Adaptation of a transmitted/founder simian-human immunodeficiency virus for enhanced replication in rhesus macaques

Transmitted/founder (TF) simian-human immunodeficiency viruses (SHIVs) express HIV-1 envelopes modified at position 375 to efficiently infect rhesus macaques while preserving authentic HIV-1 Env biology. SHIV.C.CH505 is an extensively characterized virus encoding the TF HIV-1 Env CH505 mutated at position 375 shown to recapitulate key features of HIV-1 immunobiology, including CCR5-tropism, a tier 2 neutralization profile, reproducible early viral kinetics, and authentic immune responses. SHIV.C.CH505 is used frequently in nonhuman primate studies of HIV, but viral loads after months of infection are variable and typically lower than those in people living with HIV. We hypothesized that additional mutations besides Δ375 might further enhance virus fitness without compromising essential components of CH505 Env biology. From sequence analysis of SHIV.C.CH505-infected macaques across multiple experiments, we identified a signature of envelope mutations associated with higher viremia. We then used short-term in vivo mutational selection and competition to identify a minimally adapted SHIV.C.CH505 with just five amino acid changes that substantially improve virus replication fitness in macaques. Next, we validated the performance of the adapted SHIV in vitro and in vivo and identified the mechanistic contributions of selected mutations. In vitro, the adapted SHIV shows improved virus entry, enhanced replication on primary rhesus cells, and preserved neutralization profiles. In vivo, the minimally adapted virus rapidly outcompetes the parental SHIV with an estimated growth advantage of 0.14 days-1 and persists through suppressive antiretroviral therapy to rebound at treatment interruption. Here, we report the successful generation of a well-characterized, minimally adapted virus, termed SHIV.C.CH505.v2, with enhanced replication fitness and preserved native Env properties that can serve as a new reagent for NHP studies of HIV-1 transmission, pathogenesis, and cure.

Spontaneous Glycan Reattachment Following N-Glycanase Treatment of Influenza and HIV Vaccine Antigens

In cells, asparagine/N-linked glycans are added to glycoproteins cotranslationally, in an attachment process that supports proper folding of the nascent polypeptide. We found that following pruning of N-glycan by the amidase PNGase F, the principal influenza vaccine antigen and major viral spike protein hemagglutinin (HA) spontaneously reattached N-glycan to its de-N-glycosylated positions when the amidase was removed from solution. This reaction, which we term N-glycanation, was confirmed by site-specific analysis of HA glycoforms by mass spectrometry prior to PNGase F exposure, during exposure to PNGase F, and after amidase removal. Iterative rounds of de-N-glycosylation followed by N-glycanation could be repeated at least three times and were observed for other viral glycoproteins/vaccine antigens, including the envelope glycoprotein (Env) from HIV. Covalent N-glycan reattachment was nonenzymatic as it occurred in the presence of metal ions that inhibit PNGase F activity. Rather, N-glycanation relied on a noncovalent assembly between protein and glycan, formed in the presence of the amidase, where linearization of the glycoprotein prevented this retention and subsequent N-glycanation. This reaction suggests that under certain experimental conditions, some glycoproteins can organize self-glycan addition, highlighting a remarkable self-assembly principle that may prove useful for re-engineering therapeutic glycoproteins such as influenza HA or HIV Env, where glycan sequence and structure can markedly affect bioactivity and vaccine efficacy.

Therapeutic antibody discovery in lung tumors by B-cell receptor sequencing

Malignancies of the lung are expected to be responsible for over 25% of all cancer-associated mortalities in the United States in 2019. Clinical treatment of lung cancer is complicated by both poor detection of early disease activity and relapse or unresponsiveness to administered therapy. Taken together, these realities of patient outcome underscore the need for alternative therapeutic strategies. Research efforts in the cancer immunology field focus primarily on T cells in the tumor microenvironment, however, there is evidence that B cells may impart a clinical benefit in patients. The formation of tertiary lymphoid structures and antibody secretion in lung tumors associate with positive clinical outcomes yet remain understudied and poorly characterized. In an effort to expand upon these observations, we isolated B cells from cryopreserved human lung cancer tissue and recovered B-cell receptor (BCR) sequences by paired heavy and light chain single cell RNA sequencing. From these experiments, we identified clonally expanded B-cell populations and convergent BCR sequences shared between different patients. We further demonstrated that recombinant antibodies derived from lung cancer patients bind cultured lung cancer cell lines in a dose-dependent manner. This preliminary data supports the notion that tumor-resident B-cells secrete functional antibodies that may additionally be tumor-reactive. Future characterization of these antibodies includes antigen identification and the measurement of in vitro and in vivo cytotoxic activity. Human patient-derived antibodies not only could serve as a novel source for therapeutic and diagnostic agents but may also help inform vaccine design in lung cancer indications.

