Domain Fragment Research Articles

Thrombin cleaves recombinant soluble thrombomodulin into a lectin-like domain fragment and a fragment with protein C-activating cofactor activity.

Thrombomodulin (TM) is a transmembrane protein that plays an important role in regulating the coagulation system by acting as a cofactor for thrombin in protein C activation. Additionally, TM is involved in inflammation. Previous studies have shown that soluble fragments of TM of varying sizes, which are derived from membrane-bound TM, are present in plasma and urine. Soluble fragments of TM are speculated to exhibit biological activity. Among these, a lectin-like domain fragment (TMD1) is of particular importance. Recombinant TMD1 has previously been shown to attenuate lipopolysaccharide-induced inflammation. Here, we report that thrombin cleaves recombinant soluble TM, which is used for the treatment of disseminated intravascular coagulation associated with sepsis, into TMD1 and a fragment comprising the C-terminal portion of TM (TMD23), the latter of which retains the cofactor activity for activating protein C. Our findings suggest that thrombin not only activates protein C on membrane-bound TM but may also cleave TM to generate TMD1.

Myristolated Serotonin 2A Receptor Peptide Promotes Long-Lasting Blood Pressure-Lowering and Reno protection in Hypertensive Rat Species.

The aim of the present study was to test whether conjugation of a synthetic peptide corresponding to a fragment of the second extracellular domain of the human serotonin 2A receptor substantially alters the in vivo pharmacodynamic blood pressure-lowering profile of the peptide in different hypertensive rat strains. Sertuercept (SCLLADDN) was synthesized and modified using pegylation or myristolation. The two different peptide conjugates were tested in male Zucker diabetic fatty rats for acute and long-lasting blood pressure-lowering effects following single intraperitoneal administration. The myristolated Sertuercept was administered intraperitoneally to female Zucker fatty and male spontaneously hypertensive rats (SHR) and blood pressure was monitored either using tail cuff measurement (female Zucker) or by telemetry (SHR) rats. Plasma immunoglobulin G obtained by Protein G affinity chromatography in 25-week-old female Zucker or male spontaneously hypertensive rats was tested for binding to a linear synthetic peptide corresponding to the second extracellular loop of the serotonin 2A receptor. A cohort of male Zucker diabetic fatty rats was randomized to seven weeks of once-weekly myristolated Sertuercept or scrambled peptide (injections) and the kidneys were examined histologically for differences in total kidney lesions or fibrosis. Pegylated Sertuercept promoted substantial blood pressure-lowering lasting approximately 30-48 hours in male Zucker diabetic fatty rats. Blood pressure-lowering following a single injection of Myristolated Sertuercept was much longer-lasting (6-11 days) and it was effective in male Zucker diabetic fatty rats, male spontaneously hypertensive rats and in a subset of hypertensive female Zucker fatty rats. Seven weeks' treatment with once-weekly Myristolated Sertuercept (2mg/kg) was associated with significantly fewer kidney lesions and less interstitial fibrosis compared to scrambled peptide in 25-week-old male Zucker diabetic fatty rats. Male spontaneously hypertensive rats (4 of 4 tested) harbored plasma IgG which bound significantly to serotonin 2A receptor peptide, and a subset of female Zucker fatty rats harboring IgG were responsive to blood pressure-lowering from the myristolated Sertuercept peptide. Myristolated-Sertuercept, an epitope-specific peptide comprised of a portion of second extracellular loop of the human serotonin 2A receptor was safe, well-tolerated and effectively lowered blood pressure for one week or longer in two different strains of male hypertensive rats. These data provide proof-of-concept that once-weekly systemic drug administration is feasible to achieve not only long-lasting hypertension control, but also substantial renoprotection.

Efficient Multiple Domain Ligation for Proteins Using Asparaginyl Endopeptidase by Selection of Appropriate Ligation Sites Based on Steric Hindrance.

Three domain fragments of a multi-domain protein, ER-60, were ligated in two short linker regions using asparaginyl endopeptidase not involving denaturation. To identify appropriate ligation sites, by selecting several potential ligation sites with fewer mutations around two short linker regions, their ligation efficiencies and the functions of the ligated ER-60s were examined experimentally. To evaluate the dependence of ligation efficiencies on the ligation sites computationally, steric hinderances around the sites for the ligation were calculated through molecular dynamics simulations. Utilizing the steric hindrance, a site-dependent ligation potential index was introduced as reproducing the experimental ligation efficiency. Referring to this index, the reconstruction of ER-60 was succeeded by the ligation of the three domains for the first time. In addition, the new ligation potential index well-worked for application to other domain ligations. Therefore, the index may serve as a more time-effective tool for multi-site ligations.

