Individual Amino Acid Residues Research Articles

Editor's Highlight: Sequence Alignment to Predict Across Species Susceptibility (SeqAPASS): A Web-Based Tool for Addressing the Challenges of Cross-Species Extrapolation of Chemical Toxicity.

Conservation of a molecular target across species can be used as a line-of-evidence to predict the likelihood of chemical susceptibility. The web-based Sequence Alignment to Predict Across Species Susceptibility (SeqAPASS; https://seqapass.epa.gov/seqapass/) application was developed to simplify, streamline, and quantitatively assess protein sequence/structural similarity across taxonomic groups as a means to predict relative intrinsic susceptibility. The intent of the tool is to allow for evaluation of any potential protein target while remaining amenable to variable degrees of protein characterization, in the context of available information about the chemical/protein interaction and the molecular target itself. To accommodate this flexibility in the analysis, 3 levels of evaluation were developed. The first level of the SeqAPASS analysis compares primary amino acid sequences to a query sequence, calculating a metric for sequence similarity (including detection of orthologs); the second level evaluates sequence similarity within selected functional domains (eg, ligand-binding domain); and the third level of analysis compares individual amino acid residue positions of importance for protein conformation and/or interaction with the chemical upon binding. Each level of the SeqAPASS analysis provides additional evidence to apply toward rapid, screening-level assessments of probable cross species susceptibility. Such analyses can support prioritization of chemicals for further evaluation, selection of appropriate species for testing, extrapolation of empirical toxicity data, and/or assessment of the cross-species relevance of adverse outcome pathways. Three case studies are described herein to demonstrate application of the SeqAPASS tool: the first 2 focused on predictions of pollinator susceptibility to molt-accelerating compounds and neonicotinoid insecticides, and the third on evaluation of cross-species susceptibility to strobilurin fungicides. These analyses illustrate challenges in species extrapolation and demonstrate the broad utility of SeqAPASS for risk-based decision making and research.

A Modified Reverse One-Hybrid Screen Identifies Transcriptional Activation Domains in PHYTOCHROME-INTERACTING FACTOR 3.

Transcriptional activation domains (TADs) are difficult to predict and identify, since they are not conserved and have little consensus. Here, we describe a yeast-based screening method that is able to identify individual amino acid residues involved in transcriptional activation in a high throughput manner. A plant transcriptional activator, PIF3 (phytochrome interacting factor 3), was fused to the yeast GAL4-DNA-binding Domain (BD), driving expression of the URA3 (Orotidine 5′-phosphate decarboxylase) reporter, and used for negative selection on 5-fluroorotic acid (5FOA). Randomly mutagenized variants of PIF3 were then selected for a loss or reduction in transcriptional activation activity by survival on FOA. In the process, we developed a strategy to eliminate false positives from negative selection that can be used for both reverse-1- and 2-hybrid screens. With this method we were able to identify two distinct regions in PIF3 with transcriptional activation activity, both of which are functionally conserved in PIF1, PIF4, and PIF5. Both are collectively necessary for full PIF3 transcriptional activity, but neither is sufficient to induce transcription autonomously. We also found that the TAD appear to overlap physically with other PIF3 functions, such as phyB binding activity and consequent phosphorylation. Our protocol should provide a valuable tool for identifying, analyzing and characterizing novel TADs in eukaryotic transcription factors, and thus potentially contribute to the unraveling of the mechanism underlying transcriptional activation.

Interplay between Intrinsic Conformational Propensities and Intermolecular Interactions in the Self-Assembly of Short Surfactant-like Peptides Composed of Leucine/Isoleucine.

