Cluster Of Residues Research Articles

Molecular mechanism of pH-dependent modulation of Sup35 phase separation by intrinsically disordered M domain.

In budding yeast, starvation stress can trigger a protective response where most cellular processes are downregulated. The transition to this fully reversible state is accompanied by cytoplasmic acidification and subsequent reorganization. Sup35, a translation termination factor with two intrinsically disordered regions (N and M domains), is known to phase separate upon cytoplasmic acidification. Previous work showed the pH dependence of Sup35's phase separation could be attributed to a particularly dense ionizable cluster of negatively-charged residues in the intrinsically disordered M domain, which is proposed to regulate the phase separation properties of the N domain. In this work, we use NMR spectroscopy to probe the pH sensitivity of the ionizable residues in the IDR regions and their interactions. Our aim is to determine the molecular mechanism by which the M domain regulates Sup35's phase separation.

Probing P(T/S)XP peptides for novel structural interactions with Tsg101 UEV.

To complete their lifecycle, enveloped viruses such as human immunodeficiency virus type-1 (HIV-1) recruit host machinery to facilitate budding and egress. For HIV-1, this involves an interaction between a PTAP motif in the HIV-1 Gag polyprotein and the ubiquitin E2 variant (UEV) domain of tumor susceptibility gene 101 (Tsg101). The latter is part of the native endosomal sorting complex required for transport (ESCRT) machinery, which functions in endosomal cargo sorting but is hijacked by HIV-1 for plasma membrane budding. The interaction between the PTAP signal of HIV-1 Gag and the UEV domain of Tsg101 is well characterized biochemically and structurally, with the PTAP motif binding into a groove in the UEV domain. The HIV-1 PTAP sequence emulates similar P(T/S)XP signals that drive host protein interactions involved with ESCRT, where some host proteins may contain several potential P(T/S)XP motifs. This suggested potential competitive or cooperative action on the UEV surface, and so we screened two additional P(T/S)XP motifs from the ESCRT-0 protein Hrs and several motifs identified in other viruses for interaction with the Tsg101 UEV domain using solution nuclear magnetic resonance. In the process, we identified an additional interaction mode for P(T/S)XP peptides with the Tsg101 UEV, involving both a charged surface and a cluster of aromatic residues, neither of which are implicated in the previously characterized PTAP interaction. We identified several binding determinants of this P(T/S)XP interaction using alanine mutant peptides and combined chemical shift perturbations with distance data from paramagnetic relaxation enhancement experiments using spin-labeled peptides to build a structural model of the interaction on the UEV surface. This additional P(T/S)XP interaction may reflect a novel viral strategy to recruit Tsg101 and by extension ESCRT for egress, or hijacking of a different endogenous role of Tsg101 altogether.

Connecting sequence features within the disordered C-terminal linker of B. subtilis FtsZ to functions and bacterial cell division.

Intrinsically disordered regions (IDRs) can function as autoregulators of folded enzymes to which they are tethered. One such example is the disordered C-terminal tail (CTT) of FtsZ, an essential GTPase in bacterial cell division. FtsZs feature a folded core and a CTT that encompasses a poorly conserved, disordered C-terminal linker (CTL) and a conserved 17-residues C-terminal peptide (CT17). Sites for GTPase activity of FtsZs are formed at the interface between GTP binding sites and T7 loops on cores of adjacent subunits within dimers. Here, we explore the molecular, evolutionary, and cellular bases for how autoregulatory functions of the CTT are realized in Bacillus subtilis FtsZ (Bs-FtsZ). Molecular simulations show statistically significant CTL-mediated contacts between the T7 loop and the CT17. Statistical coupling analysis of more than 1000 orthologs reveals clear covariation of the T7 loop and the CT17 with most of the core domain whereas the CTL is under independent selection. Furthermore, we also identify a conserved set of non-random sequence patterns within the CTLs, including linear clustering of polar and acidic residues, that modulate the interaction between the core and the CTT. To test how the non-random patterns of CTLs mediate CTT-core interactions and modulate FtsZ functionalities, we designed Bs-FtsZ variants by altering the patterning of oppositely charged residues within the CTL. Such alterations disrupt the core-CTT interactions, lead to anomalous assembly and inefficient GTP hydrolysis in vitro, and protein degradation, aberrant assembly, and disruption of cell division in vivo. Our findings suggest that viable CTLs in FtsZs are likely to be IDRs that encompass the non-random, functionally relevant sequence patterns that also preserve three-way covariation of the CT17, the T7 loop, and core domain.