Antibody cross-reactivity in chronic HIV/HCV co-infection

HIV/HCV co-infected individuals fair worse than their mono-infected counterparts, experiencing rapid progression to fibrosis, and increased chance of liver damage due to HAART. Given this, novel antibody therapeutic and rational vaccine design for both viruses have become top priorities worldwide. This study seeks to understand the antibody response in chronic HIV/HCV co-infection. Normally selected against, antibodies that recognize diverse antigens confer a selective advantage against highly mutable pathogens, such as HIV and HCV. We hypothesized that chronic co-infection leads to the development of antibodies that can recognize both viruses.

In collaboration with the Vanderbilt HIV cohort, we obtained patient PBMCs from a single HIV/HCV co-infected African American man, at four timepoints between 0.5 – 3 years post HIV infection (ypi). For 0.5, and 1.5 ypi we performed antigen-specific B cell sorting and deep B cell receptor sequencing. Notably, we used fluorescently-labeled envelope proteins from each virus to isolate virus-specific B cells from infected peripheral blood. We identified multiple unique B cells positive for both HIV and HCV antigens, which we then expressed as recombinant antibodies to characterize. Intriguingly, we see antibody-mediated neutralization of diverse viral strains, suggesting a common mode of antiviral protection. Matching single cell sequencing and functional to next-generation sequencing data allows for powerful delineation and characterization of virus-specific antibody responses. Furthermore, this study presents the first evidence of antibody cross-reactivity between genetically unrelated viruses, which could have great impact on future vaccine design efforts.

Facial soft tissue thicknesses in Bulgarian adults: relation to sex, body mass index and bilateral asymmetry

BACKGROUND

The aim of the study is to measure the facial soft tissue thicknesses (STTs) in Bulgarians, to evaluate the relation of the STTs to the nutritional status, sex and bilateral asymmetry, and to examine the correlations between the separate STTs as well as between the STTs and body weight, height, and body mass index (BMI). In the present study, the facial STTs were measured on computed tomography scans of the head of Bulgarian adults.

MATERIALS AND METHODS

The STTs were measured at 7 midline and 9 bilateral landmarks. The measurements were performed in the free software InVesalius in the axial and sagittal planes. The mean, standard deviation, minimum and maximum values, median and coefficient of variation were reported for the STT at each landmark according to the sex and BMI category. The BMI, sex and bilateral differences were assessed for statistical significance. Pearson correlation analysis was applied to assess the strength and direction of the relationships between the STTs and body height, weight and BMI, as well as between separate STTs.

RESULTS AND CONCLUSIONS

The facial soft tissues in Bulgarian adults changed in accordance with the nutritional status of the individual and in both sexes all STTs augmented with the increasing BMI. For both normal and overweight BMI categories, males had more soft tissue at the majority of facial points than females, as the only exceptions were observed in the cheek zone, where STTs were thicker in females. Significant bilateral differences were observed in either sex and BMI category. Stronger correlations were established for the STTs in the jaw region and between the cheek and jaw soft tissues. Besides, the correlations between the homologous bilateral landmarks were among the strongest ones.