To study how the conformational propensities of individual amino acid residues, primary structures (i.e., adjacent residues and molecular lengths), and intermolecular interactions of peptides affect their self-assembly properties, we report the use of replica exchange molecular dynamics (REMD) to investigate the monomers, dimers, and trimers of a series of short surfactant-like peptides (I3K, L3K, L4K, and L5K). For four-residue peptides X3K (I3K and L3K), the results show that their different aggregation behaviors arise from the different intrinsic conformational propensities of isoleucine and leucine. For LmK peptides (L3K, L4K, and L5K), the molecular length is found to dictate their aggregation via primarily modulating intermolecular interactions. Increasing the number of hydrophobic amino acid residues of LmK peptides enhances their intermolecular H-bonding and promotes the formation of β-strands in dimer and trimer aggregates, overwhelming the intrinsic preference of Leu for helical structures. Thus, the interplay between the conformational propensities of individual amino acid residues for secondary structures and molecular interactions determines the self-assembly properties of the peptides, and the competition between intramolecular and intermolecular H-bonding interactions determines the probability of β-sheet alignment of peptide molecules. These results are validated by comparing simulated and experimental CD spectra of the peptides. This study will aid the design of short peptide amphiphiles and improve the mechanistic understanding of their self-assembly behavior.

Search for conserved amino acid residues of the α-crystallin proteins of vertebrates.

[Formula: see text]-crystallin is the major eye lens protein and a member of the small heat-shock protein (sHsp) family. [Formula: see text]-crystallins have been shown to support lens clarity by preventing the aggregation of lens proteins. We performed the bioinformatics analysis of [Formula: see text]-crystallin sequences from vertebrates to find conserved amino acid residues as the three-dimensional (3D) structure of [Formula: see text]-crystallin is not identified yet. We are the first who demonstrated that the N-terminal region is conservative along with the central domain for vertebrate organisms. We have found that there is correlation between the conserved and structured regions. Moreover, amyloidogenic regions also correspond to the structured regions. We analyzed the amino acid composition of [Formula: see text]-crystallin A and B chains. Analyzing the occurrence of each individual amino acid residue, we have found that such amino acid residues as leucine, serine, lysine, proline, phenylalanine, histidine, isoleucine, glutamic acid, and valine change their content simultaneously in A and B chains in different classes of vertebrates. Aromatic amino acids occur more often in [Formula: see text]-crystallins from vertebrates than on the average in proteins among 17 animal proteomes. We obtained that the identity between A and B chains in the mammalian group is 0.35, which is lower than the published 0.60.

‘Lollipop’-shaped helical structure of a hybrid antimicrobial peptide of temporin B-lipopolysaccharide binding motif and mapping cationic residues in antibacterial activity

BackgroundTemporins are attractive templates for the development of antibiotics. However, many temporins are inactive against Gram-negative bacteria. Previously, we demonstrated conjugation of a lipopolysaccharide binding motif peptide to temporins yielded hybrid non-haemolytic AMPs that killed several Gram-negative bacteria. MethodsWe carried out a systematic Ala replacement of individual cationic and polar amino acid residues of LG21, a hybrid AMP consisted of temporin B (TB) and LPS binding motif. These Ala containing analogs of LG21 were examined for antibacterial activity, cell membrane permeabilization and liposome leakage assays using optical spectroscopic methods. Atomic resolution structure of LG21 was determined in zwitterionic dodecyl phosphocholine (DPC) micelles by NMR spectroscopy. ResultsCationic residues in the LPS binding motif of LG21 were critical for bactericidal and membrane permeabilization. Detergent bound structure of LG21 revealed helical conformation containing extensive sidechain/sidechain packing including cation/π interactions in the LPS binding motif. The helical structure of LG21 resembled a ‘lollipop’ like shape that was sustained by a compacted bulky aromatic/cationic head with a comparatively thinner ‘stick’ at the N-terminal region. The ‘head’ of the structure could be localized into micelle-water interfacial region whereas the ‘stick’ region may be inserted into the hydrophobic core of micelle. ConclusionsThe LPS binding motif of LG21 played dominant roles in broad spectrum activity and the 3-D structure provided plausible mechanistic insights for permeabilization of bacterial membrane. General significanceHybrid AMPs containing LPS binding motif could be useful for the structure based development of broad spectrum antibiotics.