Investigating the sequence properties that govern disorder and secretion of bacterial virulence proteins.

Many proteins contain disordered segments that play important roles in vivo. Autotransporter (AT) proteins are key virulence proteins from pathogenic Gram-negative bacteria. AT proteins have disordered properties that have been shown to be crucial for their efficient secretion to the bacterial cell surface. We have extensively studied pertactin, a virulence protein secreted by Bordetella pertussis, the bacterium that causes whooping cough. Like several other ATs, the mature pertactin virulence protein contains two segments with distinctly different folding properties. In isolation, the more stable C-terminal segment (PCt) is stably folded whereas the N-terminal segment (PNt) is disordered. Our previous studies indicate that folding of PCt is important for the efficient secretion of pertactin. Moreover, we recently showed that local clustering of hydrophobic residues leads to a significant collapse of PNt in vitro. Interestingly, we found that the extent to which PNt adopts a disordered, highly expanded conformational ensemble regulates the efficient secretion of pertactin through the bacterial outer membrane. Taken together, these observations suggest that PNt contains sequence properties important for secretion. Because disordered properties are important for AT secretion, understanding the connections between amino acid sequence features, disordered conformations, and AT secretion will improve our understanding of virulence protein secretion. The present research project aims to build upon our recent findings to develop a predictive understanding of the sequence factors that regulate disorder in pertactin and other proteins. We are using a combination of biophysical and biochemical approaches to characterize the sequence determinants of disorder and test their impact on AT secretion. We expect that insight into the regulation of disorder in pertactin will likely also apply to other members of the AT protein family, the largest family of secreted virulence proteins in Gram-negative bacterial pathogens.

A coarse-grained molecular dynamics investigation on spontaneous binding of Aβ1–40 fibrils with cholesterol-mixed DPPC bilayers

Alzheimer's disease is the most common form of dementia. Its aetiology is characterized by the misfolding and aggregation of amyloid-β (Aβ) peptides into β-sheet-rich Aβ oligomers/fibrils. Although multiple experimental studies have suggested that Aβ oligomers/fibrils interact with the cell membranes and perturb their structures and dynamics, the molecular mechanism of this interaction is still not fully understood. In the present work, we have performed a total of 120 μs-long simulations to investigate the interaction between trimeric or hexameric Aβ1–40 fibrils with either a 100% DPPC bilayer, a 70% DPPC-30% cholesterol bilayer or a 50% DPPC-50% cholesterol bilayer. Our simulation data capture the spontaneous binding of the aqueous Aβ1–40 fibrils with the membranes and show that the central hydrophobic amino acid cluster, the lysine residue adjacent to it and the C-terminal hydrophobic residues are all involved in the process. Moreover, our data show that while the Aβ1–40 fibril does not bind to the 100% DPPC bilayer, its binding affinity for the membrane increases with the amount of cholesterol. Overall, our data suggest that two clusters of hydrophobic residues and one lysine help Aβ1–40 fibrils establish stable interactions with a cholesterol-rich DPPC bilayer. These residues are likely to represent potential target regions for the design of inhibitors, thus opening new avenues in structure-based drug design against Aβ oligomer/fibril-membrane interaction.