Efficient Multiple Domain Ligation for Proteins Using Asparaginyl Endopeptidase by Selection of Appropriate Ligation Sites Based on Steric Hindrance

AbstractThree domain fragments of a multi‐domain protein, ER‐60, were ligated in two short linker regions using asparaginyl endopeptidase not involving denaturation. To identify appropriate ligation sites, by selecting several potential ligation sites with fewer mutations around two short linker regions, their ligation efficiencies and the functions of the ligated ER‐60s were examined experimentally. To evaluate the dependence of ligation efficiencies on the ligation sites computationally, steric hinderances around the sites for the ligation were calculated through molecular dynamics simulations. Utilizing the steric hindrance, a site‐dependent ligation potential index was introduced as reproducing the experimental ligation efficiency. Referring to this index, the reconstruction of ER‐60 was succeeded by the ligation of the three domains for the first time. In addition, the new ligation potential index well‐worked for application to other domain ligations. Therefore, the index may serve as a more time‐effective tool for multi‐site ligations.

EXTH-85. TARGETING CLAUDIN 6 WITH CAR T CELL THERAPY FOR ATYPICAL TERATOID/RHABDOID TUMOR

Abstract Atypical teratoid/rhabdoid tumor (ATRT) is an aggressive brain tumor that predominantly affects young children and has an average 5-year survival under 50%. Novel, targeted therapies are desperately needed. Claudin 6 (CLDN6) is a tight junction protein present during development and expressed in up to 70% of ATRT specimens but not in normal tissue, making it a promising immunotherapeutic target. CLDN6-targeted chimeric antigen receptor (CAR) T cells in combination with a CAR T cell–amplifying mRNA vaccine have demonstrated antitumor activity against other CLDN6-expressing cancers in pre-clinical and phase I adult trial (NCT04503278; Haanen J et al AACR, 2022). To assess the effectiveness of CLDN6-targeted CAR T cells against ATRT, we utilized a second-generation mRNA CAR with a 4-1BB costimulatory domain and single-chain variable fragment against CLDN6 (Reinhard et al, 2020). Patient-derived ATRT specimens were assessed by RNAseq for CLDN6 expression (mean FPKM= 11.4) and by immunohistochemistry (positive staining in 53% of specimens). Tumor-derived cell lines were validated for CLDN6 expression by flow cytometry. Co-culture of CLDN6-directed mRNA CAR T cells with ATRT cell line 7316-2187 resulted in tumor-specific cytotoxicity compared to CD19-directed control CAR T cells (92% versus 15% at 10:1, p< 0.0001; 86% versus 0% at 5:1, p< 0.0001). Similar results were seen with ATRT cell line 7316-2141 (75% versus 7% at 10:1, p< 0.0001; 53% versus 0% at 5:1, p< 0.0001). Both CLDN6- and CD19-directed CAR T cells showed no cytotoxicity against CLDN6-negative cell line 7316-4149. Patient-derived xenograft models were also created through intracranial injection of multiple ATRT patient cell lines, and ongoing work will evaluate locoregional administration of CLDN6-directed CAR T cells in orthotopic xenograft models to test in vivo efficacy. This work highlights the potential for targeting CLDN6 via CAR T cell therapy in patients with ATRT as a novel therapeutic strategy for these devastating tumors.

Understanding the Magnetic Microstructure through Experiments and Machine Learning Algorithms.