Insight into determinants of substrate binding and transport in a multidrug efflux protein.

Multidrug resistance arising from the activity of integral membrane transporter proteins presents a global public health threat. In bacteria such as Escherichia coli, transporter proteins belonging to the major facilitator superfamily make a considerable contribution to multidrug resistance by catalysing efflux of myriad structurally and chemically different antimicrobial compounds. Despite their clinical relevance, questions pertaining to mechanistic details of how these promiscuous proteins function remain outstanding, and the role(s) played by individual amino acid residues in recognition, binding and subsequent transport of different antimicrobial substrates by multidrug efflux members of the major facilitator superfamily requires illumination. Using in silico homology modelling, molecular docking and mutagenesis studies in combination with substrate binding and transport assays, we identified several amino acid residues that play important roles in antimicrobial substrate recognition, binding and transport by Escherichia coli MdtM, a representative multidrug efflux protein of the major facilitator superfamily. Furthermore, our studies suggested that ‘aromatic clamps’ formed by tyrosine and phenylalanine residues located within the substrate binding pocket of MdtM may be important for antimicrobial substrate recognition and transport by the protein. Such ‘clamps’ may be a structurally and functionally important feature of all major facilitator multidrug efflux proteins.

Deformability of Microtubules: An Atomistic Computational Study

Thanks to their material properties, microtubules can play complex variety of biological functions. Experimental studies have shown that mechanical characteristics of microtubules are length-dependent and anisotropic, however, the origin of this feature has not been traced down to the level of tubulin sequence yet. Here we use high-resolution elastic network model to show local deformations patterns in microtubule structure up to the level of individual amino acid residues. The mechanical strain within the molecular structure of a microtubule is, according to our results, localized to interdimer contacts with energetic preference of deformation in longitudinal contacts. These findings are in agreement with reported mechanical anisotropy of microtubules, i.e. higher Young's modulus in axial direction compared to radial direction. Our results contribute to understanding the origin of deformability of microtubules on the molecular level, which is important for prospective targeting of microtubules in medical therapeutic strategies.

Ion Mobility Spectrometry-Hydrogen Deuterium Exchange Mass Spectrometry of Anions: Part 2. Assessing Charge Site Location and Isotope Scrambling

Ion mobility spectrometry (IMS) coupled with gas-phase hydrogen deuterium exchange (HDX)-mass spectrometry (MS) and molecular dynamic simulations (MDS) has been used for structural investigation of anions produced by electrospraying a sample containing a synthetic peptide having the sequence KKDDDDDIIKIIK. In these experiments the potential of the analytical method for locating charge sites on ions as well as for utilizing collision-induced dissociation (CID) to reveal the degree of deuterium uptake within specific amino acid residues has been assessed. For diffuse (i.e., more elongated) [M - 2H](2-) ions, decreased deuterium content along with MDS data suggest that the D4 and D6 residues are charge sites, whereas for the more diffuse [M - 3H](3-) ions, the data suggest that the D4, D7, and the C-terminus are deprotonated. Fragmentation of mobility-selected, diffuse [M - 2H](2-) ions to determine deuterium uptake at individual amino acid residues reveals a degree of deuterium retention at incorporation sites. Although the diffuse [M - 3H](3-) ions may show more HD scrambling, it is not possible to clearly distinguish HD scrambling from the expected deuterium uptake based on a hydrogen accessibility model. The capability of the IMS-HDX-MS/MS approach to provide relevant details about ion structure is discussed. Additionally, the ability to extend the approach for locating protonation sites on positively-charged ions is presented.