OSPREY Predicts Resistance Mutations Using Positive and Negative Computational Protein Design

Drug resistance in protein targets is an increasingly common phenomenon that reduces the efficacy of both existing and new antibiotics. However, knowledge of future resistance mutations during pre-clinical phases of drug development would enable the design of novel antibiotics that are robust against not only known resistant mutants, but also against those that have not yet been clinically observed. Computational structure-based protein design (CSPD) is a transformative field that enables the prediction of protein sequences with desired biochemical properties such as binding affinity and specificity to a target. The use of CSPD to predict previously unseen resistance mutations represents one of the frontiers of computational protein design. In a recent study (Reeve et al. Proc Natl Acad Sci U S A 112(3):749-754, 2015), we used our OSPREY (Open Source Protein REdesign for You) suite of CSPD algorithms to prospectively predict resistance mutations that arise in the active site of the dihydrofolate reductase enzyme from methicillin-resistant Staphylococcus aureus (SaDHFR) in response to selective pressure from an experimental competitive inhibitor. We demonstrated that our top predicted candidates are indeed viable resistant mutants. Since that study, we have significantly enhanced the capabilities of OSPREY with not only improved modeling of backbone flexibility, but also efficient multi-state design, fast sparse approximations, partitioned continuous rotamers for more accurate energy bounds, and a computationally efficient representation of molecular-mechanics and quantum-mechanical energy functions. Here, using SaDHFR as an example, we present a protocol for resistance prediction using the latest version of OSPREY. Specifically, we show how to use a combination of positive and negative design to predict active site escape mutations that maintain the enzyme's catalytic function but selectively ablate binding of an inhibitor.

Activation and lysis of human CD4 cells latently infected with HIV-1

The treatment of AIDS with combination antiretroviral therapy (cART) remains lifelong largely because the virus persists in latent reservoirs. Elimination of latently infected cells could therefore reduce treatment duration and facilitate immune reconstitution. Here we report an approach to reduce the viral reservoir by activating dormant viral gene expression and directing T lymphocytes to lyse previously latent, HIV-1-infected cells. An immunomodulatory protein was created that combines the specificity of a HIV-1 broadly neutralizing antibody with that of an antibody to the CD3 component of the T-cell receptor. CD3 engagement by the protein can stimulate T-cell activation that induces proviral gene expression in latently infected T cells. It further stimulates CD8 T-cell effector function and redirects T cells to lyse these previously latent-infected cells through recognition of newly expressed Env. This immunomodulatory protein could potentially help to eliminate latently infected cells and deplete the viral reservoir in HIV-1-infected individuals.

The elimination of latently infected cells is a sought after goal in the treatment of HIV-1 infections. Here the authors develop an approach to eliminate latently HIV-1 infected cells by using an immunomodulatory protein, which can activate viral gene expression in these cells and direct T lymphocytes to lyse them in vitro.

EPIDEMIOLOGICAL REGISTRY OF NEUROENDOCRINE TUMORS IN BULGARIA--A PILOT SURVEY

The National registry of patients with neuroendocrine tumors (NET) in Bulgaria was established in 2013 as a joint initiative of the Bulgarian Surgical Society and the Institute for Rare Diseases. The register aims to explore the epidemiology of NET in Bulgaria, as well as the different diagnostic and treatment approaches for the disease throughout the country. This the first of its kind retrospective study of NET in the country is covering the period January 2012 - January 2013. A total of 127 patients with NET were identified. At the time of the survey the average age of patients with NET was 58.61 ± 15.59 years. The data show almost equal distribution between the genders with a slight predominance of women. The largest relative part of NET is those of NET located in the gastrointestinal tract (54.10 ± 4.51%), followed by those located in the pancreas (12.30 ± 2.97%) and in the lungs (10.66 ± 2.79%). In 72.44 ± 3.96% of the patients a immunohistochemical diagnosis was performed. The study confirmed the leading role of the surgery method of the NET management. In 65.83 ± 4.33% of the patients a radical removal of the tumor was conducted, while the relative part of the undertaken partial resection was 7.50 ± 2.40%. A statistically significant association between the type of surgical treatment and during the follow-up of patients was found. An update of the information in the register will allow a more precise determining of the distribution and management of NET in Bulgaria.

OSPREY: protein design with ensembles, flexibility, and provable algorithms

We have developed a suite of protein redesign algorithms that improves realistic in silico modeling of proteins. These algorithms are based on three characteristics that make them unique: (1) improved flexibility of the protein backbone, protein side-chains, and ligand to accurately capture the conformational changes that are induced by mutations to the protein sequence; (2) modeling of proteins and ligands as ensembles of low-energy structures to better approximate binding affinity; and (3) a globally optimal protein design search, guaranteeing that the computational predictions are optimal with respect to the input model. Here, we illustrate the importance of these three characteristics. We then describe OSPREY, a protein redesign suite that implements our protein design algorithms. OSPREY has been used prospectively, with experimental validation, in several biomedically relevant settings. We show in detail how OSPREY has been used to predict resistance mutations and explain why improved flexibility, ensembles, and provability are essential for this application.

