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Hydrophobic interactions have long been established as essential for stabilizing structured proteins as well as drivers of aggregation, but the impact of hydrophobicity on the functional significance of sequence variants has rarely been considered in a genomewide context. Here we test the role of hydrophobicity on functional impact across 70,000 disease- and non–disease-associated single-nucleotide polymorphisms (SNPs), using enrichment of disease association as an indicator of functionality. We find that functional impact is uncorrelated with hydrophobicity of the SNP itself and only weakly correlated with the average local hydrophobicity, but is strongly correlated with both the size and minimum hydrophobicity of the contiguously hydrophobic sequence (or “blob”) that contains the SNP. Disease association is found to vary by more than sixfold as a function of contiguous hydrophobicity parameters, suggesting utility as a prior for identifying causal variation. We further find signatures of differential selective constraint on hydrophobic blobs and that SNPs splitting a long hydrophobic blob or joining two short hydrophobic blobs are particularly likely to be disease associated. Trends are preserved for both aggregating and nonaggregating proteins, indicating that the role of contiguous hydrophobicity extends well beyond aggregation risk. [ABSTRACT FROM AUTHOR]

All proteomes contain both proteins and polypeptide segments that don't form a defined three-dimensional structure yet are biologically active—called intrinsically disordered proteins and regions (IDPs and IDRs). Most of these IDPs/IDRs lack useful functional annotation limiting our understanding of their importance for organism fitness. Here we characterized IDRs using protein sequence annotations of functional sites and regions available in the UniProt knowledgebase ("UniProt features": active site, ligand-binding pocket, regions mediating protein-protein interactions, etc.). By measuring the statistical enrichment of twenty-five UniProt features in 981 IDRs of 561 human proteins, we identified eight features that are commonly located in IDRs. We then collected the genetic variant data from the general population and patient-based databases and evaluated the prevalence of population and pathogenic variations in IDPs/IDRs. We observed that some IDRs tolerate 2 to 12-times more single amino acid-substituting missense mutations than synonymous changes in the general population. However, we also found that 37% of all germline pathogenic mutations are located in disordered regions of 96 proteins. Based on the observed-to-expected frequency of mutations, we categorized 34 IDRs in 20 proteins (DDX3X, KIT, RB1, etc.) as intolerant to mutation. Finally, using statistical analysis and a machine learning approach, we demonstrate that mutation-intolerant IDRs carry a distinct signature of functional features. Our study presents a novel approach to assign functional importance to IDRs by leveraging the wealth of available genetic data, which will aid in a deeper understating of the role of IDRs in biological processes and disease mechanisms. Author summary: Intrinsically disordered regions (IDRs) in proteins are typically not considered to be functionally as important as the structured parts. However, it is becoming evident that both structured and disordered regions are essential for the repertoire of protein functions. Nevertheless, most of these largely flexible and functionally dynamic protein regions remain uncharacterized. Nevertheless, most of these largely flexible and functionally dynamic protein regions remain uncharacterized. Here, informed by human genetic diversity (i.e., genetic variations from the general population and patients), we identified the IDRs that are more frequently mutated in patients than in relatively healthy individuals, and further show that they carry a set of characteristic functional features. This approach provides a different and effective means to identify unannotated disordered protein segments that are biologically important and lead to pathogenesis upon mutation. [ABSTRACT FROM AUTHOR]

The role of electrostatic interactions and mutations that change charge states in intrinsically disordered proteins (IDPs) is well-established, but many disease-associated mutations in IDPs are charge-neutral. The Val66Met single nucleotide polymorphism (SNP) in precursor brain-derived neurotrophic factor (BDNF) is one of the earliest SNPs to be associated with neuropsychiatric disorders, and the underlying molecular mechanism is unknown. Here we report on over 250 μs of fully-atomistic, explicit solvent, temperature replica-exchange molecular dynamics (MD) simulations of the 91 residue BDNF prodomain, for both the V66 and M66 sequence. The simulations were able to correctly reproduce the location of both local and non-local secondary structure changes due to the Val66Met mutation, when compared with NMR spectroscopy. We find that the change in local structure is mediated via entropic and sequence specific effects. We developed a hierarchical sequence-based framework for analysis and conceptualization, which first identifies "blobs" of 4-15 residues representing local globular regions or linkers. We use this framework within a novel test for enrichment of higher-order (tertiary) structure in disordered proteins; the size and shape of each blob is extracted from MD simulation of the real protein (RP), and used to parameterize a self-avoiding heterogenous polymer (SAHP). The SAHP version of the BDNF prodomain suggested a protein segmented into three regions, with a central long, highly disordered polyampholyte linker separating two globular regions. This effective segmentation was also observed in full simulations of the RP, but the Val66Met substitution significantly increased interactions across the linker, as well as the number of participating residues. The Val66Met substitution replaces β-bridging between V66 and V94 (on either side of the linker) with specific side-chain interactions between M66 and M95. The protein backbone in the vicinity of M95 is then free to form β-bridges with residues 31-41 near the N-terminus, which condenses the protein. A significant role for Met/Met interactions is consistent with previously-observed non-local effects of the Val66Met SNP, as well as established interactions between the Met66 sequence and a Met-rich receptor that initiates neuronal growth cone retraction. Intrinsically disordered proteins are proteins that have no well-defined structure in at least one functional form. Mutations in one amino acid may still affect their function significantly, especially in subtle ways with cumulative adverse effects on health. Here we report on molecular dynamics simulations of a protein that is critical for neuronal health throughout adulthood (brain-derived neurotrophic factor). We investigate the effects of a mutation carried by 30% of human population, which has been widely studied for its association with aging-related and stress-related disorders, reduced volume of the hippocampus, and variations in episodic memory. We identify a molecular mechanism in which the mutation may change the global conformations of the protein and its ability to bind to receptors. [ABSTRACT FROM AUTHOR]