Intra- and Intersubunit Dynamic Binding in Kv4.2 Channel Closed-State Inactivation

We studied the kinetics and structural determinants of closed-state inactivation (CSI) in Kv4.2 channels, considering a multistep process and the possibility that both intra- and intersubunit dynamic binding (i.e., loss and restoration of physical contact) may occur between the S4-S5 linker, including the initial S5 segment (S4S5), and the S6 gate. We expressed Kv4.2 channels in Xenopus oocytes and measured the onset of low-voltage inactivation under two-electrode voltage clamp. Indicative of a transitory state, the onset kinetics were best described by a double-exponential function. To examine the involvement of individual S4S5 and S6 amino acid residues in dynamic binding, we studied S4S5 and S6 single alanine mutants and corresponding double mutants. Both transitory and steady-state inactivation were modified by these mutations, and we quantified the mutational effects based on apparent affinities for the respective inactivated states. Double-mutant cycle analyses revealed strong functional coupling of the S6 residues V404 and I412 to all tested S4S5 residues. To examine whether dynamic S4S5/S6 binding occurs within individual α-subunits or between neighboring α-subunits, we performed a double-mutant cycle analysis with Kv4.2 tandem-dimer constructs. The constructs carried either an S4S5/S6 double mutation in the first α-subunit and no mutation in the second (concatenated) α-subunit or an S4S5 point mutation in the first α-subunit and an S6 point mutation in the second α-subunit. Our results support the notion that CSI in Kv4.2 channels is a multistep process that involves dynamic binding both within individual α-subunits and between neighboring α-subunits.

Influence of single amino acid substitutions in the hemagglutinin on the antigenic and receptor-binding properties of influenza virus B/Florida/04/2006 of Yamagata-like evolutionary lineage

ABSTRACT Influenza A and B viruses use sialylated oligosaccharide chains expressed on the surface of a host cell as the cell entry receptors. The type of the bond between sialic acid (SA) and the neighboring galactose residue (Gal) is one of the main characteristics that define the type of receptor. Influenza viruses recognize SAα2-3Gal- or SAα2-6Gal-structures on the surface of the cells. Influenza A viruses of avian origin bind α2-3-sialylated glycans, while the human strains bind preferentially α2-6-sialylated ones. However, the receptor-binding specificity of influenza B viruses has not been characterized sufficiently so far. In this study, we selected the escape mutants of influenza B/Florida/04/2006 strain (Yamagata-like lineage) using monoclonal antibodies (mAb) to hemagglutinin (HA). The analysis of the amino acid sequences of mAb-induced escape mutants revealed the single amino acid substitutions 40Tyr→His, 85His→Tyr, 202Asn→Lys and 242Ser→Arg in 10F4-, 8Н11-, 8Н3- and 9A3-induced HA variants, correspondingly. It was shown that the single amino acid substitutions 202Asn→Lys and 242Ser→Arg alter the receptor-binding specificity of the influenza B virus. These findings are important for the understanding of the influence of individual amino acid residues in HA on the receptor-binding properties of influenza B Yamagata-like lineage viruses and allow us to predict the possible ways of their evolution.

Genetic mosaics and time-lapse imaging identify functions of histone H3.3 residues in mouse oocytes and embryos.

During development from oocyte to embryo, genetic programs in mouse germ cells are reshaped by chromatin remodeling to orchestrate the onset of development. Epigenetic modifications of specific amino acid residues of core histones and their isoforms can dramatically alter activation and suppression of gene expression. H3.3 is a histone H3 variant that plays essential roles in mouse oocytes and early embryos, but the functional role of individual amino acid residues has been unclear because of technical hurdles. Here, we describe two strategies that successfully investigated the functions of three individual H3.3 residues in oogenesis, cleavage-stage embryogenesis and early development. We first generated genetic mosaic ovaries and blastocysts with stochastic expression of wild-type or mutant H3.3 alleles and showed dominant negative effects of H3.3R26 and H3.3K27 in modulating oogenesis and partitioning cells to the inner cell mass of the early embryo. Time-lapse imaging assays also revealed the essential roles of H3.3K56 in efficient H2B incorporation and paternal pronuclei formation. Application of these strategies can be extended to investigate roles of additional H3.3 residues and has implications for use in other developmental systems.