AVAILABILITY

OSPREY is free and open source under a Lesser GPL license. The latest version is OSPREY 2.0. The program, user manual, and source code are available at www.cs.duke.edu/donaldlab/software.php.

CONTACT

osprey@cs.duke.edu.

Increased HIV-1 vaccine efficacy against viruses with genetic signatures in Env V2

The RV144 trial demonstrated 31% vaccine efficacy at preventing human immunodeficiency virus (HIV)-1 infection. Antibodies against the HIV-1 envelope variable loops 1 and 2 (Env V1 and V2) correlated inversely with infection risk. We proposed that vaccine-induced immune responses against V1/V2 would have a selective effect against, or sieve, HIV-1 breakthrough viruses. A total of 936 HIV-1 genome sequences from 44 vaccine and 66 placebo recipients were examined. We show that vaccine-induced immune responses were associated with two signatures in V2 at amino acid positions 169 and 181. Vaccine efficacy against viruses matching the vaccine at position 169 was 48% (confidence interval 18% to 66%; P = 0.0036), whereas vaccine efficacy against viruses mismatching the vaccine at position 181 was 78% (confidence interval 35% to 93%; P = 0.0028). Residue 169 is in a cationic glycosylated region recognized by broadly neutralizing and RV144-derived antibodies. The predicted distance between the two signature sites (21 ± 7 Å) and their match/mismatch dichotomy indicate that multiple factors may be involved in the protection observed in RV144. Genetic signatures of RV144 vaccination in V2 complement the finding of an association between high V1/V2-binding antibodies and reduced risk of HIV-1 acquisition, and provide evidence that vaccine-induced V2 responses plausibly had a role in the partial protection conferred by the RV144 regimen.

The role of local backrub motions in evolved and designed mutations

Amino acid substitutions in protein structures often require subtle backbone adjustments that are difficult to model in atomic detail. An improved ability to predict realistic backbone changes in response to engineered mutations would be of great utility for the blossoming field of rational protein design. One model that has recently grown in acceptance is the backrub motion, a low-energy dipeptide rotation with single-peptide counter-rotations, that is coupled to dynamic two-state sidechain rotamer jumps, as evidenced by alternate conformations in very high-resolution crystal structures. It has been speculated that backrubs may facilitate sequence changes equally well as rotamer changes. However, backrub-induced shifts and experimental uncertainty are of similar magnitude for backbone atoms in even high-resolution structures, so comparison of wildtype-vs.-mutant crystal structure pairs is not sufficient to directly link backrubs to mutations. In this study, we use two alternative approaches that bypass this limitation. First, we use a quality-filtered structure database to aggregate many examples for precisely defined motifs with single amino acid differences, and find that the effectively amplified backbone differences closely resemble backrubs. Second, we directly apply a provably-accurate, backrub-enabled protein design algorithm to idealized versions of these motifs, and discover that the lowest-energy computed models match the average-coordinate experimental structures. These results support the hypothesis that backrubs participate in natural protein evolution and validate their continued use for design of synthetic proteins.

Protein design has the potential to generate useful molecules for medicine and chemistry, including sensors, drugs, and catalysts for arbitrary reactions. When protein design is carried out starting from an experimentally determined structure, as is often the case, one important aspect to consider is backbone flexibility, because in response to a mutation the backbone often must shift slightly to reconcile the new sidechain with its environment. In principle, one may model the backbone in many ways, but not all are physically realistic or experimentally validated. Here we study the "backrub" motion, which has been previously documented in atomic detail, but only for sidechain movements within single structures. By a twopronged approach involving both structural bioinformatics and computation with a principled design algorithm, we demonstrate that backrubs are sufficient to explain the backbone differences between mutation-related sets of very precisely defined motifs from the protein structure database. Our findings illustrate that backrubs are useful for describing evolutionary sequence change and, by extension, suggest that they are also appropriate for rational protein design calculations.

