Penta-L-lysine Potentiates Fibrin-Independent Activity of Human Tissue Plasminogen Activator

Global shape of SvGT, a metal-dependent bacteriocin modifying S/O-HexNActransferase from actinobacteria: c -terminal dimerization modulates the function of this GT

Here, we describe hitherto unknown shape-function of S/O-HexNActransferase SvGT (ORF AQF52_3101) instrumental in glycosylation of bacteriocin SvC (ORF AQF52_3099) in Streptomyces venezuelae ATCC 15439. Data from gel filtration, mass spectrometry, analytical ultracentrifugation, and Small Angle X-ray Scattering (SAXS), experiments confirmed elongated dimeric shape in solution for SvGT protein. Enzyme assays confirmed the dependence of SvGT on the availability of Mg2+ ions to be functionally activated. SAXS data analysis provided that apo and Mg2+-activated protein adopt a shape characterized by a radius of gyration and maximum linear dimension of 5.2 and 17.0 nm, and 5.3 and 17.8 nm, respectively. Alphafold2 server was used to model the monomeric chain of this protein which was docked on self to obtain different poses of the dimeric entity. Experimental SAXS data was used to select and refine the structure of SvGT dimer. Results showed that Mg2+ ions induce reorientation of the GT domain of one chain leading to a dimer with C2 symmetry, and the C-terminal portion entangles with each other in all states. Mutation-rendered alteration in activity profiles confirmed the role of conserved residues around catalytic motif. Global structure analysis puts forth the need to understand the role of constitutionally diverse C-terminal portion in regulating substrate selectivity.Communicated by Ramaswamy H. Sarma.

Development and Testing of Thrombolytics in Stroke

Despite recent advances in recanalization therapy, mechanical thrombectomy will never be a treatment for every ischemic stroke because access to mechanical thrombectomy is still limited in many countries. Moreover, many ischemic strokes are caused by occlusion of cerebral arteries that cannot be reached by intra-arterial catheters. Reperfusion using thrombolytic agents will therefore remain an important therapy for hyperacute ischemic stroke. However, thrombolytic drugs have shown limited efficacy and notable hemorrhagic complication rates, leaving room for improvement. A comprehensive understanding of basic and clinical research pipelines as well as the current status of thrombolytic therapy will help facilitate the development of new thrombolytics. Compared with alteplase, an ideal thrombolytic agent is expected to provide faster reperfusion in more patients; prevent re-occlusions; have higher fibrin specificity for selective activation of clot-bound plasminogen to decrease bleeding complications; be retained in the blood for a longer time to minimize dosage and allow administration as a single bolus; be more resistant to inhibitors; and be less antigenic for repetitive usage. Here, we review the currently available thrombolytics, strategies for the development of new clot-dissolving substances, and the assessment of thrombolytic efficacies in vitro and in vivo.

Monomeric human soluble CD4 dimerizes at physiological temperature: VTSAXS data based modeling and screening of retardant molecules

Earlier, solution small angle X-ray scattering (SAXS) data at 10 °C showed that soluble CD4 (sCD4; 1 mg/ml) is monomer with shape similar to single chain in crystal structures of its dimer. Query remained whether the dimeric state of CD4 can form independent of packing effects of crystal? Taking cue from other systems, we explored heat induced possible association of native shapes of sCD4 by variable temperature SAXS (VTSAXS) experiments. The predominant particle size increased consistently with temperature and around 35-40 °C, the estimated mass indicated dimeric state in solution. Furthermore, the observed association was found to be reversible to certain extent. Using SAXS profile representing dimer and crystal structure of monomer, we solved models of CD4 dimers which were dominated by D4-D4 interactions and appeared "wobbling" about the crystal structure of dimeric CD4, convincing pre-existence of crystal-like association in solution. To break the dimerization, we theoretically screened for small molecules binding to dimeric interface of D4 domain. Additionally, as negative control or not expecting to interfere, we searched molecules preferentially docking on the apex of D1 domain. VTSAXS experiments of CD4 + molecules at ∼1:3 molar ratio showed that as expected few D4 reactive hits could retard dimerization, yet surprisingly molecules which docked at D1 domain could also derail dimerization. Additional analysis led to conclusion that there lies a systematic communication network across the structural length of sCD4 which senses binding to self and other molecules, and our work can be used to develop new (or re-purpose known) molecules as CD4-reactive immunosuppressive agents.Communicated by Ramaswamy H. Sarma.

Structural Biology and Protein Engineering of Thrombolytics

Myocardial infarction and ischemic stroke are the most frequent causes of death or disability worldwide. Due to their ability to dissolve blood clots, the thrombolytics are frequently used for their treatment. Improving the effectiveness of thrombolytics for clinical uses is of great interest. The knowledge of the multiple roles of the endogenous thrombolytics and the fibrinolytic system grows continuously. The effects of thrombolytics on the alteration of the nervous system and the regulation of the cell migration offer promising novel uses for treating neurodegenerative disorders or targeting cancer metastasis. However, secondary activities of thrombolytics may lead to life-threatening side-effects such as intracranial bleeding and neurotoxicity. Here we provide a structural biology perspective on various thrombolytic enzymes and their key properties: (i) effectiveness of clot lysis, (ii) affinity and specificity towards fibrin, (iii) biological half-life, (iv) mechanisms of activation/inhibition, and (v) risks of side effects. This information needs to be carefully considered while establishing protein engineering strategies aiming at the development of novel thrombolytics. Current trends and perspectives are discussed, including the screening for novel enzymes and small molecules, the enhancement of fibrin specificity by protein engineering, the suppression of interactions with native receptors, liposomal encapsulation and targeted release, the application of adjuvants, and the development of improved production systems.