KIR signaling is regulated by electrostatic interaction of its cytosolic tail with the plasma membrane despite being neutral polyampholyte

Many receptors signal upon phosphorylation of tyrosine-based motifs in their cytosolic tail, with intrinsic disorder as a common feature. Studies on CD3ζ and CD3ε tails, which are disordered and polybasic, suggested regulation of phosphorylation through accessibility of tyrosines, governed by electrostatic interactions with membrane anionic lipids. We noticed characteristics of intrinsic disorder and previously unappreciated features in tyrosine-based motif-bearing cytosolic tails of many, especially, inhibitory receptors. They are neutral or acidic polyampholytes, with acidic and basic residues linearly segregated. To explore roles of these electrostatic features, we studied inhibitory killer-cell immunoglobulin-like receptor (KIR). Its cytosolic tail is a disordered neutrally charged polyampholyte, wherein juxtamembrane and membrane distal stretches are basic, and the intervening stretch is acidic. Despite lacking net charge, it interacted electrostatically with the plasma membrane. The juxtamembrane stretch was crucial for overall binding, which sequestered tyrosines in the lipid bilayer and restrained their constitutive phosphorylation. Human leukocyte antigen-C ligand binding to KIR released its tail from the plasma membrane to initiate signaling. Tail release occurred independently of KIR polymerization, clustering, or tyrosine phosphorylation, but required acidic residues of the acidic stretch. Tail interaction with the plasma membrane dictated signaling strength of KIR. These results revealed an electrostatic protein-lipid interaction that is unusual in being governed by segregated clusters of acidic and basic residues in polyampholytic disordered region of protein. In contrast to previously known, segregated distribution of oppositely charged residues made both binding and unbinding modules inherent to receptor tail, which could make the interaction an independent signaling switch.

Mutational Insight into Allosteric Regulation of Kir Channel Activity.

Potassium (K+) channels are regulated in part by allosteric communication between the helical bundle crossing, or inner gate, and the selectivity filter, or outer gate. This network is triggered by gating stimuli. In concert, there is an allosteric network which is a conjugated set of interactions which correlate long-range structural rearrangements necessary for channel function. Inward-rectifier K+ (Kir) channels favor inward K+ conductance, are ligand-gated, and help establish resting membrane potentials. KirBac1.1 is a bacterial Kir (KirBac) channel homologous to human Kir (hKir) channels. Additionally, KirBac1.1 is gated by the anionic phospholipid ligand phosphatidylglycerol (PG). In this study, we use site-directed mutagenesis to investigate residues involved in the KirBac1.1 gating mechanism and allosteric network we previously proposed using detailed solid-state NMR (SSNMR) measurements. Using fluorescence-based K+ and sodium (Na+) flux assays, we identified channel mutants with impaired function that do not alter selectivity of the channel. In tandem, we performed coarse grain molecular dynamics simulations, observing changes in PG-KirBac1.1 interactions correlated with mutant channel activity and contacts between the two transmembrane helices and pore helix tied to this behavior. Lipid affinity is closely tied to the proximity of two tryptophan residues on neighboring subunits which lure anionic lipids to a cationic pocket formed by a cluster of arginine residues. Thus, these simulations establish a structural and functional basis for the role of each mutated site in the proposed allosteric network. The experimental and simulated data provide insight into key functional residues involved in gating and lipid allostery of K+ channels. Our findings also have direct implications on the physiology of hKir channels due to conservation of many of the residues identified in this work from KirBac1.1.

GIS-Based Cluster and Suitability Analysis of Crop Residues: A Case Study in Yangon Region, Myanmar

In the study of biomass assessment, geospatial modeling-based analysis becomes crucial for the sustainable management of agriculture. Currently, there is no integrated sustainability assessment of the geographic information system (GIS) cluster or suitability analysis for the feedstock of crop residues. In order to fill this research gap and support the strategy of bioenergy formulation with the circular economy concept in agriculture residues in Myanmar, this study aims to assess the energy generation potential and site locations of treatment facilities for crop residue, utilizing the integrated assessment of GIS cluster and suitability modeling. The cluster analysis identifies the rice straw as the highest feedstock of crop residues and township-based high/low clusters. In addition, the electricity generation potential is estimated at 279.14 MW for different clusters of rice straw. Moreover, the suitability analysis in the study uses the conceptual model of variables for constraints and factors with the analytical hierarchy process (AHP) technique to evaluate the weights. The suitability analysis found high suitability areas of 14,603 hectares for treatment facilities within the high/low cluster of feedstock for rice straw. The multicriteria and GIS integrated assessment model adopted in this research can support the decision-makers in developing spatial-based strategic planning for bioenergy promotion which will support sustainable farming practices in Myanmar. Additionally, the proposed model is adaptable in study areas with similar feedstock.