Computational prediction of N-linked glycosylation incorporating structural properties and patterns

MOTIVATION

N-linked glycosylation occurs predominantly at the N-X-T/S motif, where X is any amino acid except proline. Not all N-X-T/S sequons are glycosylated, and a number of web servers for predicting N-linked glycan occupancy using sequence and/or residue pattern information have been developed. None of the currently available servers, however, utilizes protein structural information for the prediction of N-glycan occupancy.

RESULTS

Here, we describe a novel classifier algorithm, NGlycPred, for the prediction of glycan occupancy at the N-X-T/S sequons. The algorithm utilizes both structural as well as residue pattern information and was trained on a set of glycosylated protein structures using the Random Forest algorithm. The best predictor achieved a balanced accuracy of 0.687 under 10-fold cross-validation on a curated dataset of 479 N-X-T/S sequons and outperformed sequence-based predictors when evaluated on the same dataset. The incorporation of structural information, including local contact order, surface accessibility/composition and secondary structure thus improves the prediction accuracy of glycan occupancy at the N-X-T/S consensus sequon.

AVAILABILITY AND IMPLEMENTATION

NGlycPred is freely available to non-commercial users as a web-based server at http://exon.niaid.nih.gov/nglycpred/.

Early low-titer neutralizing antibodies impede HIV-1 replication and select for virus escape

Single genome sequencing of early HIV-1 genomes provides a sensitive, dynamic assessment of virus evolution and insight into the earliest anti-viral immune responses in vivo. By using this approach, together with deep sequencing, site-directed mutagenesis, antibody adsorptions and virus-entry assays, we found evidence in three subjects of neutralizing antibody (Nab) responses as early as 2 weeks post-seroconversion, with Nab titers as low as 1∶20 to 1∶50 (IC(50)) selecting for virus escape. In each of the subjects, Nabs targeted different regions of the HIV-1 envelope (Env) in a strain-specific, conformationally sensitive manner. In subject CH40, virus escape was first mediated by mutations in the V1 region of the Env, followed by V3. HIV-1 specific monoclonal antibodies from this subject mapped to an immunodominant region at the base of V3 and exhibited neutralizing patterns indistinguishable from polyclonal antibody responses, indicating V1-V3 interactions within the Env trimer. In subject CH77, escape mutations mapped to the V2 region of Env, several of which selected for alterations of glycosylation. And in subject CH58, escape mutations mapped to the Env outer domain. In all three subjects, initial Nab recognition was followed by sequential rounds of virus escape and Nab elicitation, with Nab escape variants exhibiting variable costs to replication fitness. Although delayed in comparison with autologous CD8 T-cell responses, our findings show that Nabs appear earlier in HIV-1 infection than previously recognized, target diverse sites on HIV-1 Env, and impede virus replication at surprisingly low titers. The unexpected in vivo sensitivity of early transmitted/founder virus to Nabs raises the possibility that similarly low concentrations of vaccine-induced Nabs could impair virus acquisition in natural HIV-1 transmission, where the risk of infection is low and the number of viruses responsible for transmission and productive clinical infection is typically one.

Structure of HIV-1 gp120 V1/V2 domain with broadly neutralizing antibody PG9

Variable regions 1 and 2 (V1/V2) of human immunodeficiency virus-1 (HIV-1) gp120 envelope glycoprotein are critical for viral evasion of antibody neutralization, and are themselves protected by extraordinary sequence diversity and N-linked glycosylation. Human antibodies such as PG9 nonetheless engage V1/V2 and neutralize 80% of HIV-1 isolates. Here we report the structure of V1/V2 in complex with PG9. V1/V2 forms a four-stranded β-sheet domain, in which sequence diversity and glycosylation are largely segregated to strand-connecting loops. PG9 recognition involves electrostatic, sequence-independent and glycan interactions: the latter account for over half the interactive surface but are of sufficiently weak affinity to avoid autoreactivity. The structures of V1/V2-directed antibodies CH04 and PGT145 indicate that they share a common mode of glycan penetration by extended anionic loops. In addition to structurally defining V1/V2, the results thus identify a paradigm of antibody recognition for highly glycosylated antigens, which-with PG9-involves a site of vulnerability comprising just two glycans and a strand.