Advanced machine learning techniques have unfurled their applications in various interdisciplinary areas of research and development. This paper highlights the use of image regression algorithms based on advanced neural networks to understand the magnetic properties directly from the magnetic microstructure. In this study, Co/Pd multilayers have been chosen as a reference material system that displays maze-like magnetic domains in pristine conditions. Irradiation of Ar+ ions with two different energies (50 and 100 keV) at various fluences was used as an external perturbation to investigate the modification of magnetic and structural properties from a state of perpendicular magnetic anisotropy to the vicinity of the spin reorientation transition. Magnetic force microscopy revealed domain fragmentation with a smaller periodicity and weaker magnetic contrast up to the fluence of 1014 ions/cm2. Further increases in the ion fluence result in the formation of feather-like domains with a variation in local magnetization distribution. The experimental results were complemented with micromagnetic simulations, where the variations of effective magnetic anisotropy and exchange constant result in qualitatively similar changes in magnetic domains, as observed experimentally. Importantly, a set of 960 simulated domain images was generated to train, validate, and test the convolutional neural network (CNN) that predicts the magnetic properties directly from the domain images with a high level of accuracy (maximum 93.9%). Our work has immense importance in promoting the applications of image regression methods through the CNN in understanding integral magnetic properties obtained from the microscopic features subject to change under external perturbations.

Strengthening of enterococcal biofilms by Esp.

Multidrug-resistant (MDR) Enterococcus faecalis are major causes of hospital-acquired infections. Numerous clinical strains of E. faecalis harbor a large pathogenicity island that encodes enterococcal surface protein (Esp), which is suggested to promote biofilm production and virulence, but this remains controversial. To resolve this issue, we characterized the Esp N-terminal region, the portion implicated in biofilm production. Small angle X-ray scattering indicated that the N-terminal region had a globular head, which consisted of two DEv-Ig domains as visualized by X-ray crystallography, followed by an extended tail. The N-terminal region was not required for biofilm production but instead significantly strengthened biofilms against mechanical or degradative disruption, greatly increasing retention of Enterococcus within biofilms. Biofilm strengthening required low pH, which resulted in Esp unfolding, aggregating, and forming amyloid-like structures. The pH threshold for biofilm strengthening depended on protein stability. A truncated fragment of the first DEv-Ig domain, plausibly generated by a host protease, was the least stable and sufficient to strengthen biofilms at pH ≤ 5.0, while the entire N-terminal region and intact Esp on the enterococcal surface was more stable and required a pH ≤ 4.3. These results suggested a virulence role of Esp in strengthening enterococcal biofilms in acidic abiotic or host environments.

A CHCHD6–APP axis connects amyloid and mitochondrial pathology in Alzheimer’s disease

The mechanistic relationship between amyloid-beta precursor protein (APP) processing and mitochondrial dysfunction in Alzheimer’s disease (AD) has long eluded the field. Here, we report that coiled-coil-helix-coiled-coil-helix domain containing 6 (CHCHD6), a core protein of the mammalian mitochondrial contact site and cristae organizing system, mechanistically connects these AD features through a circular feedback loop that lowers CHCHD6 and raises APP processing. In cellular and animal AD models and human AD brains, the APP intracellular domain fragment inhibits CHCHD6 transcription by binding its promoter. CHCHD6 and APP bind and stabilize one another. Reduced CHCHD6 enhances APP accumulation on mitochondria-associated ER membranes and accelerates APP processing, and induces mitochondrial dysfunction and neuronal cholesterol accumulation, promoting amyloid pathology. Compensation for CHCHD6 loss in an AD mouse model reduces AD-associated neuropathology and cognitive impairment. Thus, CHCHD6 connects APP processing and mitochondrial dysfunction in AD. This provides a potential new therapeutic target for patients.

An ACE2-IgG4 Fc Fusion Protein Demonstrates Strong Binding to All Tested SARS-CoV-2 Variants and Reduced Lung Inflammation in Animal Models of SARS-CoV-2 and Influenza.

Background:The continued emergence of SARS-CoV-2 variants has caused concern that a constantly evolving virus will escape vaccines and antibody therapies. New approaches are needed.Methods:We created and manufactured an ACE2 extracellular domain (ECD) fragment Fc fusion drug candidate, G921, and engineered the compound for enhanced delivery of drug to peripheral tissues by minimizing the size of the ACE2 ECD and by incorporating an Fc domain to enhance transcytosis. G921 was assessed for binding, neutralization, in vivo anti-inflammatory effect, and pharmacokinetic profile.Results:G921 was expressed as an IgG4 Fc fusion protein presenting two ACE2 domains to ACE2 ligands while avoiding risk of infection via antibody-dependent enhancement. G921 strongly binds to the SARS-CoV-2 Wuhan-Hu-1 spike protein and demonstrates further diminished off rate to the spike protein from each of the currently identified variants of concern. G921 demonstrates ACE2 enzymatic activity comparable to positive control and binding to the neonatal Fc receptor (FcRn) without binding to low affinity Fc-gamma receptors (FcγRs). G921 is effective in a concentration-dependent manner in a focus reduction neutralization assay with EC50=16.3±4.2 µg/mL without cytotoxicity in Vero E6 cells when tested at 200 µg/mL in an MTS cell proliferation assay. G921 demonstrates statistically significant reduction of lung inflammation in relevant models of both SARS-CoV-2 and influenza. The pharmacokinetic profile demonstrated dose-dependent exposure with a multi-day half-life in monkeys and rats.Conclusion:G921 data are consistent with both antiviral and anti-inflammatory modes of action. G921 is a novel approach for the prevention and treatment of COVID-19 and possible other diseases characterized by deficiency of ACE2.