Non-specificity as the sticky problem in therapeutic antibody development.

Antibodies are highly potent therapeutic scaffolds with more than a hundreddifferent products approved on the market. Successful development of antibody-based drugs requires a trade-off between high target specificity and target binding affinity. In order to better understand this problem, we here review non-specific interactions and explore their fundamental physicochemical origins. We discuss the role of surface patches - clusters of surface-exposed amino acid residues with similar physicochemical properties - as inducers of non-specific interactions. These patches collectively drive interactions including dipole-dipole, π-stacking and hydrophobic interactions to complementary moieties. We elucidate links between these supramolecular assembly processes and macroscopic development issues, such as decreased physical stability and poor in vivo half-life. Finally, we highlight challenges and opportunities for optimizing protein binding specificity and minimizing non-specificity for future generations of therapeutics.

Structure and dynamic simulation-based interactions of benzenoids, pyrroles and organooxygen compounds for effective targeting of GPX4 in ischemic stroke

The discovery of a novel drug for ischemic stroke is plagued by expensive and unsuccessful outcomes. FDA-approved drugs could be a viable repurposing strategy for stroke therapy. Emerging evidence suggests the regulating role of Glutathione peroxidase (GPX4) in stroke and attracts as a potential target. To overcome limited therapeutic interventions, a drug repurposing in silico investigation of FDA-approved drugs is proposed for the GPX4 receptor in distinctive species (Homo sapiens and Mus musculus). The GPX4 UniProt wild type ids, that is, P36969 (Homo sapiens), P36970 (Rattus norvegicus) and O70325 (Mus musculus) are Swiss modelled, and resultant templates are 2OBI and 6HN3 for Homo sapiens, and 5L71 for Mus musculus with a sequence identity of ∼88%. Enrichment analysis reveals high sensitivity and ranked actives with ROC and AUC values of 0.59 and 0.61, respectively. Virtual screening at extra precision resulted hit Acarbosum, is similar between 2OBI and 6HN3, demonstrating a multiple-target specificity and Iopromide, targeting 2OBI. MD simulation at 100 ns following trajectory analysis provides RMSD (∼1.2–1.8Å), RMSF (∼1.6–2.7Å), Rgyr (∼15–15.6Å) depicting stabilisation of receptor–ligand complexes. Furthermore, average B-factor value of 2OBI, 6HN3 and 5L71 is 25Å, 24Å and 60Å with a defined resolution of 1.55Å, 1.01Å and 1.80Å, respectively, depicting the thermodynamic stability of the protein structures. The dynamic cross-correlation and principal component analysis of residual fluctuations reveal more positive correlation, high atomic displacements and greater residual clustering of residues from atomic coordinates. Therefore, Acarbosum, an FDA-approved drug, could act as a potential repurposing drug with a multi-target approach translating from preclinical to clinical stages. Communicated by Ramaswamy H. Sarma

Evolution of an Iron-Detoxifying Protein: Eukaryotic and Rickettsia Frataxins Contain a Conserved Site Which Is Not Present in Their Bacterial Homologues.

Friedreich's ataxia is a neurodegenerative disease caused by mutations in the frataxin gene. Frataxin homologues, including bacterial CyaY proteins, can be found in most species and play a fundamental role in mitochondrial iron homeostasis, either promoting iron assembly into metaloproteins or contributing to iron detoxification. While several lines of evidence suggest that eukaryotic frataxins are more effective than bacterial ones in iron detoxification, the residues involved in this gain of function are unknown. In this work, we analyze conservation of amino acid sequence and protein structure among frataxins and CyaY proteins to identify four highly conserved residue clusters and group them into potential functional clusters. Clusters 1, 2, and 4 are present in eukaryotic frataxins and bacterial CyaY proteins. Cluster 3, containing two serines, a tyrosine, and a glutamate, is only present in eukaryotic frataxins and on CyaY proteins from the Rickettsia genus. Residues from cluster 3 are blocking a small cavity of about 40 Å present in E. coli's CyaY. The function of this cluster is unknown, but we hypothesize that its tyrosine may contribute to prevent formation of reactive oxygen species during iron detoxification. This cluster provides an example of gain of function during evolution in a protein involved in iron homeostasis, as our results suggests that Cluster 3 was present in the endosymbiont ancestor of mitochondria and was conserved in eukaryotic frataxins.

