ResMAP-a saturation mutagenesis platform enabling parallel profiling of target-specific resistance-conferring mutations in .

Unlabelled: New and improved drugs are required for the treatment and ultimate eradication of malaria. The efficacy of front-line therapies is now threatened by emerging drug resistance; thus, new tools to support the development of drugs with a lower propensity for resistance are needed. Here, we describe the development of a RESistance Mapping And Profiling (ResMAP) platform for the identification of resistance-conferring mutations in drug targets.

A unified analysis of evolutionary and population constraint in protein domains highlights structural features and pathogenic sites.

Protein evolution is constrained by structure and function, creating patterns in residue conservation that are routinely exploited to predict structure and other features. Similar constraints should affect variation across individuals, but it is only with the growth of human population sequencing that this has been tested at scale. Now, human population constraint has established applications in pathogenicity prediction, but it has not yet been explored for structural inference.

Classification of likely functional class for ligand binding sites identified from fragment screening.

Fragment screening is used to identify binding sites and leads in drug discovery, but it is often unclear which binding sites are functionally important. Here, data from 37 experiments, and 1309 protein structures binding to 1601 ligands were analysed. A method to group ligands by binding sites is introduced and sites clustered according to profiles of relative solvent accessibility.

Missense variants in human ACE2 strongly affect binding to SARS-CoV-2 Spike providing a mechanism for ACE2 mediated genetic risk in Covid-19: A case study in affinity predictions of interface variants.

SARS-CoV-2 Spike (Spike) binds to human angiotensin-converting enzyme 2 (ACE2) and the strength of this interaction could influence parameters relating to virulence. To explore whether population variants in ACE2 influence Spike binding and hence infection, we selected 10 ACE2 variants based on affinity predictions and prevalence in gnomAD and measured their affinities and kinetics for Spike receptor binding domain through surface plasmon resonance (SPR) at 37°C. We discovered variants that reduce and enhance binding, including three ACE2 variants that strongly inhibited (p.

Effects of common mutations in the SARS-CoV-2 Spike RBD and its ligand, the human ACE2 receptor on binding affinity and kinetics.

The interaction between the SARS-CoV-2 virus Spike protein receptor binding domain (RBD) and the ACE2 cell surface protein is required for viral infection of cells. Mutations in the RBD are present in SARS-CoV-2 variants of concern that have emerged independently worldwide. For example, the B.

Ankyrin repeats in context with human population variation.

Ankyrin protein repeats bind to a wide range of substrates and are one of the most common protein motifs in nature. Here, we collate a high-quality alignment of 7,407 ankyrin repeats and examine for the first time, the distribution of human population variants from large-scale sequencing of healthy individuals across this family. Population variants are not randomly distributed across the genome but are constrained by gene essentiality and function.

The Dundee Resource for Sequence Analysis and Structure Prediction.

The Dundee Resource for Sequence Analysis and Structure Prediction (DRSASP; http://www.compbio.dundee.

Disease related single point mutations alter the global dynamics of a tetratricopeptide (TPR) α-solenoid domain.

Tetratricopeptide repeat (TPR) proteins belong to the class of α-solenoid proteins, in which repetitive units of α-helical hairpin motifs stack to form superhelical, often highly flexible structures. TPR domains occur in a wide variety of proteins, and perform key functional roles including protein folding, protein trafficking, cell cycle control and post-translational modification. Here, we look at the TPR domain of the enzyme O-linked GlcNAc-transferase (OGT), which catalyses O-GlcNAcylation of a broad range of substrate proteins.

NCoR1-independent mechanism plays a role in the action of the unliganded thyroid hormone receptor.

Nuclear receptor corepressor 1 (NCoR1) is considered to be the major corepressor that mediates ligand-independent actions of the thyroid hormone receptor (TR) during development and in hypothyroidism. We tested this by expressing a hypomorphic NCoR1 allele (NCoR1ΔID), which cannot interact with the TR, in Pax8-KO mice, which make no thyroid hormone. Surprisingly, abrogation of NCoR1 function did not reverse the ligand-independent action of the TR on many gene targets and did not fully rescue the high mortality rate due to congenital hypothyroidism in these mice.

Contribution of bacteriochlorophyll conformation to the distribution of site-energies in the FMO protein.

The structural data for the Fenna-Matthews-Olson (FMO) protein indicate that the bacteriochlorophylls (BChls) display a significant degree of conformational heterogeneity of their peripheral substituents and the protein-induced nonplanar skeletal deformations of the tetrapyrrole macrocycle. As electronic properties of chromophores are altered by such differences, a conformational effect may influence the site-energies of specific pigments and thus play a role in mediating the excitation energy transfer dynamics, but this has not yet been established. The difficulty of assessing this question is shown to be partly the result of the inability of the sequential truncation approach usually employed to account for interactions between the conformations of the macrocycle and its substituents and an alternative approach is suggested.

Expanding the clinical spectrum of hereditary fibrosing poikiloderma with tendon contractures, myopathy and pulmonary fibrosis due to FAM111B mutations.

Background: Hereditary Fibrosing Poikiloderma (HFP) with tendon contractures, myopathy and pulmonary fibrosis (POIKTMP [MIM 615704]) is a very recently described entity of syndromic inherited poikiloderma. Previously by using whole exome sequencing in five families, we identified the causative gene, FAM111B (NM_198947.3), the function of which is still unknown.