Abstract 607: Humanized mice model for efficacy and toxicity evaluation of drugs targeting CD47-SIRPα-PD1-PD-L1 axes

Abstract CD47 is widely expressed on the surface of cells. CD47 interacts with inhibitory receptor signaling protein alpha (SIRPα) to mediate a series of activities such as apoptosis, proliferation, and immune response. Tumor cells can escape the immune surveillance of macrophages through the CD47-SIRPa signaling pathway. Blocking CD47-SIRPα interactions has been shown to promote the destruction of cancer cells by phagocytes. Furthermore, there is growing evidence that targeting of the CD47-SIRPα axis may also promote antigen-presenting cell function. These identify the CD47-SIRPα axis as a promising innate immune checkpoint in cancer. We have generated humanized SIRPα and double humanized CD47/SIRPα mice model for drug efficacy and toxicity evaluation. The humanized mice with human extracellular domain and mouse cytoplasmic fragment of target protein showed similar immune cell population compared with wild type mice. The anti-CD47 antibody, Magrolimab (5F9) analog, displayed anti-tumor effect when administrated to humanized SIRPα mice bearing MC38-hCD47 (MC38 cells engineered to express human CD47) tumor cells. The tumor regression was also observed when treating humanized CD47/SIRPα mice bearing MC38-hCD47 with tested anti-CD47 antibody. Dual checkpoint blockade of CD47 and PD-L1 or PD1 have been reported as a synergistic therapy that activates both innate and adaptive immune response against tumors.We also generated humanized PD1/SIRPα and PD1/PDL1/SIRPα/CD47 mice model for efficacy and toxicity evaluation of drugs targeting for CD47/SIRPα-PD1/PD-L1 axes. Treatment with anti-CD47, anti-SIRPα and anti-PD-L1 alone showed tumor regression efficacy, and combination of anti-PD-L1 and anti-SIRPα or anti-CD47 showed improved anti-tumor effect compared with alone treatment. Those data suggested the humanized syngeneic mice model are useful for the efficacy evaluation of drugs targeting of axes.However, the administration of anti-CD47 blocking antibodies may cause haematotoxicity, including anaaemia and thrombocytopenia, because of the ubiquitous expression of CD47.In vitro Erythrocyte binding activity analysis showed that red blood cells(RBC) collected from humanized CD47/SIRPα mice could bind with Magrolimab analog, while another anti-CD47 antibody has low affinity with RBC. Furthermore, treatment with Magrolimab analog in CD47/SIRPα humanized mice caused haemagglutination and Hemolysis of human RBCs, which were not observed when treating with tested anti-CD47 antibody. Thus, the humanized CD47 and double humanized CD47/SIRPα mice are also suitable for CD47 antibody toxicity evaluation. In conclusion, humanized CD47/SIRPα and quadruple humanized PD1/PDL1/SIRPα/CD47 mice model provide a validated preclinical mouse model to interrogate new therapeutic agents targeting SIRPα-PD1 axes in immune oncology therapy. Citation Format: Juan Liang, Cunxiang Ju, Song Li, Weiwei Yu, Hongyan Sun, Santi Suryani Chen, Jing Zhao, Xiang Gao, Mark Moore. Humanized mice model for efficacy and toxicity evaluation of drugs targeting CD47-SIRPα-PD1-PD-L1 axes [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 607.

Enhanced Nuclear Magnetic Resonance Spectroscopy with Isotropic Mixing as a Pseudodimension.

