Binding induced conformational changes of proteins correlate with their intrinsic fluctuations: a case study of antibodies

<p>Abstract</p> <p>Background</p> <p>How antibodies recognize and bind to antigens can not be totally explained by rigid shape and electrostatic complimentarity models. Alternatively, pre-existing equilibrium hypothesis states that the native state of an antibody is not defined by a single rigid conformation but instead with an ensemble of similar conformations that co-exist at equilibrium. Antigens bind to one of the preferred conformations making this conformation more abundant shifting the equilibrium.</p> <p>Results</p> <p>Here, two antibodies, a germline antibody of 36–65 Fab and a monoclonal antibody, SPE7 are studied in detail to elucidate the mechanism of antibody-antigen recognition and to understand how a single antibody recognizes different antigens. An elastic network model, Anisotropic Network Model (ANM) is used in the calculations. Pre-existing equilibrium is not restricted to apply to antibodies. Intrinsic fluctuations of eight proteins, from different classes of proteins, such as enzymes, binding and transport proteins are investigated to test the suitability of the method. The intrinsic fluctuations are compared with the experimentally observed ligand induced conformational changes of these proteins. The results show that the intrinsic fluctuations obtained by theoretical methods correlate with structural changes observed when a ligand is bound to the protein. The decomposition of the total fluctuations serves to identify the different individual modes of motion, ranging from the most cooperative ones involving the overall structure, to the most localized ones.</p> <p>Conclusion</p> <p>Results suggest that the pre-equilibrium concept holds for antibodies and the promiscuity of antibodies can also be explained this hypothesis: a limited number of conformational states driven by intrinsic motions of an antibody might be adequate to bind to different antigens.</p

Comparing interfacial dynamics in protein-protein complexes: an elastic network approach

<p>Abstract</p> <p>Background</p> <p>The transient, or permanent, association of proteins to form organized complexes is one of the most common mechanisms of regulation of biological processes. Systematic physico-chemical studies of the binding interfaces have previously shown that a key mechanism for the formation/stabilization of dimers is the steric and chemical complementarity of the two semi-interfaces. The role of the fluctuation dynamics at the interface of the interacting subunits, although expectedly important, proved more elusive to characterize. The aim of the present computational study is to gain insight into salient dynamics-based aspects of protein-protein interfaces.</p> <p>Results</p> <p>The interface dynamics was characterized by means of an elastic network model for 22 representative dimers covering three main interface types. The three groups gather dimers sharing the same interface but with good (type I) or poor (type II) similarity of the overall fold, or dimers sharing only one of the semi-interfaces (type III). The set comprises obligate dimers, which are complexes for which no structural representative of the free form(s) is available. Considerations were accordingly limited to bound and unbound forms of the monomeric subunits of the dimers. We proceeded by first computing the mobility of amino acids at the interface of the bound forms and compare it with the mobility of (i) other surface amino acids (ii) interface amino acids in the unbound forms. In both cases different dynamic patterns were observed across interface types and depending on whether the interface belongs to an obligate or non-obligate complex.</p> <p>Conclusions</p> <p>The comparative investigation indicated that the mobility of amino acids at the dimeric interface is generally lower than for other amino acids at the protein surface. The change in interfacial mobility upon removing "in silico" the partner monomer (unbound form) was next found to be correlated with the interface type, size and obligate nature of the complex. In particular, going from the unbound to the bound forms, the interfacial mobility is noticeably reduced for dimers with type I interfaces, while it is largely unchanged for type II ones. The results suggest that these structurally- and biologically-different types of interfaces are stabilized by different balancing mechanisms between enthalpy and conformational entropy.</p

Primary Percutaneous Coronary Intervention for Acute Myocardial Infarction in a Young Female with Idiopathic Thrombocytopenic Purpura: A Case Report and Review

A 23-year-old female with the diagnosis of idiopathic thrombocytopenic purpura (ITP) was admitted to our hospital with severe chest pain. The electrocardiogram (ECG) revealed acute anterior myocardial infarction. She underwent an immediate cardiac catheterization. An occluded left anterior descending (LAD) was detected by coronary angiography. Reperfusion was performed successfully by angioplasty and stenting with optimal distal flow without any complications. In this report we discussed the management strategies of acute myocardial infarction (AMI) in a patient with ITP

Enriching Traditional Protein-protein Interaction Networks with Alternative Conformations of Proteins

Traditional Protein-Protein Interaction (PPI) networks, which use a node and edge representation, lack some valuable information about the mechanistic details of biological processes. Mapping protein structures to these PPI networks not only provides structural details of each interaction but also helps us to find the mutual exclusive interactions. Yet it is not a comprehensive representation as it neglects the conformational changes of proteins which may lead to different interactions, functions, and downstream signalling. In this study, we proposed a new representation for structural PPI networks inspecting the alternative conformations of proteins. We performed a large-scale study by creating breast cancer metastasis network and equipped it with different conformers of proteins. Our results showed that although 88% of proteins in our network has at least two structures in Protein Data Bank (PDB), only 22% of them have alternative conformations and the remaining proteins have different regions saved in PDB. However, using even this small set of alternative conformations we observed a considerable increase in our protein docking predictions. Our protein-protein interaction predictions increased from 54% to 76% using the alternative conformations. We also showed the benefits of investigating structural data and alternative conformations of proteins through three case studies

