Knowledge of protein structure can be used to predict the phenotypic consequence of a missense variant. Since structural coverage of the human proteome can be roughly tripled to over 50% of the residues if homology-predicted structures are included in addition to experimentally determined coordinates, it is important to assess the reliability of using predicted models when analyzing missense variants. Accordingly, we assess whether a missense variant is structurally damaging by using experimental and predicted structures. We considered 606 experimental structures and show that 40% of the 1965 disease-associated missense variants analyzed have a structurally damaging change in the mutant structure. Only 11% of the 2134 neutral variants are structurally damaging. Importantly, similar results are obtained when 1052 structures predicted using Phyre2 algorithm were used, even when the model shares low (< 40%) sequence identity to the template. Thus, structure-based analysis of the effects of missense variants can be effectively applied to homology models. Our in-house pipeline, Missense3D, for structurally assessing missense variants was made available at http://www.sbg.bio.ic.ac.uk/~missense3d

Dietary fat is an important source of nutrition. Here we identify eight mutations in SARA2 that are associated with three severe disorders of fat malabsorption. The Sar1 family of proteins initiates the intracellular transport of proteins in COPII (coat protein)-coated vesicles. Our data suggest that chylomicrons, which vastly exceed the size of typical COPII vesicles, are selectively recruited by the COPII machinery for transport through the secretory pathways of the cell.

No abstract

The promyelocytic leukemia (PML) protein is aggregated into nuclear bodies that are associated with diverse nuclear processes. Here, we report that the distance between a locus and its nearest PML body correlates with the transcriptional activity and gene density around the locus. Genes on the active X chromosome are more significantly associated with PML bodies than their silenced homologues on the inactive X chromosome. We also found that a histone-encoding gene cluster, which is transcribed only in S-phase, is more strongly associated with PML bodies in S-phase than in G0/G1 phase of the cell cycle. However, visualization of specific RNA transcripts for several genes showed that PML bodies were not themselves sites of transcription for these genes. Furthermore, knock-down of PML bodies by RNA interference did not preferentially change the expression of genes closely associated with PML bodies. We propose that PML bodies form in nuclear compartments of high transcriptional activity, but they do not directly regulate transcription of genes in these compartments.

Amide bond formation is one of the most important reactions in both chemistry and biology 1-4 , but there is currently no chemical method to achieve α-peptide ligation in water that tolerates all twenty proteinogenic amino acids at the peptide ligation site. The universal genetic code establishes the biological role of peptides predates Life's last universal common ancestor and that peptides played an essential role in the origins of Life 5-9 . The essential role of sulfur in the citric acid cycle, non-ribosomal peptide synthesis and polyketide biosynthesis points towards thioester-dependent peptide ligations preceding RNA-dependent protein synthesis during the evolution of Life 5,9-13 . However, a robust mechanism for aminoacyl thioester formation has never been demonstrated 13 . Here, we report a chemoselective, high yielding a-aminonitrile ligation that exploits only prebiotically plausible molecules-hydrogen sulfide, thioacetate 12,14 and ferricyanide 12,14-17 or cyanoacetylene 8,14 -to yield apeptides in water. The ligation is extremely selective for a-aminonitrile coupling and tolerates all 20 proteinogenic amino acid residues. Two essential features enable the peptide ligation in water: 1) the reactivity and pKaH of a-aminonitriles makes them compatible with ligation at neutral pH, and 2) Nacylation stabilises the peptide product and activates the peptide precursor to (biomimetic) N®C peptide ligation. Our model unites prebiotic aminonitrile synthesis and biological a-peptides, suggesting short N-acyl peptide nitriles were plausible substrates during early evolution.To improve the efficiency and selectivity of peptide ligation in water we sought to develop a novel mechanism for non-enzymatic peptide synthesis, which would operate via biomimetic N®C ligation in near-neutral pH water, and we suspected that a combination of sulfur and nitrile chemistry would be required ( Fig. 1a) 8,9,14,[18][19][20][21] . Proteinogenic a-aminonitriles (AA-CN) are readily synthesised 8,18 , and their direct ligation would provide the simplest prebiotic pathway to peptides. Unfortunately, incubation of AA-CN in water results in extremely ineffective peptide synthesis 22 . a-Amino acids (AA) are widely assumed to be prebiotic precursors of peptides, but the harsh conditions (typically strongly acidic or alkaline solutions) required for AA formation from AA-CN are incompatible with the integrity of both peptides and electrophilic activating agents. Therefore, we sought a more congruent and direct pathway from a-aminonitriles to a-peptides, and although the conversion of AA-CN to AA-SH has never been reported 23 , harnessing the AA-CN nitrile moiety for thioacid synthesis seemed more prudent than dissipating its activation through exhaustive hydrolysis.Orgel has previously suggested that a-aminothioacids (AA-SH) 16 might offer an interesting alternative to biological thioesters 10,11 . AA-SH unite excellent aqueous stability with highly selective (electrophilic or oxidative) activation 12,14,16,24 , but their prebiotic synthesis...