Влияние единичных аминокислотных замен в гемагглютинине вируса гриппа В/Флорида/04/2006 ямагатской эволюционной линии на антигенные и рецепторсвязывающие свойства

Известно, что рецептором для проникновения в клетку хозяина для вирусов гриппа A и В служат углеводные цепи, терминированные остатками нейраминовой кислоты. Тип связи между сиаловой кислотой (sialic acid, SA) и соседним остатком галактозы (Gal) является одной из главных характеристик, определяющих тип рецептора. Вирусы гриппа узнают на поверхности клетки SAα2-3Gal-или SAα2-6Gal-структуры. Птичьи изоляты вирусов гриппа A связываются с SAα2-3сиалированными цепями, тогда как вирусы гриппа А человека – с SAα2-6Gal. Рецепторсвязывающая специфичность вирусов гриппа B изучена мало, однако известно, что вирусы разновидности Ямагата преимущественно узнают олигосахариды, терминированные SAα2-6Gal, тогда как вирусы генетической линии Виктория узнают оба типа сиалозидов. Используя четыре вируснейтрализующих моноклональных антитела (монАТ): 10F4, 8Н11, 8Н3 и 9А3, – мы получили эскейп-мутанты вируса гриппа В/Флорида/04/2006 ямагатской линии. При анализе последовательности гемагглютинина (HA) выявлено, что НА эскейп-мутантов, индуцированных монАТ 10F4, 8Н11, 8Н3 и 9А3, несут следующие единичные аминокислотные замены: 40Tyr→His, 85His→Tyr, 202Asn→Lys и 242Ser→Arg соответственно. Показано, что замены 202Asn→Lys и 242Ser→Arg приводят к изменению рецепторсвязывающей специфичности вируса. Полученные данные имеют важное значение для понимания роли отдельных аминокислотных остатков HA в формировании рецепторсвязывающих свойств вирусов грип-па В ямагатской эволюционной линии, что позволяет прогнозировать возможные пути эволюции этих вирусов.

Molecular evolution of ion channels: Amino acid sequences and 3D structures

An integral part of modern evolutionary biology is comparative analysis of structure and function of macromolecules such as proteins. The first and critical step to understand evolution of homologous proteins is their amino acid sequence alignment. However, standard algorithms fop not provide unambiguous sequence alignments for proteins of poor homology. More reliable results can be obtained by comparing experimental 3D structures obtained at atomic resolution, for instance, with the aid of X-ray structural analysis. If such structures are lacking, homology modeling is used, which may take into account indirect experimental data on functional roles of individual amino-acid residues. An important problem is that the sequence alignment, which reflects genetic modifications, does not necessarily correspond to the functional homology. The latter depends on three-dimensional structures which are critical for natural selection. Since alignment techniques relying only on the analysis of primary structures carry no information on the functional properties of proteins, including 3D structures into consideration is very important. Here we consider several examples involving ion channels and demonstrate that alignment of their three-dimensional structures can significantly improve sequence alignments obtained by traditional methods.

Reformatting Rituximab into Human IgG2 and IgG4 Isotypes Dramatically Improves Apoptosis Induction In Vitro.

The direct induction of cell death, or apoptosis, in target cells is one of the effector mechanisms for the anti CD20 antibody Rituximab. Here we provide evidence that Rituximab’s apoptotic ability is linked to the antibody IgG isotype. Reformatting Rituximab from the standard human IgG1 heavy chain into IgG2 or IgG4 boosted in vitro apoptosis induction in the Burkitt’s lymphoma B cell line Ramos five and four-fold respectively. The determinants for this behavior are located in the hinge region and CH1 domain of the heavy chain. By transplanting individual IgG2 or IgG4 specific amino acid residues onto otherwise IgG1 like backbones, thereby creating hybrid antibodies, the same enhancement of apoptosis induction could be achieved. The cysteines at position 131 of the CH1 domain and 219 in the hinge region, involved in IgG2 and IgG4 disulfide formation, were found to be of particular structural importance. Our data indicates that the hybrid antibodies possess a different CD20 binding mode than standard Rituximab, which appears to be key in enhancing apoptotic ability. The presented work opens up an interesting engineering route for enhancing the direct cytotoxic ability of therapeutic antibodies.

