Crowding Promotes the Switch from Hairpin to Pseudoknot Conformation in Human Telomerase RNA

Formation of a pseudoknot in the conserved RNA core domain in the ribonucleoprotein human telomerase is required for function. In vitro experiments show that the pseudoknot (PK) is in equilibrium with an extended hairpin (HP) structure. We use molecular simulations of a coarse-grained model, which reproduces most of the salient features of the experimental melting profiles of PK and HP, to show that crowding enhances the stability of PK relative to HP in the wild type and in a mutant associated with dyskeratosis congenita. In monodisperse suspensions, small crowding particles increase the stability of compact structures to a greater extent than larger crowders. If the sizes of crowders in a binary mixture are smaller than the unfolded RNA, the increase in melting temperature due to the two components is additive. In a ternary mixture of crowders that are larger than the unfolded RNA, which mimics the composition of ribosome, large enzyme complexes and proteins in E. coli, the marginal increase in stability is entirely determined by the smallest component. We predict that crowding can restore partially telomerase activity in mutants, which dramatically decrease the PK stability.Comment: File "JACS_MAIN_archive_PDF_from_DOC.pdf" (PDF created from DOC) contains the main text of the paper File JACS_SI_archive.tex + 7 figures are the supplementary inf

Local molecular field theory for the treatment of electrostatics

We examine in detail the theoretical underpinnings of previous successful applications of local molecular field (LMF) theory to charged systems. LMF theory generally accounts for the averaged effects of long-ranged components of the intermolecular interactions by using an effective or restructured external field. The derivation starts from the exact Yvon-Born-Green hierarchy and shows that the approximation can be very accurate when the interactions averaged over are slowly varying at characteristic nearest-neighbor distances. Application of LMF theory to Coulomb interactions alone allows for great simplifications of the governing equations. LMF theory then reduces to a single equation for a restructured electrostatic potential that satisfies Poisson's equation defined with a smoothed charge density. Because of this charge smoothing by a Gaussian of width sigma, this equation may be solved more simply than the detailed simulation geometry might suggest. Proper choice of the smoothing length sigma plays a major role in ensuring the accuracy of this approximation. We examine the results of a basic confinement of water between corrugated wall and justify the simple LMF equation used in a previous publication. We further generalize these results to confinements that include fixed charges in order to demonstrate the broader impact of charge smoothing by sigma. The slowly-varying part of the restructured electrostatic potential will be more symmetric than the local details of confinements.Comment: To be published in J Phys-Cond Matt; small misprint corrected in Eq. (12) in V

Conformational dynamics and internal friction in homopolymer globules: equilibrium vs. non-equilibrium simulations

We study the conformational dynamics within homopolymer globules by solvent-implicit Brownian dynamics simulations. A strong dependence of the internal chain dynamics on the Lennard-Jones cohesion strength ε and the globule size N [subscript G] is observed. We find two distinct dynamical regimes: a liquid-like regime (for ε ε[subscript s] with slow internal dynamics. The cohesion strength ε[subscript s] of this freezing transition depends on N G . Equilibrium simulations, where we investigate the diffusional chain dynamics within the globule, are compared with non-equilibrium simulations, where we unfold the globule by pulling the chain ends with prescribed velocity (encompassing low enough velocities so that the linear-response, viscous regime is reached). From both simulation protocols we derive the internal viscosity within the globule. In the liquid-like regime the internal friction increases continuously with ε and scales extensive in N [subscript G] . This suggests an internal friction scenario where the entire chain (or an extensive fraction thereof) takes part in conformational reorganization of the globular structure.American Society for Engineering Education. National Defense Science and Engineering Graduate Fellowshi

Mixing A and B homopolymers with AC diblock copolymers: Phase behaviour of asymmetric polymer blends

We use grand-canonical-ensemble self-consistent field theory to study blends of both moderately and strongly segregated homopolymers A and B with some diblock copolymer AC, where C is attracted to B. We derive an analytical condition for the Flory-Huggins interaction parameters, which describes a balanced copolymer surfactant AC. We then calculate ternary phase diagrams mainly for blends containing such balanced surfactants. Among the ordered structures, we generally consider lamellar and hexagonal phases, whereas cubic phases are included in the calculation when the polymer blends are studied far from the Lifshitz point. The resulting phase diagrams are highly asymmetric. In particular we show that even a compositionally symmetric polymer blends - that is with equal concentrations and molecular weights of the two homopolymers and with identical polymerization degrees of the copolymer blocks - may organize into either of the two distinct hexagonal structures, as well as into the lamellar structure. One of these hexagonal phases, with the B-rich matrix, has a rather low content of the stabilizing copolymer and may therefore, under experimental conditions, disorder into a polymeric microemulsion. Overall we conclude that the AC diblock can provide a slightly more efficient compatibilizer than its AB counterpart, provided that the incompatibility of homopolymers A and B is not too strong