UK 2A central problem for prebiotic synthesis of the biological amino acids and nucleotides is avoiding the concomitant synthesis of undesired or irrelevant byproducts. Additionally, multistep pathways require mechanisms that enable the sequential addition of reactants and purification of intermediates that are consistent with reasonable geochemical scenarios. Here, we show that 2-aminothiazole reacts selectively with two-and three-carbon sugars (glycolaldehyde and glyceraldehyde, respectively), which results in their accumulation and purification as stable crystalline aminals. This permits ribonucleotide synthesis, even from complex sugar mixtures. Remarkably, aminal formation also overcomes the thermodynamically favoured isomerisation of glyceraldehyde to dihydroxyacetone because only the aminal of glyceraldehyde separates from the equilibrating mixture. Finally, we show that aminal formation provides a novel pathway to amino acids that avoids synthesis of the non-proteinogenic α,α-disubstituted analogues. The common physicochemical mechanism that controls proteinogenic amino acid and ribonucleotide assembly from prebiotic mixtures suggests these essential classes of metabolite had a unified chemical origin. 3The conservation of the genetic code, amino acids, and nucleotides in biology suggests a single origin of life on Earth. [1][2][3][4][5][6][7][8][9][10][11][12][13] Proteins are built from a highly restricted set of about 20 amino acids according to a universal triplet code of four ribonucleotides. Therefore, it is essential to learn how this specific small constellation of molecules became irrevocably linked at the advent of life. In contrast to the narrow distribution of universal metabolites observed in biology, typical prebiotic reactions are notorious for their complex product distributions. Accordingly, it has been recognised that "the chief obstacle to understanding the origin of RNA-based life is identifying a plausible mechanism for overcoming the clutter wrought by prebiotic chemistry". [4][5][6][7] For example, the most-efficient and specific proposed prebiotic pathway to the pyrimidine ribonucleotides requires synthesis of the key intermediate pentose aminooxazoline (1) (Fig. 1a). [2][3][4][5][6][22][23][24] However, the plausibility of this proposed prebiotic synthesis of pentose aminooxazoline (1) has been questioned because it is contingent upon the strictly controlled sequential delivery of pure glycolaldehyde (2a) to cyanamide (3) to yield 2-aminooxazole (4), followed by pure glyceraldehyde (2b) to 2-aminooxazole (4) to yield the desired product (Fig. 1a). This is a serious problem because both of these reactions lack the intrinsic selectivity required to exclusively yield their respective products (2-aminooxazole (4) and pentose aminooxazoline (1)) from mixtures of glycolaldehyde (2a) and glyceraldehyde (2b). The problem becomes increasingly worse in the presence of other sugars. Without a separate and sequential delivery of glycolaldehyde (2a) and glyceraldehyde (2b), a complex mixture...