Focused evolution of HIV-1 neutralizing antibodies revealed by structures and deep sequencing

Antibody VRC01 is a human immunoglobulin that neutralizes about 90% of HIV-1 isolates. To understand how such broadly neutralizing antibodies develop, we used x-ray crystallography and 454 pyrosequencing to characterize additional VRC01-like antibodies from HIV-1-infected individuals. Crystal structures revealed a convergent mode of binding for diverse antibodies to the same CD4-binding-site epitope. A functional genomics analysis of expressed heavy and light chains revealed common pathways of antibody-heavy chain maturation, confined to the IGHV1-2*02 lineage, involving dozens of somatic changes, and capable of pairing with different light chains. Broadly neutralizing HIV-1 immunity associated with VRC01-like antibodies thus involves the evolution of antibodies to a highly affinity-matured state required to recognize an invariant viral structure, with lineages defined from thousands of sequences providing a genetic roadmap of their development.

Structural basis for broad and potent neutralization of HIV-1 by antibody VRC01

During HIV-1 infection, antibodies are generated against the region of the viral gp120 envelope glycoprotein that binds CD4, the primary receptor for HIV-1. Among these antibodies, VRC01 achieves broad neutralization of diverse viral strains. We determined the crystal structure of VRC01 in complex with a human immunodeficiency virus HIV-1 gp120 core. VRC01 partially mimics CD4 interaction with gp120. A shift from the CD4-defined orientation, however, focuses VRC01 onto the vulnerable site of initial CD4 attachment, allowing it to overcome the glycan and conformational masking that diminishes the neutralization potency of most CD4-binding-site antibodies. To achieve this recognition, VRC01 contacts gp120 mainly through immunoglobulin V-gene regions substantially altered from their genomic precursors. Partial receptor mimicry and extensive affinity maturation thus facilitate neutralization of HIV-1 by natural human antibodies.

The minimized dead-end elimination criterion and its application to protein redesign in a hybrid scoring and search algorithm for computing partition functions over molecular ensembles

One of the main challenges for protein redesign is the efficient evaluation of a combinatorial number of candidate structures. The modeling of protein flexibility, typically by using a rotamer library of commonly-observed low-energy side-chain conformations, further increases the complexity of the redesign problem. A dominant algorithm for protein redesign is dead-end elimination (DEE), which prunes the majority of candidate conformations by eliminating rigid rotamers that provably are not part of the global minimum energy conformation (GMEC). The identified GMEC consists of rigid rotamers (i.e., rotamers that have not been energy-minimized) and is thus referred to as the rigid-GMEC. As a postprocessing step, the conformations that survive DEE may be energy-minimized. When energy minimization is performed after pruning with DEE, the combined protein design process becomes heuristic, and is no longer provably accurate: a conformation that is pruned using rigid-rotamer energies may subsequently minimize to a lower energy than the rigid-GMEC. That is, the rigid-GMEC and the conformation with the lowest energy among all energy-minimized conformations (the minimized-GMEC) are likely to be different. While the traditional DEE algorithm succeeds in not pruning rotamers that are part of the rigid-GMEC, it makes no guarantees regarding the identification of the minimized-GMEC. In this paper we derive a novel, provable, and efficient DEE-like algorithm, called minimized-DEE (MinDEE), that guarantees that rotamers belonging to the minimized-GMEC will not be pruned, while still pruning a combinatorial number of conformations. We show that MinDEE is useful not only in identifying the minimized-GMEC, but also as a filter in an ensemble-based scoring and search algorithm for protein redesign that exploits energy-minimized conformations. We compare our results both to our previous computational predictions of protein designs and to biological activity assays of predicted protein mutants. Our provable and efficient minimized-DEE algorithm is applicable in protein redesign, protein-ligand binding prediction, and computer-aided drug design.

Algorithm for backrub motions in protein design

Motivation: The Backrub is a small but kinematically efficient side-chain-coupled local backbone motion frequently observed in atomic-resolution crystal structures of proteins. A backrub shifts the C_α–C_β orientation of a given side-chain by rigid-body dipeptide rotation plus smaller individual rotations of the two peptides, with virtually no change in the rest of the protein. Backrubs can therefore provide a biophysically realistic model of local backbone flexibility for structure-based protein design. Previously, however, backrub motions were applied via manual interactive model-building, so their incorporation into a protein design algorithm (a simultaneous search over mutation and backbone/side-chain conformation space) was infeasible.