The temperature in the Arctic region has been increasing in the recent past accompanied by melting of its glaciers. We took a snapshot of the current microbial inhabitation of an Alaskan glacier (which can be considered as one of the simplest possible ecosystems) by using metagenomic sequencing of 16S rRNA recovered from ice/snow samples. Somewhat contrary to our expectations and earlier estimates, a rich and diverse microbial population of more than 2,500 species was revealed including several species of Archaea that has been identified for the first time in the glaciers of the Northern hemisphere. The most prominent bacterial groups found were Proteobacteria, Bacteroidetes, and Firmicutes. Firmicutes were not reported in large numbers in a previously studied Alpine glacier but were dominant in an Antarctic subglacial lake. Representatives of Cyanobacteria, Actinobacteria and Planctomycetes were among the most numerous, likely reflecting the dependence of the ecosystem on the energy obtained through photosynthesis and close links with the microbial community of the soil. Principal component analysis (PCA) of nucleotide word frequency revealed distinct sequence clusters for different taxonomic groups in the Alaskan glacier community and separate clusters for the glacial communities from other regions of the world. Comparative analysis of the community composition and bacterial diversity present in the Byron glacier in Alaska with other environments showed larger overlap with an Arctic soil than with a high Arctic lake, indicating patterns of community exchange and suggesting that these bacteria may play an important role in soil development during glacial retreat. [ABSTRACT FROM AUTHOR]

The theory of receptor-ligand binding equilibria has long been well-established in biochemistry, and was primarily constructed to describe dilute aqueous solutions. Accordingly, few computational approaches have been developed for making quantitative predictions of binding probabilities in environments other than dilute isotropic solution. Existing techniques, ranging from simple automated docking procedures to sophisticated thermodynamics-based methods, have been developed with soluble proteins in mind. Biologically and pharmacologically relevant protein-ligand interactions often occur in complex environments, including lamellar phases like membranes and crowded, nondilute solutions. Here, we revisit the theoretical bases of ligand binding equilibria, avoiding overly specific assumptions that are nearly always made when describing receptor-ligand binding. Building on this formalism, we extend the asymptotically exact Alchemical Free Energy Perturbation technique to quantifying occupancies of sites on proteins in a complex bulk, including phase-separated, anisotropic, or nondilute solutions, using a thermodynamically consistent and easily generalized approach that resolves several ambiguities of current frameworks. To incorporate the complex bulk without overcomplicating the overall thermodynamic cycle, we simplify the common approach for ligand restraints by using a single distance-from-bound-configuration (DBC) ligand restraint during AFEP decoupling from protein. DBC restraints should be generalizable to binding modes of most small molecules, even those with strong orientational dependence. We apply this approach to compute the likelihood that membrane cholesterol binds to known crystallographic sites on three GPCRs (β 2 -adrenergic, 5HT-2B, and μ-opioid) at a range of concentrations. Nonideality of cholesterol in a binary cholesterol:phosphatidylcholine (POPC) bilayer is characterized and consistently incorporated into the interpretation. We find that the three sites exhibit very different affinities for cholesterol: The site on the adrenergic receptor is predicted to be high affinity, with 50% occupancy for 1:10 9 CHOL:POPC mixtures. The sites on the 5HT-2B and μ-opioid receptor are predicted to be lower affinity, with 50% occupancy for 1:10 3 CHOL:POPC and 1:10 2 CHOL:POPC, respectively. These results could not have been predicted from the crystal structures alone.