Chemical analysis based on liquid-state nuclear magnetic resonance spectroscopy exploits numerous observables, mainly chemical shifts, relaxation rates, and internuclear coupling constants. Regarding the latter, the efficiencies of internuclear coherence transfers may be encoded in spectral peak intensities. The dependencies of these intensities on the experimental parameter that influences the transfer, for example, mixing time, are an important source of structural information. Yet, they are costly to measure and difficult to analyze. Here, we show that peak intensity build-up curves in two-dimensional total correlation spectroscopy (2D TOCSY) experiments may be quickly measured by employing nonuniform sampling and that their analysis can be effective if supported by quantum mechanical calculations. Thus, such curves can be used to form a new, third pseudodimension of the TOCSY spectrum. Similarly to the other two frequency dimensions, this one also resolves ambiguities and provides characteristic information. We show how the approach supports the analysis of a fragment of protein Tau Repeat-4 domain. Yet, its potential applications are far broader, including the analysis of complex mixtures or other polymers.

Development of an Enzyme-Linked Immunosorbent Assay for Detection of the Native Conformation of Enterovirus A71.

ABSTRACTEnterovirus A71 (EVA71) is a medically important virus that is commonly associated with hand, foot, and mouth disease (HFMD). It is responsible for periodic outbreaks, resulting in significant economic impact and loss of life. Vaccination offers the potential to control future outbreaks, and vaccine development has been increasingly the focus of global research efforts. However, antigenic characterization of vaccine candidates is challenging because there are few tools to characterize the different antigenic forms of the virus. As with other picornaviruses, EVA71 virions exist in two antigenic states, native (NAg) and expanded (HAg). It is likely that the composition of vaccines, in terms of the proportions of NAg and HAg, will be important for vaccine efficacy and batch-to-batch consistency. This paper describes the development of a single-chain fused variable (scFv) domain fragment and the optimization of a sandwich enzyme-linked immunosorbent assay (ELISA) for the specific detection of the NAg conformation of EVA71. NAg specificity of the scFv was demonstrated using purified EVA71, and conversion of NAg to HAg by heating resulted in a loss of binding. We have thus developed an effective tool for characterization of the specific antigenic state of EVA71.IMPORTANCE EVA71 is a medically important virus that is commonly associated with HFMD, resulting in periodic outbreaks, significant economic impact, and loss of life. Vaccination offers the potential to curtail future outbreaks, and vaccine development has been increasingly the focus of global research efforts. However, antigenic characterization of vaccine candidates is challenging because there are very limited effective tools to characterize the different antigenic forms of EV71. As with other picornaviruses, EVA71 virions exist in two antigenic states, native and expanded. This paper describes the development of an scFv and the optimization of a sandwich ELISA for the specific detection of the native conformation of EVA71 as an effective tool for characterization of the specific antigenic state of EVA71.

Expanding PAM recognition and enhancing base editing activity of Cas9 variants with non‐PI domain mutations derived from xCas9

The recognition of protospacer adjacent motif (PAM) is a key factor for the CRISPR (i.e. clustered regularly interspaced short palindromic repeats)/CRISPR-associated 9 (Cas9) system to distinguish foreign DNAs from the host genome, and also significantly restricts the targeting scope of the system during genome-editing applications. Structurally, the PAM interacting (PI) domain, which usually is located in the C-terminus of Cas9 proteins, directly binds to PAM and plays a key role in determining the recognition specificity. However, several lines of evidence showed that other regions of Cas9 protein beyond the PI domain might also play roles in PAM interaction. Here, we constructed a mosaic SpCas9 protein (xCas9-NG) by fusing the PI domain of SpCas9 PAM variant, Cas9-NG with the non-PI fragment of xCas9 protein that contains multiple amino acid substitutions. We found that non-PI fragment of xCas9 expanded PAM recognition of the Cas9-NG PI domain. In addition, xCas9-NG showed an improved editing efficiency in the majority of targets harboring xCas9 and Cas9-NG PAMs. Importantly, this finding was also successfully extended to other Cas9 variants, including SpRY and the non-G SpCas9 series. Together, our work expands the target scope of SpCas9 editing system and demonstrates the notion that the non-PI domain fragment plays an important role in PAM restriction.