PRISM: protein interactions by structural matching

Prism () is a website for protein interface analysis and prediction of putative protein–protein interactions. It is composed of a database holding protein interface structures derived from the Protein Data Bank (PDB). The server also includes summary information about related proteins and an interactive protein interface viewer. A list of putative protein–protein interactions obtained by running our prediction algorithm can also be accessed. These results are applied to a set of protein structures obtained from the PDB at the time of algorithm execution (January 2004). Users can browse through the non-redundant dataset of representative interfaces on which the prediction algorithm depends, retrieve the list of similar structures to these interfaces or see the results of interaction predictions for a particular protein. Another service provided is interactive prediction. This is done by running the algorithm for user input structures

CCRXP: exploring clusters of conserved residues in protein structures

Conserved residues forming tightly packed clusters have been shown to be energy hot spots in both protein–protein and protein–DNA complexes. A number of analyses on these clusters of conserved residues (CCRs) have been reported, all pointing to a crucial role that these clusters play in protein function, especially protein–protein and protein–DNA interactions. However, currently there is no publicly available tool to automatically detect such clusters. Here, we present a web server that takes a coordinate file in PDB format as input and automatically executes all the steps to identify CCRs in protein structures. In addition, it calculates the structural properties of each residue and of the CCRs. We also present statistics to show that CCRs, determined by these procedures, are significantly enriched in ‘hot spots’ in protein–protein and protein–RNA complexes, which supplements our more detailed similar results on protein–DNA complexes. We expect that CCRXP web server will be useful in studies of protein structures and their interactions and selecting mutagenesis targets. The web server can be accessed at http://ccrxp.netasa.org

Recent Developments in CRISPR/Cas9 Genome-Editing Technology Related to Plant Disease Resistance and Abiotic Stress Tolerance

The revolutionary CRISPR/Cas9 genome-editing technology has emerged as a powerful tool for plant improvement, offering unprecedented precision and efficiency in making targeted gene modifications. This powerful and practical approach to genome editing offers tremendous opportunities for crop improvement, surpassing the capabilities of conventional breeding techniques. This article provides an overview of recent advancements and challenges associated with the application of CRISPR/Cas9 in plant improvement. The potential of CRISPR/Cas9 in terms of developing crops with enhanced resistance to biotic and abiotic stresses is highlighted, with examples of genes edited to confer disease resistance, drought tolerance, salt tolerance, and cold tolerance. Here, we also discuss the importance of off-target effects and the efforts made to mitigate them, including the use of shorter single-guide RNAs and dual Cas9 nickases. Furthermore, alternative delivery methods, such as protein- and RNA-based approaches, are explored, and they could potentially avoid the integration of foreign DNA into the plant genome, thus alleviating concerns related to genetically modified organisms (GMOs). We emphasize the significance of CRISPR/Cas9 in accelerating crop breeding processes, reducing editing time and costs, and enabling the introduction of desired traits at the nucleotide level. As the field of genome editing continues to evolve, it is anticipated that CRISPR/Cas9 will remain a prominent tool for crop improvement, disease resistance, and adaptation to challenging environmental conditions

Evaluation of the consistency ratios of cervical smear, cervical biopsy and conization results

Objectives: Possible discrepancies between the cervical smear, biopsy histology and loop electrosurgical excision procedure (LEEP) results of the same patient is a matter of debate in the literature. In this study, we investigate the degree to which these results differ, and the clinical reasons for these differences. Material and methods: With a retrospective design, cervical smear, cervical biopsy and LEEP results of patients were compared in terms of consistency. One hundred sixty-four patients who underwent till LEEP procedure due to pathologic initial smear and biopsy results between January 2015 and March 2020 were included in the study. Results: Exact diagnosis discrepancy and high grade squamous intraepithelial lesion (HSIL) discrepancy were 78.9% and 50.0% between smear and cervical biopsy, 64.6% and 31.7% between cervical smear and LEEP and 43.8% and 28.1% between cervical biopsy and LEEP results, respectively. Age did not affect the consistency rates of pathologic results between smear-biopsy (p = 0.408) and biopsy-LEEP (p = 0.590). However, the probability of the consistency of smear and LEEP results exhibited a statistically significant linear relation with age (OR = 1.043, p = 0.015). HPV infections did not affect the discrepancy between smear-biopsy (p = 0.533), smear-LEEP (p = 1.000) and biopsy-LEEP (p = 0.529) Conclusions: Smear technique has a serious discrepancy and under-diagnosis problem when its results are compared with biopsy and LEEP. The consistency between smear and LEEP results appears to improve with age. When HSIL is evaluated in terms of detection, this discrepancy decreases. A smear test can detect HSIL and carcinoma with a higher accuracy than low-grade lesions

Life-Threatening Hypercalcemia due to Graves&apos; Disease and Concomitant Adrenal Failure: A Case Report and Review of the Literature

A 47-year-old woman presented with the complaints of nausea, vomiting, and weight loss. She had a history of bilateral surrenalectomy due to Cushing&apos;s syndrome. On examination she had tachycardia and orthostatic hypotension. Laboratory examinations revealed hypercalcemia and suppressed parathyroid hormone levels. She also had thyrotoxicosis due to Graves&apos; disease. The investigations to rule out a malignancy were negative. With steroid, zoledronic acid, and antithyroid drug treatment her symptoms were resolved and calcium level was normalized. This case highlights the importance of recognizing thyrotoxicosis and concomitant adrenal failure as a possible cause of severe hypercalcemia