Severe dermatitis, multiple allergies, and metabolic wasting syndrome caused by a novel mutation in the N-terminal plakin domain of desmoplakin.

Background: Severe dermatitis, multiple allergies, and metabolic wasting (SAM) syndrome is a recently recognized syndrome caused by mutations in the desmoglein 1 gene (DSG1). To date, only 3 families have been reported.

Objective: We studied a new case of SAM syndrome known to have no mutations in DSG1 to detail the clinical, histopathologic, immunofluorescent, and ultrastructural phenotype and to identify the underlying molecular mechanisms in this rare genodermatosis.

Ultrasound mapping of the long saphenous vein in coronary artery bypass graft surgery.

Long saphenous vein is the most common conduit utilized for surgical coronary revascularization. Ultrasound-assisted vein assessment is superior to traditional clinical examination of the long saphenous vein in discerning path and suitability for use as a conduit. Preoperative ultrasound mapping of the long saphenous vein is easy and rapidly accomplished allowing optimal surgical site selection, avoiding unnecessary surgical dissection and potential wound complications.

Computational quantification of the physicochemical effects of heme distortion: redox control in the reaction center cytochrome subunit of Blastochloris viridis.

A facile, experimentally calibrated computational procedure is described that affords the relative ordering of heme cofactor reduction potentials with respect to intrinsic shifts brought about by apoprotein induced heme-macrocycle distortion. The method utilizes heme-Fe partial atomic charges and is useful with the computationally inexpensive B3LYP/3-21g method calculated for simplified heme models extracted from the Protein Data Bank incorporating only the effects of varying macrocycle conformations and thereby delineating their physicochemical effects. The procedure was successfully calibrated using the atomic coordinates and published midpoint potentials from the heme cofactors in wild-type and a series of heme-NO and -O(2) binding domain mutants and thus confirmed the sole conformational modulation of the redox potentials in these complexes.

Malignant primary cardiac tumours.

Objectives: Management of malignant tumours of the heart remains a poorly investigated clinical area due to the scarcity of presentations. The purpose of this series and review is to present an outline of the management emphasized by our personal experience in a regional cardiothoracic centre.

Methods: We reviewed all cases presenting with primary cardiac tumours in our institution within the last 10 years, looking at presentation, management and outcomes.

Conformational control of cofactors in nature--functional tetrapyrrole conformations in the photosynthetic reaction centers of purple bacteria.

Chemically identical tetrapyrrole cofactors such as hemes and chlorophylls participate in functionally diverse biological roles. An analysis of the available protein structural data for the bacteriochlorophylls in the photosynthetic reaction center gives statistically reliable evidence of the hypothesis that the protein induced cofactor conformation is a modulator of the bio-molecular function of each reaction center. The results serve as a general model to illustrate conformational control of tetrapyrrole cofactors in other proteins.

Impact of coronary artery bypass grafting on survival after aortic valve replacement.

Treatment of coronary artery disease by coronary artery bypass grafting (CABG) concurrently with aortic valve replacement (AVR) improves outcome but survival compared to isolated AVR remains uncertain, as does the role of the left internal mammary artery (LIMA) graft to the left anterior descending (LAD) artery. All 799 patients undergoing elective primary AVR, using the St. Jude Medical mechanical prosthesis, with or without CABG, between March 1986 and May 2000, were reviewed with 100% follow-up.

An absent carotid pulse may indicate critical aortic stenosis.

In severe valvular aortic stenosis, obstruction to ventricular contraction results in prolonged ventricular systole and diminished peak flow velocity. This may translate into weak or impalpable peripheral arterial pulses. We report a case of severe aortic stenosis associated with an impalpable carotid pulse (in the absence of local carotid artery disease) that became easily detectable following aortic valve replacement.

Concomitant mitral valve surgery with aortic valve replacement: a 21-year experience with a single mechanical prosthesis.

Background: Long-term survival for combined aortic and mitral valve replacement appears to be determined by the mitral valve prosthesis from our previous studies. This 21-year retrospective study assess long-term outcome and durability of aortic valve replacement (AVR) with either concomitant mitral valve replacement (MVR) or mitral valve repair (MVrep). We consider only a single mechanical prosthesis.

Treatment of a persistent false lumen with aneurysm formation following surgical repair of type a dissection.

We describe the case of a 68-year-old man who developed aneurysmal dilatation of the proximal descending thoracic aorta 8 years after repair of a type A dissection. The aneurysm was due to an anastomotic leak at the distal end of the previous repair in the ascending aorta with antegrade perfusion of the false lumen. Surgical repair of the anastomotic leak partially obliterated the false lumen and computed tomography scan demonstrated thrombosis in a large proportion of the false lumen aneurysm.

A clinical, renal and immunological assessment of surface modifying additive treated (SMART) cardiopulmonary bypass circuits.

Biocompatible cardiopulmonary bypass (CPB) circuits aim to reduce contact activation and its physiological consequences. We investigated the hypothesis that use of Surface Modifying Additive (SMA)-treated circuits (Sorin Group Ltd) compared with non-SMA circuits would be associated with preservation of blood pressure during CPB and modulation of perioperative subclinical renal function (urinary alpha-1-microglobulin (alpha-1-m)) and plasma and urinary cytokine changes. In a study of low-risk CABG patients (n=40), randomized to SMA (n=20) versus non-SMA circuits (n=20), we found better preserved blood pressure at CPB initiation in SMA patients (p <0.