PD1 CD44 antiviral peptide as an inhibitor of the protein-protein interaction in dengue virus invasion

Dengue virus (DENV) infection is mediated by the interaction between the virus envelope protein and cellular receptors of the host cells. In this study, we designed peptides to inhibit protein-protein interaction between dengue virus and CD44 receptor, which is one of the receptors used by DENV for entry. In silico model complexes were designed between domain III of the viral envelope protein of dengue virus 2 and the domain of human CD44 receptor using ClusPro 2.0, (https://cluspro.bu.edu/login.php), and inhibition peptides were designed with Rosetta Online-Server(http://rosie.rosettacommons.org/peptiderive). We identified one linear antiviral peptide of 18 amino acids derived from the human CD44 receptor, PD1 CD44. It did not show hemolysis or toxicity in HepG2 or BHK cell lines, nor did it stimulate the release of IL-1β, IL-6, TNF-α, and IFN-γ, below 100 µM. It had an IC50 of 13.8 µM and maximum effective dose of 54.9 µM evaluated in BHK cells. The decrease in plaque-forming units/mL for DENV1, DENV2, DENV3, and DENV4 was 99.60%, 99.40%, 97.80%, and 70.50%, respectively, and similar results were obtained by RT-qPCR. Non-structural protein 1 release was decreased in pre- and co-treatment but not in post-treatment. Competition assays between the DN59 peptide, envelope protein, and the fragment of domain III "MDKLQLKGMSYSMCTGKF" of the viral envelope of DENV2 and PD1 CD44 showed that our peptide lost its antiviral activity. We demonstrated that our peptide decreased endosome formation, and we propose that it binds to the envelope protein of DENV, inhibiting viral invasion/fusion.

A map of neurofilament light chain species in brain and cerebrospinal fluid and alterations in Alzheimer's disease.

Neurofilament light is a well-established marker of both acute and chronic neuronal damage and is increased in multiple neurodegenerative diseases. However, the protein is not well characterized in brain tissue or body fluids, and it is unknown what neurofilament light species are detected by commercial assays and whether additional species exist. We developed an immunoprecipitation-mass spectrometry assay using custom antibodies targeting various neurofilament light domains, including antibodies targeting Coil 1A/1B of the rod domain (HJ30.13), Coil 2B of the rod domain (HJ30.4) and the tail region (HJ30.11). We utilized our assay to characterize neurofilament light in brain tissue and CSF of individuals with Alzheimer’s disease dementia and healthy controls. We then validated a quantitative version of our assay and measured neurofilament light concentrations using both our quantitative immunoprecipitation-mass spectrometry assay and the commercially available immunoassay from Uman diagnostics in individuals with and without Alzheimer’s disease dementia. Our validation cohort included CSF samples from 30 symptomatic amyloid-positive participants, 16 asymptomatic amyloid-positive participants, 10 symptomatic amyloid-negative participants and 25 amyloid-negative controls. We identified at least three major neurofilament light species in CSF, including N-terminal and C-terminal truncations, and a C-terminal fragment containing the tail domain. No full-length neurofilament light was identified in CSF. This contrasts with brain tissue, which contained mostly full-length neurofilament and a C-terminal tail domain fragment. We observed an increase in neurofilament light concentrations in individuals with Alzheimer’s disease compared with healthy controls, with larger differences for some neurofilament light species than for others. The largest differences were observed for neurofilament light fragments including NfL165 (in Coil 1B), NfL324 (in Coil 2B) and NfL530 (in the C-terminal tail domain). The Uman immunoassay correlated most with NfL324. This study provides a comprehensive evaluation of neurofilament light in brain and CSF and enables future investigations of neurofilament light biology and utility as a biomarker.

Microsecond dynamics during the binding-induced folding of an intrinsically disordered protein

Tau is an intrinsically disordered protein implicated in many neurodegenerative diseases. The repeat domain fragment of tau, tau-K18, is known to undergo a disorder to order transition in the presence of lipid micelles and vesicles, in which helices form in each of the repeat domains. Here, the mechanism of helical structure formation, induced by a phospholipid mimetic, sodium dodecyl sulfate (SDS) at sub-micellar concentrations, has been studied using multiple biophysical probes. A study of the conformational dynamics of the disordered state, using photoinduced electron transfer coupled to fluorescence correlation spectroscopy (PET-FCS) has indicated the presence of an intermediate state, I, in equilibrium with the unfolded state, U.