SUMMARYLiving organisms are the most complex chemical system known to exist, yet exploit only a small constellation of universally conserved metabolites to support indefinite evolution. The conserved chemical simplicity belying biological diversity strongly indicates a unified origin of life. Thus, the chemical relationship between metabolites suggests that a simple set of predisposed chemical reactions predicated the appearance of life on Earth. Conversely, if prebiotic chemistry produces highly complex mixtures, this then implies that the feasibility of elucidating life's origins is an insurmountable task. Prebiotic systems chemistry, however, has recently been exploiting the chemical links between different metabolites to provide unprecedented scope for exploration of the origins of life, and an exciting new perspective on a 4 billion-year-old problem. At the heart of the systems approach is an understanding that individual classes of metabolites cannot be considered in isolation. This review highlights several recent advances suggesting that the canonical nucleotides and proteinogenic amino acids are predisposed chemical structures. KEYWORDSOrigins of life, prebiotic chemistry, systems chemistry, predisposed chemistry, RNA, nucleotides, amino acids, sugars, metabolism, crystallization. BIGGER PICTUREAdvancing our understanding of the spontaneous emergence of life requires innovation across scientific disciplines as broad as astrophysics to phylogenetics, yet the primacy of chemistry cannot be overestimated. Cellular life is a chemical system of awe-inspiring complexity yet, perhaps surprisingly, life exploits only a 2 small constellation of universally conserved metabolites working in concert to support indefinite evolution.The conserved chemical simplicity that belies biodiversity is a strong indication that a simple set of predisposed reactions predicated the sudden appearance of life on Earth. The wonder of nature's greatest feat of invention-the self-assembly of living cells-positions the origins of life as one of the greatest challenges in chemistry. Building chemical systems that can self-assemble, process information, control the transport and accumulation of chemicals, orchestrate reaction pathways, and ultimately self-replicate will no doubt have a major impact on evolving technology, but nature has had a 4 billion-year head start in implementing controlled chemical evolution, and the lessons to be learnt from its prior art merely await discovery. eTOCPrebiotic systems chemistry is providing unprecedented scope for exploring the origins of life and an exciting new perspective on a 4 billion-year-old problem. At the heart of this new systems approach is an understanding that individual classes of metabolites cannot be considered in isolation if the chemical origin of life on Earth is to be successfully elucidated. This review aims to highlight several recent advances that suggest the canonical nucleotides and proteinogenic amino acids are predisposed chemical structures.

Non-equilibrium conditions must have been crucial for the assembly of the first informational polymers of early life-by supporting their formation and continuous enrichment in a long-lasting environment. Here we explored how gas bubbles in water subjected to a thermal gradient, a likely scenario within crustal mafic rocks on the early Earth, drive a complex, continuous enrichment of prebiotic molecules. RNA precursors, monomers, active ribozymes, oligonucleotides, and lipids are shown to (1) cycle between dry and wet states, enabling the central step of RNA phosphorylation, (2) accumulate at the gas-water interface to drastically increase ribozymatic activity, (3) condense into hydrogels, (4) form pure crystals, and (5) encapsulate into protecting vesicle aggregates that subsequently undergo fission. These effects occurred within less than 30 minutes. The findings unite physical conditions in one location which were crucial for the chemical emergence of biopolymers.They suggest that heated microbubbles could have hosted the first cycles of molecular evolution.Life is a non-equilibrium system. By evolution, modern life has created a complex protein machinery to maintain the nonequilibrium of crowded molecules inside dividing vesicles. Based on entropy arguments, equilibrium conditions were unlikely to trigger the evolutionary processes during the origin of life 1 . External non-equilibria had to be provided for the accumulation, encapsulation, and replication of the first informational molecules. They can locally reduce entropy, give rise to patterns 2 , and lean the system towards a continuous, dynamic self-organization 3 . Non-equilibrium dynamics can be found in many fluid systems, including gravity-driven instabilities in the atmosphere 4 , the accumulation of particles in nonlinear flow 5,6 , and shear-dependent platelet activation in blood 7 . Our experiments discuss whether gas-water interfaces in a thermal gradient could have provided such a nonequilibrium setting for the emergence of life on early Earth.Non-equilibrium systems in the form of heat flows were a very common and simplistic setting, found ubiquitously on the planet 8 . Hydrothermal activity is considered abundant on early Earth and intimately linked to volcanic activity 9 . Water is thereby circulating through the pore space of the volcanic rocks, which is formed by magmatic vesiculation (primary origin) and fractures (secondary origin). These systems have been studied as non-equilibrium driving forces for biological molecules in a variety of processes 10-17 .Gases originating from degassing of deeper magma bodies percolate through these water-filled pore networks. At shallow depths bubbles are formed by gases dissolved in water and formation of vapor where sufficient heat is supplied by the hydrothermal system. The bubbles create gas-water interfaces, which previously have been discussed in connection with atmospheric bubble-aerosol-droplet cycles 18 , the adsorption of lipid monolayers and DNA to the interface 19,20 , or the formation of pep...