Results: We present a combinatorial search algorithm for protein design that incorporates an automated procedure for local backbone flexibility via backrub motions. We further derive a dead-end elimination (DEE)-based criterion for pruning candidate rotamers that, in contrast to previous DEE algorithms, is provably accurate with backrub motions. Our backrub-based algorithm successfully predicts alternate side-chain conformations from ≤0.9 Å resolution structures, confirming the suitability of the automated backrub procedure. Finally, the application of our algorithm to redesign two different proteins is shown to identify a large number of lower-energy conformations and mutation sequences that would have been ignored by a rigid-backbone model.

Availability: Contact authors for source code.

Contact:brd+ismb08@cs.duke.edu

Dead-end elimination with backbone flexibility

MOTIVATION

Dead-End Elimination (DEE) is a powerful algorithm capable of reducing the search space for structure-based protein design by a combinatorial factor. By using a fixed backbone template, a rotamer library, and a potential energy function, DEE identifies and prunes rotamer choices that are provably not part of the Global Minimum Energy Conformation (GMEC), effectively eliminating the majority of the conformations that must be subsequently enumerated to obtain the GMEC. Since a fixed-backbone model biases the algorithm predictions against protein sequences for which even small backbone movements may result in a significantly enhanced stability, the incorporation of backbone flexibility can improve the accuracy of the design predictions. If explicit backbone flexibility is incorporated into the model, however, the traditional DEE criteria can no longer guarantee that the flexible-backbone GMEC, the lowest-energy conformation when the backbone is allowed to flex, will not be pruned.

RESULTS

We derive a novel DEE pruning criterion, flexible-backbone DEE (BD), that is provably accurate with backbone flexibility, guaranteeing that no rotamers belonging to the flexible-backbone GMEC are pruned; we also present further enhancements to BD for improved pruning efficiency. The results from applying our novel algorithms to redesign the beta1 domain of protein G and to switch the substrate specificity of the NRPS enzyme GrsA-PheA are then compared against the results from previous fixed-backbone DEE algorithms. We confirm experimentally that traditional-DEE is indeed not provably-accurate with backbone flexibility and that BD is capable of generating conformations with significantly lower energies, thus confirming the feasibility of our novel algorithms.

AVAILABILITY

Contact authors for source code.

Redesigning the PheA domain of gramicidin synthetase leads to a new understanding of the enzyme's mechanism and selectivity

The PheA domain of gramicidin synthetase A, a non-ribosomal peptide synthetase, selectively binds phenylalanine along with ATP and Mg2+ and catalyzes the formation of an aminoacyl adenylate. In this study, we have used a novel protein redesign algorithm, K*, to predict mutations in PheA that should exhibit improved binding for tyrosine. Interestingly, the introduction of two predicted mutations to PheA did not significantly improve KD, as measured by equilibrium fluorescence quenching. However, the mutations improved the specificity of the enzyme for tyrosine (as measured by kcat/KM), primarily driven by a 56-fold improvement in KM, although the improvement did not make tyrosine the preferred substrate over phenylalanine. Using stopped-flow fluorometry, we examined binding of different amino acid substrates to the wild-type and mutant enzymes in the pre-steady state in order to understand the improvement in KM. Through these investigations, it became evident that substrate binding to the wild-type enzyme is more complex than previously described. These experiments show that the wild-type enzyme binds phenylalanine in a kinetically selective manner; no other amino acids tested appeared to bind the enzyme in the early time frame examined (500 ms). Furthermore, experiments with PheA, phenylalanine, and ATP reveal a two-step binding process, suggesting that the PheA-ATP-phenylalanine complex may undergo a conformational change toward a catalytically relevant intermediate on the pathway to adenylation; experiments with PheA, phenylalanine, and other nucleotides exhibit only a one-step binding process. The improvement in KM for the mutant enzyme toward tyrosine, as predicted by K*, may indicate that redesigning the side-chain binding pocket allows the substrate backbone to adopt productive conformations for catalysis but that further improvements may be afforded by modeling an enzyme:ATP:substrate complex, which is capable of undergoing conformational change.