Spectroscopic analysis of metal ions effect on the aggregation of a λ6aJL2R24G protein variant

Light-chain amyloidosis (AL) is one of the most common forms of amyloidosis. It is characterized by the extracellular deposition of variable domain fragments of immunoglobulin light chains. The clinical manifestations of this disease vary because the deposits can be found in almost all the organs of the human body causing various failures. Approximately 30% of AL cases contain a λ6a germline and 25% of those cases presents a Glycine at position 24 instead of Arginine (R24G). This mutation causes the protein to be thermodynamically more unstable and to be more amyloidogenic.

SIRT2 regulates proliferation and chemotherapy response of MLL-ENL-driven acute myeloid leukemia

Both MLL-AF9 and MLL-ENL leukemia fusion proteins drive oncogenic transformation of hematopoietic cells through their N-terminal DNA/histone binding mixed-lineage leukemia 1 domain and C-terminal fragment of AF9 or ENL containing an unstructured linker region and the ANC1 homology domain, which recruits transcription factors. Despite of their structural similarity, acute myeloid leukemia (AML) patients bearing MLL-ENL show more adverse outcomes compared to those with MLL-AF9. We recapitulated the clinical patterns of these two MLL-fusions driven AMLs using murine models and found that MLL-ENL AML cells showed slower cell cycle progression and more resistance to standard chemotherapy than MLL-AF9 cells. These phenotypes were primarily controlled by the linker regions of ENL and a highly conserved lysine residue K469 within. Substitution of K469 with an acetylated mimic glutamine abolished the ability of MLL-ENL to suppress proliferation and promote chemo-resistance. We showed that deacetylase Sirt2 might act as an upstream regulator of MLL-ENL. Deletion of Sirt2 promoted proliferation of AML cells with either MLL fusions. Importantly, loss of Sirt2 greatly enhanced the sensitivity of the MLL-ENL AML cells to chemo-treatment. Taken together, our study uncovered a unique regulatory role of Sirt2 in leukemogenesis and suggested targeting SIRT2 as a new way to sensitize MLL-ENL AML patience for chemotherapy.

Molecular dynamics simulations of an α-synuclein NAC domain fragment with a ff14IDPSFF IDP-specific force field suggest β-sheet intermediate states of fibrillation.

For the discovery of treatments against synucleinopathies, it is necessary to unravel and fully understand the mechanism of fibrillation of proteins involved. Among them, α-synuclein (αS) plays a key role in the development of these diseases through its aggregation into oligomers found in Lewy bodies. However, its structural disorder as an intrinsically disordered protein (IDP) makes its characterization by experimental techniques arduously difficult. Atomistic simulations aim to provide insights into this blank canvas and, fortunately, some studies have already suggested promising mechanisms. Still, it is urgent to consider the IDP features in simulations, so recently a lot of force fields designed to deal with IDPs have been developed. In this study, we have carried out a total of 12 μs simulations of an αS core fragment using a popular ff14SB AMBER force field and the ff14IDPSFF variation that includes a grid-based energy correction map (CMAP) method. The predicted chemical shifts from the simulations and those measured from the αS protein in the NMR solution indicate that ff14IDPSFF reproduces the experimental data more accurately. Moreover, structural analysis exhibits opposite trends between secondary structure propensities. The ff14SB force field preserves the α-helices found in the micelle-bound αS structure, which is used as an initial conformation, while ff14IDPSFF stands out with increased structural disorder and the formation of β-sheets, which suggests that the IDP-specific force field can capture more suitable conformations representing the possible intermediate states of the fibrillation process.

Allosteric control of ACE2 peptidase domain dynamics.

The Angiotensin Converting Enzyme 2 (ACE2) assists the regulation of blood pressure and is the main target of the coronaviruses responsible for SARS and COVID19. The catalytic function of ACE2 relies on the opening and closing motion of its peptidase domain (PD). In this study, we investigated the possibility of allosterically controlling the ACE2 PD functional dynamics. After confirming that ACE2 PD binding site opening-closing motion is dominant in characterizing its conformational landscape, we observed that few mutations in the viral receptor binding domain fragments were able to impart different effects on the binding site opening of ACE2 PD. This showed that binding to the solvent exposed area of ACE2 PD can effectively alter the conformational profile of the protein, and thus likely its catalytic function. Using a targeted machine learning model and relative entropy-based statistical analysis, we proposed the mechanism for the allosteric perturbation that regulates the ACE2 PD binding site dynamics at atomistic level. The key residues and the source of the allosteric regulation of ACE PD dynamics are also presented.