Characterization of the Escherichia coli pyridoxal 5'-phosphate homeostasis protein (YggS): Role of lysine residues in PLP binding and protein stability.

The pyridoxal 5′‐phosphate (PLP) homeostasis protein (PLPHP) is a ubiquitous member of the COG0325 family with apparently no catalytic activity. Although the actual cellular role of this protein is unknown, it has been observed that mutations of the PLPHP encoding gene affect the activity of PLP‐dependent enzymes, B6 vitamers and amino acid levels. Here we report a detailed characterization of the Escherichia coli ortholog of PLPHP (YggS) with respect to its PLP binding and transfer properties, stability, and structure. YggS binds PLP very tightly and is able to slowly transfer it to a model PLP‐dependent enzyme, serine hydroxymethyltransferase. PLP binding to YggS elicits a conformational/flexibility change in the protein structure that is detectable in solution but not in crystals. We serendipitously discovered that the K36A variant of YggS, affecting the lysine residue that binds PLP at the active site, is able to bind PLP covalently. This observation led us to recognize that a number of lysine residues, located at the entrance of the active site, can replace Lys36 in its PLP binding role. These lysines form a cluster of charged residues that affect protein stability and conformation, playing an important role in PLP binding and possibly in YggS function.

Host protein kinases required for SARS-CoV-2 nucleocapsid phosphorylation and viral replication.

Multiple coronaviruses have emerged independently in the past 20 years that cause lethal human diseases. Although vaccine development targeting these viruses has been accelerated substantially, there remain patients requiring treatment who cannot be vaccinated or who experience breakthrough infections. Understanding the common host factors necessary for the life cycles of coronaviruses may reveal conserved therapeutic targets. Here, we used the known substrate specificities of mammalian protein kinases to deconvolute the sequence of phosphorylation events mediated by three host protein kinase families (SRPK, GSK-3, and CK1) that coordinately phosphorylate a cluster of serine and threonine residues in the viral N protein, which is required for viral replication. We also showed that loss or inhibition of SRPK1/2, which we propose initiates the N protein phosphorylation cascade, compromised the viral replication cycle. Because these phosphorylation sites are highly conserved across coronaviruses, inhibitors of these protein kinases not only may have therapeutic potential against COVID-19 but also may be broadly useful against coronavirus-mediated diseases.

Does Tyrosine Protect S. coelicolor Laccase from Oxidative Degradation or Act as an Extended Catalytic Site?

We have investigated the roles of tyrosine (Tyr) and tryptophan (Trp) residues in the four-electron reduction of oxygen catalyzed by Streptomyces coelicolor laccase (SLAC). During normal enzymatic turnover in laccases, reducing equivalents are delivered to a type 1 Cu center (CuT1) and then are transferred over 13 Å to a trinuclear Cu site (TNC: (CuT3)2CuT2) where O2 reduction occurs. The TNC in SLAC is surrounded by a large cluster of Tyr and Trp residues that can provide reducing equivalents when the normal flow of electrons is disrupted. Prior studies by Canters and co-workers [J. Am. Chem. Soc. 2009, 131 (33), 11680-11682] have shown that when O2 reacts with a reduced SLAC variant lacking the CuT1 center, a Tyr108• radical near the TNC forms rapidly. We have found that the Tyr108• radical is reduced 10 times faster than CuT12+ by excess ascorbate, possibly because of radical transfer along Tyr/Trp chains.

