using numerous examples, Georgi Mitrinov reveals the study’s lack of scientific competence and objectivity in presenting the characteristic features of the Bulgarian Rhodope dialects. The issue concludes with a paper that remains outside its thematic scope. Stative Predicates in Contemporary Linguistic Theories by Svetlozara Leseva, Hristina Kukova and Ivelina Stoyanova offers a critical overview of the thematic classes of stative verbs based on a contrastive study of several thematic classifications. The authors analyse the different views of the properties of stative predicates from an aspectual and semantic perspective.

2022 ◽  
Leiye Yu ◽  
Licong He ◽  
Bing Gan ◽  
Rujuan Ti ◽  
Qingjie Xiao ◽  

As a critical sphingolipid metabolite, sphingosine-1-phosphate (S1P) plays an essential role in immune and vascular systems. There are five S1P receptors, designated as S1PR1-5, encoded in the human genome, and their activities are governed by endogenous S1P, lipid-like S1P mimics, or non-lipid-like therapeutic molecules. Among S1PRs, S1PR1 stands out due to its non-redundant functions, such as the egress of T and B cells from the thymus and secondary lymphoid tissues, making it a potential therapeutic target. However, the structural basis of S1PR1 activation and regulation by various agonists remains unclear. Here we reported four atomic resolution cryo-EM structures of Gi-coupled human S1PR1 complexes: bound to endogenous agonist d18:1 S1P, benchmark lipid-like S1P mimic phosphorylated Fingolimod ((S)-FTY720-P), or non-lipid-like therapeutic molecule CBP-307 in two binding modes. Our results revealed the similarities and differences of activation of S1PR1 through distinct ligands binding to the amphiphilic orthosteric pocket. We also proposed a two-step "shallow to deep" transition process of CBP-307 for S1PR1 activation. Both binding modes of CBP-307 could activate S1PR1, but from shallow to deep transition may trigger the rotation of the N-terminal helix of Gαi and further stabilize the complex by increasing the Gαi interaction with the cell membrane. We combine with extensive biochemical analysis and molecular dynamic simulations to suggest key steps of S1P binding and receptor activation. The above results decipher the common feature of the S1PR1 agonist recognition and activation mechanism and will firmly promote the development of therapeutics targeting S1P receptors.

2022 ◽  
Andrea Piserchio ◽  
Eta A Isiroho ◽  
Kimberly Long ◽  
Amanda L Bohanon ◽  
Eric A Kumar ◽  

Translation is a highly energy consumptive process tightly regulated for optimal protein quality and adaptation to energy and nutrient availability. A key facilitator of this process is the α-kinase eEF-2K that specifically phosphorylates the GTP-dependent translocase eEF-2, thereby reducing its affinity for the ribosome and suppressing the elongation phase of protein synthesis. eEF-2K activation requires calmodulin binding and auto-phosphorylation at the primary stimulatory site, T348. Biochemical studies have predicted that calmodulin activates eEF-2K through a unique allosteric process mechanistically distinct from other calmodulin-dependent kinases. Here we resolve the atomic details of this mechanism through a 2.3 Å crystal structure of the heterodimeric complex of calmodulin with the functional core of eEF-2K (eEF-2KTR). This structure, which represents the activated T348-phosphorylated state of eEF-2KTR, highlights how through an intimate association with the calmodulin C-lobe, the kinase creates a spine that extends from its N-terminal calmodulin-targeting motif through a conserved regulatory element to its active site. Modification of key spine residues has deleterious functional consequences.

Pathogens ◽  
2022 ◽  
Vol 11 (1) ◽  
pp. 99
Stephane Delbecq

Human babesiosis results from a combination of tick tropism for humans, susceptibility of a host to sustain Babesia development, and contact with infected ticks. Climate modifications and increasing diagnostics have led to an expanded number of Babesia species responsible for human babesiosis, although, to date, most cases have been attributed to B. microti and B. divergens. These two species have been extensively studied, and in this review, we mostly focus on the antigens involved in host–parasite interactions. We present features of the major antigens, so-called Bd37 in B. divergens and BmSA1/GPI12 in B. microti, and highlight the roles of these antigens in both host cell invasion and immune response. A comparison of these antigens with the major antigens found in some other Apicomplexa species emphasizes the importance of glycosylphosphatidylinositol-anchored proteins in host–parasite relationships. GPI-anchor cleavage, which is a property of such antigens, leads to soluble and membrane-bound forms of these proteins, with potentially differential recognition by the host immune system. This mechanism is discussed as the structural basis for the protein-embedded immune escape mechanism. In conclusion, the potential consequences of such a mechanism on the management of both human and animal babesiosis is examined.