Gas-Phase Hydrogen-Deuterium Exchange Labeling of Select Peptide Ion Conformer Types: a Per-Residue Kinetics Analysis.

The per-residue, gas-phase hydrogen deuterium exchange (HDX) kinetics for individual amino acid residues on selected ion conformer types of the model peptide KKDDDDDIIKIIK have been examined using ion mobility spectrometry (IMS) and HDX-tandem mass spectrometry (MS/MS) techniques. The [M + 4H](4+) ions exhibit two major conformer types with collision cross sections of 418 Å(2) and 446 Å(2); the [M + 3H](3+) ions also yield two different conformer types having collision cross sections of 340 Å(2) and 367 Å(2). Kinetics plots of HDX for individual amino acid residues reveal fast- and slow-exchanging hydrogens. The contributions of each amino acid residue to the overall conformer type rate constant have been estimated. For this peptide, N- and C-terminal K residues exhibit the greatest contributions for all ion conformer types. Interior D and I residues show decreased contributions. Several charge state trends are observed. On average, the D residues of the [M + 3H](3+) ions show faster HDX rate contributions compared with [M + 4H](4+) ions. In contrast the interior I8 and I9 residues show increased accessibility to exchange for the more elongated [M + 4H](4+) ion conformer type. The contribution of each residue to the overall uptake rate showed a good correlation with a residue hydrogen accessibility score model calculated using a distance from charge site and initial incorporation site for nominal structures obtained from molecular dynamic simulations (MDS).

The a subunit of the A1AO ATP synthase of Methanosarcina mazei Gö1 contains two conserved arginine residues that are crucial for ATP synthesis

Like the evolutionary related F1FO ATP synthases and V1VO ATPases, the A1AO ATP synthases from archaea are multisubunit, membrane-bound transport machines that couple ion flow to the synthesis of ATP. Although the subunit composition is known for at least two species, nothing is known so far with respect to the function of individual subunits or amino acid residues. To pave the road for a functional analysis of A1AO ATP synthases, we have cloned the entire operon from Methanosarcina mazei into an expression vector and produced the enzyme in Escherichia coli. Inverted membrane vesicles of the recombinants catalyzed ATP synthesis driven by NADH oxidation as well as artificial driving forces. Δμ˜H+ as well as ΔpH were used as driving forces which is consistent with the inhibition of NADH-driven ATP synthesis by protonophores. Exchange of the conserved glutamate in subunit c led to a complete loss of ATP synthesis, proving that this residue is essential for H+ translocation. Exchange of two conserved arginine residues in subunit a has different effects on ATP synthesis. The role of these residues in ion translocation is discussed.

Assessing backbone solvation effects in the conformational propensities of amino acid residues in unfolded peptides.

Conformational ensembles of individual amino acid residues within model GxG peptides (x representing different amino acid residues) are dominated by a mixture of polyproline II (pPII) and β-strand like conformations. We recently discovered rather substantial differences between the enthalpic and entropic contributions to this equilibrium for different amino acid residues. Isoleucine and valine exceed all other amino acid residues in terms of their rather large enthalpic stabilization and entropic destabilization of polyproline II. In order to shed light on these underlying physical mechanisms, we performed high-level DFT calculations to explore the energetics of four representative GxG peptides where x = alanine (A), leucine (L), valine (V), and isoleucine (I) in explicit water (10 H2O molecules with a polarizable continuum water model) and in vacuo. We found that the large energetic contributions to the stabilization of pPII result, to a major extent, from peptide-water, water-water interactions, and changes of the solvent self-energy. Differences between the peptide-solvent interaction energies of hydration in pPII and β-strand peptides are particularly important for the pPII ⇌ β equilibria of the more aliphatic peptides GIG and GLG. Furthermore, we performed a vibrational analysis of the four peptides in both conformations and discovered a rather substantial mixing between water motions and peptide vibrations below 700 cm(-1). We found that the respective vibrational entropies are substantially different for the considered conformations, and their contributions to the Gibbs/Helmholtz energy stabilize β-strand conformations. Taken together, our results underscore the notion of the solvent being the predominant determinant of peptide (and protein) conformations in the unfolded state.