A Cluster Sequencing Strategy To Determine the Consensus Affinity Domains in Heparin for Its Binding to Specific Proteins.

Glycosaminoglycans (GAGs) have high negative charge and are biologically and pharmaceutically important because their high charge promotes a strong interaction with many proteins. Due to the inherent heterogeneity of GAGs, multiple oligosaccharides, containing certain common domains, often can interact with clusters of basic amino acid residues on a target protein. The specificity of many GAG-protein interactions remains undiscovered since there is insufficient structural information on the interacting GAGs. Herein, we establish a cluster sequencing strategy to simultaneously deduce all major sequences of the affinity GAG oligosaccharides, leading to a definition of the consensus sequence they share that corresponds to the specific binding domain for the target protein. As a proof of concept, antithrombin III-binding oligosaccharides were examined, resulting in a heptasaccharide domain containing the well-established anticoagulant pentasaccharide sequence. Repeating this approach, a new pentasaccharide domain was discovered corresponding to the heparin motif responsible for binding interferon-γ (IFNγ). Our strategy is fundamentally important for the discovery of saccharide sequences needed in the development of novel GAG-based therapeutics.

Molecular Identification and Pathogenicity of Novel Duck-Origin Goose Parvovirus Isolated from Beak Atrophy and Dwarfism Syndrome of Waterfowls in the North of Vietnam.

The aim of this study is to identify and characterize virus isolates (which are named for Bacgiang Agriculture and Forestry University [BAFU]) from diseased Cherry Valley duck and mule duck flocks and investigate the damage caused by a novel parvovirus-related virus (DuPV) to tissues and organs, including the brain, cerebellum, kidney, liver, lung, spleen, and spinal cord. The results of phylogenetic analysis show that DuPV-BAFU evolved from a goose lineage and duck parvoviruses rather than from Muscovy duck parvoviruses. In the genetic lineages, DuPVs were identified from the DuPV samples analyzed, and DuPV-BAFU was found to be closely clustered with two known goose origin parvoviruses (GPVa2006 and GPV1995) and a duck GPVs. Finally, structural modeling revealed that DuPV-BAFU and the closely related viruses GPVa2006 and GPV1995 possessed identical clusters of receptor-interacting amino acid residues in the VP3 protein, a major determinant of viral receptor binding and host specificity. Significantly, these three viruses differed from DuPVs, Muscovy duck parvoviruses, and other goose parvoviruses at these positions. These results also demonstrated that DuPV-BAFU represents a new variant of goose-origin parvovirus that currently circulates in ducklings and causes beak atrophy and dwarfism syndrome, as noted in the previous reports in Europe, Taiwan, and China. This new finding highlights the need for future surveillance of DuPV-BAFU in waterfowl in order to gain a better understanding of both the evolution and the biology of this emerging parvovirus in waterfowl.

Ab initio modelling of an essential mammalian protein: Transcription Termination Factor 1 (TTF1)

Transcription Termination Factor 1 (TTF1) is an essential mammalian protein that regulates transcription, replication fork arrest, DNA damage repair, chromatin remodelling etc. TTF1 interacts with numerous cellular proteins to regulate various cellular phenomena which play a crucial role in maintaining normal cellular physiology, and dysregulation of this protein has been reported to induce oncogenic transformation of the cells. However, despite its key role in many cellular processes, the complete structure of human TTF1 has not been elucidated to date, neither experimentally nor computationally. Therefore, understanding the structure of human TTF1 is crucial for studying its functions and interactions with other cellular factors. The aim of this study was to construct the complete structure of human TTF1 protein, using molecular modelling approaches. Owing to the lack of suitable homologues in the Protein Data Bank (PDB), the complete structure of human TTF1 was constructed by ab initio modelling. The structural stability was determined with molecular dynamics (MD) simulations in explicit solvent, and trajectory analyses. The frequently occurring conformation of human TTF1 was selected by trajectory clustering, and the central residues of this conformation were determined by centrality analyses of the Residue Interaction Network (RIN) of TTF1. Two residue clusters, one in the oligomerization domain and other in the C-terminal domain, were found to be central to the structural stability of human TTF1. To the best of our knowledge, this study is the first to report the complete structure of this essential mammalian protein, and the results obtained herein will provide structural insights for future research including that in cancer biology and related studies. Communicated by Ramaswamy H. Sarma