Improved Pruning algorithms and Divide-and-Conquer strategies for Dead-End Elimination, with application to protein design

MOTIVATION

Structure-based protein redesign can help engineer proteins with desired novel function. Improving computational efficiency while still maintaining the accuracy of the design predictions has been a major goal for protein design algorithms. The combinatorial nature of protein design results both from allowing residue mutations and from the incorporation of protein side-chain flexibility. Under the assumption that a single conformation can model protein folding and binding, the goal of many algorithms is the identification of the Global Minimum Energy Conformation (GMEC). A dominant theorem for the identification of the GMEC is Dead-End Elimination (DEE). DEE-based algorithms have proven capable of eliminating the majority of candidate conformations, while guaranteeing that only rotamers not belonging to the GMEC are pruned. However, when the protein design process incorporates rotameric energy minimization, DEE is no longer provably-accurate. Hence, with energy minimization, the minimized-DEE (MinDEE) criterion must be used instead.

RESULTS

In this paper, we present provably-accurate improvements to both the DEE and MinDEE criteria. We show that our novel enhancements result in a speedup of up to a factor of more than 1000 when applied in redesign for three different proteins: Gramicidin Synthetase A, plastocyanin, and protein G.

AVAILABILITY

Contact authors for source code.

ABH blood group antigen significance as markers of endothelial differentiation of mesenchymal cells

The expression pattern of A, B and H blood group antigens was evaluated by staining frozen sections with specific monoclonal antibodies developed by us and using the indirect immunoperoxidase method. The expression of blood group antigens was ubiquitously upregulated in the endothelial cells of fetal organs. In the process of their differentiation to endothelial naive embryonic mesenchymal cells expressed cytoplasmic ABH antigens. They were assumed as products of the activation of the respective genes. ABH antigen expression was considered as suggestive evidence for the assumption that blood group antigens could serve as early immunomorphologic markers of endothelial differentiation of mesenchymal cells, thus specifying the location of future blood vessels. Extending the conceptual framework of blood group antigens' significance we consider them as being possibly involved in the process of fetal morphogenesis.

Wavelets as alternative to short-time Fourier transform in signal-averaged electrocardiography

The paper reports experience of using the wavelet transform to build time-frequency distributions of the terminal portion of the QRS-complex. We used wavelets of Morlet at 12 scales, grouped in three sets, to analyse the frequency range 33-404 Hz. On the same patient data we applied the short-time Fourier transform and compared the results. Both representations reflected the time-frequency contents and detected irregular structures in the terminal portion of the QRS complex. The wavelet transform revealed more adequately QRS prolongations characteristic of patients prone to ventricular tachycardia. We may conclude that the wavelet transform can be a flexible alternative to short-time Fourier transform.

[Determination of the turbidity temperature of solutions of the nonionogenic surface-active agent LF-57 after the action on urinary calculi in uric acid]

Non-ionogenic surfactant LF-57 contributes solving of urinary calculi from uric acid and is a component of the drug Pharmalit for curing kidney-stone disease. Turbidity temperature was determined of the solution LF-57-78, 1C, and in the presence of uric acid--80.2C.

[Clinical multiplicity of cerebrovascular disorders in childhood]

A group of 107 children with vascular diseases of the nervous system aged 3-14 years have been studied. In 100 children of the study group acute disturbances of the brain blood circulation have been found, out of which 37 children were with transitory ischemic attacks; 29 were found to be with brain ischaemia; 22-with haemorrhages (7 cases with subarchnoidal, 9 cases with intracerebral and 6 cases with subarachnoidal-parenchimatose); 5 children had wenous thromboses; 7 children were with spinal strokes. In other 7 children we found the presence of Sturge-Weber syndrome. Congenital vascular malformations have been found in 32 children (30%), out of which 16 children (15%) with loops and stenosis of the extracranial segments of the internal carotid artery, and another 16 children (15%) with AV-malformations. Congenital and acquired heart diseases are found to be primary cause for the strokes in 12 children (11%). Considerable is the rate of the epileptic seizures in the acute stage of the strokes as well as of the residual epileptic syndromes.