Liganded Hb ζ2βS2 Exhibits Antipolymer Activity Despite a T-like Quaternary Structure

Important therapeutic approaches to sickle-cell disease (SCD) are based upon the observation that the abnormal properties of Hb S (Hb α2βS2) can be mitigated by exchanging the pathological βS-globin subunit for a related β-like subunit. We previously demonstrated that exchange of the non-pathological α-globin subunit for a ζ-globin subunit (a developmentally silenced globin that can be derepressed both by natural and experimental conditions) inhibits deoxyHb S polymer assembly in vitro and reverses hematological, biochemical, and physiological characteristics of SCD in mouse models in vivo. While its therapeutic potential is clear, the underlying structural basis for the profound antipolymer activity of ζ-substituted Hb S (Hb ζ2βS2) is less certain. X-ray crystallographic studies conducted at 1.95Å resolution revealed that liganded (CO-) Hb ζ2βS2 is trapped in a tense (T-state) quaternary structure, rather than in a relaxed (R-state) structure that is characteristic of nearly all liganded hemoglobins. Specifically, CO-Hb ζ2βS2 exhibited several intact T-state intersubunit salt-bridge/hydrogen-bond interactions, a preserved T-state ζ1-β2 (ζ2-β1) interface, and a characteristically enlarged T-state central water cavity and β-cleft. This structure wrongly predicts that liganded Hb ζ2βS2 will be included, rather than excluded, from the deoxyHb S polymer; and suggests that changes in the positions or the biochemical identities of individual amino acids, rather than the overall quaternary structure of liganded Hb ζ2βS2, are the chief determinants of its antipolymer activity.To define key differences in the structures of T-state deoxyHb α2βS2 and CO-Hb ζ2βS2, we superposed their corresponding globin subunits and calculated the specific displacement of individual amino-acid residues as root mean square deviation (rmsd) values. Among βS-chain residues, α→ζ exchange effects a significant 1.9Å shift in the position of the pathological βSVal6, and correspondingly large displacements of βThr4 (2.2Å) and βAsn19 (1.4Å); each repositioning predicts weakening of an intermolecular interaction that would otherwise stabilize the deoxyHb S polymer. Similar superposition analyses of the α and ζ chains reveal a significant displacement of αPro114 (1.3Å), a well-described determinant of deoxyHb S polymerization that is conserved between the two α-like subunits. Three additional α-chain residues that stabilize the deoxyHb S polymer undergo nonconservative replacement in the ζ-globin chain, but are not materially repositioned: αHis20→ζGln (basic→neutral polar), αAsn68→ζAsp (neutral polar→acidic), and αAsn78→ζGly (neutral polar→neutral). While all three replacements are predicted to weaken or ablate intermolecular contacts, the αHis20→ζGln substitution is particularly noteworthy as it reproduces the specific mutation that defines the naturally occurring anti-sickling variant αLe Lamentin.Finally, we considered the possibility that ζ-substituted Hb S is fully excluded from the deoxyHb S polymer–and therefore reduces the rate of its assembly–by comparing the crystal packing of the two hemoglobins. While deoxyHb α2βS2 packs in a familiar two-strand structure, CO-Hb ζ2βS2 assembles into a unique trimeric arrangement comprising three lateral heterotetramers, each of which interacts with an axial heterotetramer that is constituent to a separate trimer assembly. This remarkable structure is sustained by intermolecular interactions that are distinct from those observed for deoxyHb S. Moreover, the calculated buried solvent-accessible surface area for CO-Hb ζ2βS2 (4806Å2) is nearly two-fold higher than for deoxyHb α2βS2 (2510Å2), suggesting that Hb ζ2βS2 exists in solution as a stable trimer of heterotetramers, and validating the hypothesis that Hbs α2βS2 and ζ2βS2 do not co-assemble in solution.In sum, our crystal analyses indicate that the antipolymer activities of liganded Hb ζ2βS2 arise through movements in the positions of βS-chain residues, and through changes in the identities of α-chain residues. Our studies also demonstrate a novel packing structure for T-state liganded Hb ζ2βS2 that is consistent with its exclusion from the deoxyHb S polymer. These data account for the significant antipolymer activity of ζ-substituted Hb S, and recommend the utility of therapeutic approaches to SCD that are based upon α-globin subunit exchange. DisclosuresSafo:Baxter and AesRx companies have licensed our patented antisickling compounds. Consulted with AesRx LLC during phase I clinical studies of the antisickling compound, 5HMF for the treatment of sickle cell disease: #7160910; #7119208 Patents & Royalties, Consultancy, Research Funding.