Critical structural elements for the antigenicity of wheat allergen LTP1 (Tri a 14) revealed by site-directed mutagenesis

Lipid transfer proteins (LTPs) were identified as allergens in a large variety of pollens and foods, including cereals. LTPs belong to the prolamin superfamily and display an α-helical fold, with a bundle of four α-helices held together by four disulfide bonds. Wheat LTP1 is involved in allergic reactions to food. To identify critical structural elements of antibody binding to wheat LTP1, we used site-directed mutagenesis on wheat recombinant LTP1 to target: (i) sequence conservation and/or structure flexibility or (ii) each disulfide bond. We evaluated the modifications induced by these mutations on LTP1 secondary structure by synchrotron radiation circular dichroism and on its antigenicity with patient’s sera and with mouse monoclonal antibodies. Disruption of the C28–C73 disulfide bond significantly affected IgE-binding and caused protein denaturation, while removing C13–C27 bond decreased LTP1 antigenicity and slightly modified LTP1 overall folding. In addition, we showed Lys72 to be a key residue; the K72A mutation did not affect global folding but modified the local 3D structure of LTP1 and strongly reduced IgE-binding. This work revealed a cluster of residues (C13, C27, C28, C73 and K72), four of which embedded in disulfide bonds, which play a critical role in LTP1 antigenicity.

Mechanisms of isoform-specific residue influence on GTP-bound HRas, KRas, and NRas

HRas, KRas, and NRas are GTPases with a common set of effectors that control many cell-signaling pathways, including proliferation through Raf kinase. Their G-domains are nearly identical in sequence, with a few isoform-specific residues that have an effect on dynamics and biochemical properties. Here, we use accelerated molecular dynamics (aMD) simulations consistent with solution x-ray scattering experiments to elucidate mechanisms through which isoform-specific residues associated with each Ras isoform affects functionally important regions connected to the active site. HRas-specific residues cluster in loop 8 to stabilize the nucleotide-binding pocket, while NRas-specific residues on helix 3 directly affect the conformations of switch I and switch II. KRas, the most globally flexible of the isoforms, shows greatest fluctuations in the switch regions enhanced by a KRas-specific residue in loop 7 and a highly dynamic loop 8 region. The analysis of isoform-specific residue effects on Ras proteins is supported by NMR experiments and is consistent with previously published biochemical data.

Describing auxin solid state intermolecular interactions using contact descriptors, shape property and molecular fingerprint: comparison of pure auxin crystal and auxin-TIR1 co-crystal

This work reports for the first time, the analysis of intermolecular interactions in crystal structures of auxin (Indole-3-acetic acid) crystallized as pure sample (Aux-A) or co-crystallized with transport inhibitor response 1 (Aux-B). Using crystal packing of pure auxin and a cluster of residues in a radius of 6 Å around this ligand in the transport inhibitor response 1 binding domain, various properties were calculated and mapped on the Hirshfeld surface (HS). The HSs of the two molecules are characterized by close parameters of volume, area, globularity, and asphericity revealing the efficiency of the considered cluster. The HS mapped over descriptors like de, di and dnorm showed red spots corresponding to hydrogen bonds contacts. In addition to the shape index and curvedness descriptors, the results highlight weak interactions stabilizing the auxin structures. The analyses of electrostatic potential, electron density, and deformation density maps confirm the slightly change in the electron donor and acceptor groups localization. Furthermore, the molecular fingerprint analyses revealed a notable discrepancy in the shape and percentage value of the various contacts. Decomposition of the fingerprint shows that the contributions of important contacts (H···H, H···O, and O···O) are higher in Aux-B than in Aux-A. Finally, the quantitative approach by the determination of the molecular interaction energies of the two structures in their respective crystallographic environment revealed that Aux-A is slightly more stabilized than Aux-B.