eLife ◽  
2022 ◽  
Vol 11 ◽  
Iga Kucharska ◽  
Lamia Hossain ◽  
Danton Ivanochko ◽  
Qiren Yang ◽  
John L Rubinstein ◽  

Malaria is a global health burden, with Plasmodium falciparum (Pf) and Plasmodium vivax (Pv) responsible for the majority of infections worldwide. Circumsporozoite protein (CSP) is the most abundant protein on the surface of Plasmodium sporozoites, and antibodies targeting the central repeat region of CSP can prevent parasite infection. Although much has been uncovered about the molecular basis of antibody recognition of the PfCSP repeats, data remains scarce for PvCSP. Here, we performed molecular dynamics simulations for peptides comprising the PvCSP repeats from strains VK210 and VK247 to reveal how the PvCSP central repeats are highly disordered, with minor propensities to adopt turn conformations. Next, we solved eight crystal structures to unveil the interactions of two inhibitory monoclonal antibodies (mAbs), 2F2 and 2E10.E9, with PvCSP repeats. Both antibodies can accommodate subtle sequence variances in the repeat motifs and recognize largely coiled peptide conformations that also contain isolated turns. Our structural studies uncover various degrees of Fab-Fab homotypic interactions upon recognition of the PvCSP central repeats by these two inhibitory mAbs, similar to potent mAbs against PfCSP. These findings augment our understanding of host-Plasmodium interactions, and contribute molecular details of Pv inhibition by mAbs to unlock structure-based engineering of PvCSP-based vaccines.

2022 ◽  
Zhaochun Chen ◽  
Peng Zhang ◽  
Yumiko Matsuoka ◽  
Yaroslav Tsybovsky ◽  
Kamille West ◽  

The ongoing coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has triggered a devastating global health, social and economic crisis. The RNA nature and broad circulation of this virus facilitate the accumulation of mutations, leading to the continuous emergence of variants of concern with increased transmissibility or pathogenicity1. This poses a major challenge to the effectiveness of current vaccines and therapeutic antibodies1,2. Thus, there is an urgent need for effective therapeutic and preventive measures with a broad spectrum of action, especially against variants with an unparalleled number of mutations such as the recently emerged Omicron variant, which is rapidly spreading across the globe3. Here, we used combinatorial antibody phage-display libraries from convalescent COVID-19 patients to generate monoclonal antibodies against the receptor-binding domain of the SARS-CoV-2 spike protein with ultrapotent neutralizing activity. One such antibody, NE12, neutralizes an early isolate, the WA-1 strain, as well as the Alpha and Delta variants with half-maximal inhibitory concentrations at picomolar level. A second antibody, NA8, has an unusual breadth of neutralization, with picomolar activity against both the Beta and Omicron variants. The prophylactic and therapeutic efficacy of NE12 and NA8 was confirmed in preclinical studies in the golden Syrian hamster model. Analysis by cryo-EM illustrated the structural basis for the neutralization properties of NE12 and NA8. Potent and broadly neutralizing antibodies against conserved regions of the SARS-CoV-2 spike protein may play a key role against future variants of concern that evade immune control.

2022 ◽  
Vol 23 (2) ◽  
pp. 858
Sali Anies ◽  
Vincent Jallu ◽  
Julien Diharce ◽  
Tarun J. Narwani ◽  
Alexandre G. de Brevern

Integrin αIIbβ3, a glycoprotein complex expressed at the platelet surface, is involved in platelet aggregation and contributes to primary haemostasis. Several integrin αIIbβ3 polymorphisms prevent the aggregation that causes haemorrhagic syndromes, such as Glanzmann thrombasthenia (GT). Access to 3D structure allows understanding the structural effects of polymorphisms related to GT. In a previous analysis using Molecular Dynamics (MD) simulations of αIIb Calf-1 domain structure, it was observed that GT associated with single amino acid variation affects distant loops, but not the mutated position. In this study, experiments are extended to Calf-1, Thigh, and Calf-2 domains. Two loops in Calf-2 are unstructured and therefore are modelled expertly using biophysical restraints. Surprisingly, MD revealed the presence of rigid zones in these loops. Detailed analysis with structural alphabet, the Proteins Blocks (PBs), allowed observing local changes in highly flexible regions. The variant P741R located at C-terminal of Calf-1 revealed that the Calf-2 presence did not affect the results obtained with isolated Calf-1 domain. Simulations for Calf- 1+ Calf-2, and Thigh + Calf-1 variant systems are designed to comprehend the impact of five single amino acid variations in these domains. Distant conformational changes are observed, thus highlighting the potential role of allostery in the structural basis of GT.

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