Investigation into the molecular and thermodynamic basis of protein interactions in multimodal chromatography using functionalized nanoparticles.

Although multimodal chromatography offers significant potential for bioseparations, there is a lack of molecular level understanding of the nature of protein binding in these systems. In this study a nanoparticle system is employed that can simulate a chromatographic resin surface while also being amenable to isothermal titration calorimetry (ITC) and solution NMR. ITC and NMR titration experiments are carried out with (15)N-labeled ubiquitin to investigate the interactions of ubiquitin with nanoparticles functionalized with two industrially important multimodal ligands. The ITC results suggest that binding to both multimodal ligand surfaces is entropically driven over a range of temperatures and that this is due primarily to the release of surface bound waters. In order to reveal structural details of the interaction process, binding-induced chemical shift changes obtained from the NMR experiments are employed to obtain dissociation constants of individual amino acid residues on the protein surface. The residue level information obtained from NMR is then used to identify a preferred binding face on ubiquitin for interaction to both multimodal ligand surfaces. In addition, electrostatic potential and spatial aggregation propensity maps are used to determine important protein surface property data that are shown to correlate well with the molecular level information obtained from NMR. Importantly, the data demonstrate that the cluster of interacting residues on the protein surface act co-operatively to give rise to multimodal binding affinities several orders of magnitude greater than those obtained previously for interactions with free solution ligands. The use of NMR and ITC to study protein interactions with functionalized nanoparticles offers a new tool for obtaining important molecular and thermodynamic insights into protein affinity in multimodal chromatographic systems.

A Theoretical Study of SRPK Interaction with the Flexible Domains of Hepatitis B Capsids

Hepatitis B virus (HBV) controls genome encapsidation and reverse transcription from a single-stranded RNA to a double-stranded DNA through the flexible C-terminal domain (CTD) of the capsid proteins. Although the microscopic structure of the nucleocapsid plays a critical role in the life cycle of HBV, the location of CTD residues at different stages of viral replication remains poorly understood. In this work, we report the radial distributions of individual amino-acid residues of the CTD tails for both empty and RNA-containing HBV capsids by using a coarse-grained model for the key biological components and the classical density functional theory. The density functional theory calculations reveal substantial exposure of the CTD residues outside the capsid, in particular when it is devoid of any nucleic materials. The outermost layer of the capsid surface mainly consists of residues from 170Ser-175Arg of the CTD tails, i.e., the serine-arginine protein kinase binding motif. The theoretical description corroborates recent in vitro studies that show a transient CTD distribution captured by serine-arginine protein kinase binding. We have also investigated the nucleocapsid structural changes due to phosphorylation of serine residues and shown a correlation between the CTD location and the internal distribution of RNA segments.