A mean-field theory of wetting by ionic solutions

The problem of wetting of a solid substrate by an ionic solution is examined theoretically, combining the classic Cahn theory for the solvent with the non-linear Poisson-Boltzmann treatment of the solute. The nature and location of the corresponding wetting transition are found to be particularly sensitive to the range and strength of the electrostatic interactions. These can be tuned, respectively, by changing the salt concentration and the substrate surface charge

Structural and Functional Significance of the Amino Acid Differences Val\u3csub\u3e35\u3c/sub\u3eThr, Ser\u3csub\u3e46\u3c/sub\u3eAla, Asn\u3csub\u3e65\u3c/sub\u3eSer, and Ala\u3csub\u3e94\u3c/sub\u3eSer in 3C-like Proteinases from SARS-CoV-2 and SARS-CoV

Three dimensional structures of (chymo)trypsin-like proteinase (3CLpro) from SARS-CoV-2 and SARS-CoV differ at 8 positions. We previously found that the Val86Leu, Lys88Arg, Phe134His, and Asn180Lys mutations in these enzymes can change the orientation of the N- and C-terminal domains of 3CLpro relative to each other, which leads to a change in catalytic activity. This conclusion was derived from the comparison of the structural catalytic core in 169 (chymo)trypsin-like proteinases with the serine/cysteine fold. Val35Thr, Ser46Ala, Asn65Ser, Ala94Ser mutations were not included in that analysis, since they are located far from the catalytic tetrad. In the present work, the structural and functional roles of these variable amino acids at positions 35, 46, 65, and 94 in the 3CLpro sequences of SARS-CoV-2 and SARS-CoV have been established using a comparison of the same set of proteinases leading to the identification of new conservative elements. Comparative analysis showed that, in addition to interdomain mobility, which could modulate catalytic activity, the 3CLpro(s) can use for functional regulation an autolytic loop and the unique Asp33-Asn95 region (the Asp33-Asn95 Zone) in the N-terminal domain. Therefore, all 4 analyzed mutation sites are associated with the unique structure-functional features of the 3CLpro from SARS-CoV-2 and SARS-CoV. Strictly speaking, the presented structural results are hypothetical, since at present there is not a single experimental work on the identification and characterization of autolysis sites in these proteases

On the Relationship Between the Conserved ‘black’ and ‘gray’ Structural Clusters and Intrinsic Disorder in Parvalbumins

Recently we found two highly conserved structural motifs in the members of the EF-hand protein family, which provide a supporting scaffold for their Ca2+ binding loops. Each structural motif is formed by a cluster of three amino acids. These clusters were called ‘black’ cluster (cluster I) and ‘gray’ cluster (cluster II). In the present work, we studied the relationship between the location of the ‘black’ and ‘gray’ structural clusters in parvalbumins and the location of the amino acid sequence regions with a tendency for intrinsic disorder. This analysis revealed that in parvalbumins, the residues in the vicinity of the conserved structural clusters constitute parts of the conserved motifs enriched in the disorder-promoting residues. Therefore, the clusters found in parvalbumins are characterized not only by the presence of conserved amino acid residues, but also by the conserved distribution of the intrinsic disorder predisposition within their sequences, suggesting the presence of conserved structural dynamics in the apo-forms of parvalbumins, where the black cluster appears to have greater mobility than the gray cluster

Papain-like Cysteine Proteinase Zone (PCP-zone) and PCP Structural Catalytic Core (PCP-SCC) of Enzymes with Cysteine Proteinase Fold

There are several families of cysteine proteinases with different folds – for example the (chymo)trypsin fold family and papain-like fold family – but in both families the hydrolase activity of cysteine proteinases requires a cysteine residue as the catalytic nucleophile. In this work, we have analyzed the topology of the active site regions in 146 three-dimensional structures of proteins belonging to the Papain-like Cysteine Proteinase (PCP) superfamily, which includes papain as a typical representative of this protein superfamily. All analyzed enzymes contain a unique structurally closed conformation – a “PCP-Zone” – which can be divided into two groups, Class A and Class B. Eight structurally conserved amino acids of the PCP-Zone form a common Structural Core. The Structural Core, catalytic nucleophile, catalytic base and residue Xaa – which stabilizes the side-chain conformation of the catalytic base – make up a PCP Structural Catalytic Core (PCP-SCC). The PCP-SCC of Class A and Class B are divided into 5 and 2 types, respectively. Seven variants of the mutual arrangement of the amino-acid side chains of the catalytic triad – nucleophile, base and residue Xaa – within the same fold clearly demonstrate how enzymes with the papain-like fold adapt to the need to perform diverse functions in spite of their limited structural diversity. The roles of both the PCP-Zone of SARS-CoV-2-PLpro described in this study and the NBCZone of SARS-CoV-2-3CLpro presented in our earlier article (Denesyuk AI, Johnson MS, Salo-Ahen OMH, Uversky VN, Denessiouk K. Int J Biol Macromol. 2020;153:399-411) that are in contacts with inhibitors are discussed

Structural Leitmotif and Functional Variations of the Structural Catalytic Core in (chymo)trypsin-like Serine/cysteine Fold Proteinases

Proteinases with the (chymo)trypsin-like serine/cysteine fold comprise a large superfamily performing their function through the Acid – Base – Nucleophile catalytic triad. In our previous work (Denesyuk AI, Johnson MS, Salo-Ahen OMH, Uversky VN, Denessiouk K. Int J Biol Macromol. 2020;153:399–411), we described a universal three-dimensional (3D) structural motif, NBCZone, that contains eleven amino acids: dipeptide 42 T–43 T, pentapeptide 54 T–55 T–56 T–57 T(base)–58 T, tripeptide 195 T(nucleophile)–196 T–197 T and residue 213 T (T – numeration of amino acids in trypsin). The comparison of the NBCZones among the members of the (chymo)trypsin-like protease family suggested the existence of 15 distinct groups. Within each group, the NBCZones incorporate an identical set of conserved interactions and bonds. In the present work, the structural environment of the catalytic acid at the position 102 T and the fourth member of the “catalytic tetrad” at the position 214 T was analyzed in 169 3D structures of proteinases with the (chymo)trypsin-like serine/cysteine fold. We have identified a complete Structural Catalytic Core (SCC) consisting of two classes and four groups. The proteinases belonging to different classes and groups differ from each other by the nature of the interaction between their N- and C-terminal β-barrels. Comparative analysis of the 3CLpro(s) from SARS-CoV-2 and SARS-CoV, used as an example, showed that the amino acids at positions 103 T and 179 T affect the nature of the interaction of the “catalytic acid” core (102 T-Core, N-terminal β-barrel) with the “supplementary” core (S-Core, C-terminal β-barrel), which ultimately results in the modulation of the enzymatic activity. The reported analysis represents an important standalone contribution to the analysis and systematization of the 3D structures of (chymo)trypsin-like serine/cysteine fold proteinases. The use of the developed approach for the comparison of 3D structures will allow, in the event of the appearance of new representatives of a given fold in the PDB, to quickly determine their structural homologues with the identification of possible differences

Intrinsic Disorder in S100 Proteins

Although the members of the largest subfamily of the EF-hand proteins, S100 proteins, are evolutionarily young, their functional diversity is extremely broad, partly due to their ability to adapt to various targets. This feature is a hallmark of intrinsically disordered proteins (IDPs), but none of the S100 proteins are recognized as IDPs. S100 are predicted to be enriched in intrinsic disorder, with 62% of them being predicted to be disordered by at least one of the predictors: 31% are recognized as ‘molten globules’ and 15% are shown to be in extended disordered form. The disorder level of predicted disordered S100 regions is conserved compared to that of more structured regions. The central disordered stretch corresponds to the major part of pseudo EF-hand loop, helix II, hinge region, and an initial part of helix III. It contains about half of known sites of enzymatic post-translational modifications (PTMs), confirming that this region can be flexible in vivo. Most of the internal residues missing in tertiary structures belong to the hinge. Both hinge and pseudo EF-hand loop correspond to the local maxima of the PONDR® VSL2 score and are shown to be evolutionary hotspots, leading to gain of new functional properties. The action of PTMs is shown to be destabilizing, in contrast with the effect of metal-binding or S100 dimerization. Formation of the S100 heterodimers relies on the interplay between the structural rigidity of one of the S100 monomers and the flexibility of another monomer. The ordered regions dominate in the S100 homodimerization sites. Target-binding sites generally consist of distant regions, drastically differing in their disorder level. The disordered region comprising most of the hinge and the N-terminal half of helix III is virtually not involved into dimerization, being intended solely for target recognition. The structural flexibility of this region is essential for recognition of diverse target proteins. At least 86% of multiple interactions of S100 proteins with binding partners are attributed to the S100 proteins predicted to be disordered. Overall, the intrinsic disorder is inherent to many S100 proteins and is vital for activity and functional diversity of the family