ZDOCK predictions for the CAPRI challenge

In silico protein function prediction: the rise of machine learning-based approaches

Proteins function as integral actors in essential life processes, rendering the realm of protein research a fundamental domain that possesses the potential to propel advancements in pharmaceuticals and disease investigation. Within the context of protein research, an imperious demand arises to uncover protein functionalities and untangle intricate mechanistic underpinnings. Due to the exorbitant costs and limited throughput inherent in experimental investigations, computational models offer a promising alternative to accelerate protein function annotation. In recent years, protein pre-training models have exhibited noteworthy advancement across multiple prediction tasks. This advancement highlights a notable prospect for effectively tackling the intricate downstream task associated with protein function prediction. In this review, we elucidate the historical evolution and research paradigms of computational methods for predicting protein function. Subsequently, we summarize the progress in protein and molecule representation as well as feature extraction techniques. Furthermore, we assess the performance of machine learning-based algorithms across various objectives in protein function prediction, thereby offering a comprehensive perspective on the progress within this field.

Identification and molecular modeling of novel endogenous activator proteins of Sirt-1: an in silico study

Sirt-1 is one of the most extensively studied mammalian Sirtuins that deacetylates histones and several non-histone proteins critical to cellular homeostasis. As a key sensor of cellular metabolism, it is regulated at multiple levels including transcriptional and post translational levels. As an allosteric enzyme, its activity is also modulated by ligands and certain endogenous proteins. The present study is an in silico approach to identify novel Sirt-1 binding proteins. Bioinformatic search for similarity in sequence, structure, and topology of binding region to Lamin-A, a known activator of Sirt-1, identified three proteins viz. Epididymis secretory sperm binding protein (ESSBP), xylosyltransferase 1 (XT-1), and Adenylyl cyclase 9 (ADCY-9). Molecular docking studies revealed binding of ESSBP and ADCY-9 to the N-terminal region of Sirt-1 while XT-1 docks at both N-terminal and C-terminal region of Sirt-1 with Z-Dock score better than Lamin-A; XT-1 and ADCY-9 showed better Z-Rank score as well. MD simulation studies for extended time followed by MM-PBSA analysis showed that the Sirt-1-protein complexes were stable with favourable binding energy and minimal change in RMSD relating to backbone structure and RMSF relating to residue fluctuations. Further, H-bond analysis showed only minimal changes in H bonding interactions. Docking of these proteins to Sirt-1 through interaction with several residues particularly to its N-terminal region spanning 1-243 residues, in a manner similar to the docking of the activator Lamin-A and different from the inhibitor DLBC-1 binding site, suggests that these proteins may also positively modulate Sirt-1 activity. Further experimental data would be required to validate the computational prediction and to understand its physiological role.Communicated by Ramaswamy H. Sarma.

A Novel Index of Contact Frequency from Noise Protein-Protein Interaction Data Help for Accurate Interface Residue Pair Prediction

Protein-protein interactions are important for most biological processes and have been studied for decades. However, the detailed formation mechanism of protein-protein interaction interface is still ambiguous, which makes it difficult to accurately predict the protein-protein interaction interface residue pairs. Here, we extract the interface residue-residue contacts from the decoys in the ZDOCK protein-protein complex decoy set with RMSD mostly larger than 3 Å. To accurately compute the interface residue-residue contacts, we define a new constant called interface residue pairs frequency, which counts the atom contact numbers between two interface residues. We normalize interface residue pairs frequency to pick out the top residue-residue pairs from all the possible pairs preferential to be on correct protein-protein interaction interface. When tested on 37 protein dimers from the decoy set where most decoys are incorrect, our method successfully predicts 30 protein dimers with a success rate of up to 81.1%. Higher accuracy than some other state-of-the-art methods confirmed the performance of our method.

The binding process of BmKTX and BmKTX-D33H toward to Kv1.3 channel: a molecular dynamics simulation study

The potassium channel Kv1.3 is an important pharmacological target and the Kaliotoxin-type toxins (α-KTX-3 family) are its specific blockers. Here, we study the binding process of two kinds of Kaliotoxin-type toxins:BmKTX and its mutant (BmKTX-D33H) toward to Kv1.3 channel using MD simulation and umbrella sampling simulation, respectively. The calculated binding free energies are -27 kcal/mol and -34 kcal/mol for BmKTX and BmKTX-D33H, respectively, which are consistent with experimental results. The further analysis indicate that the characteristic of electrostatic potential of the α-KTX-3 have important effect on their binding modes with Kv1.3 channel; the residue 33 in BmKTX or BmKTX-D33H plays a key role in determine their binding orientations toward to Kv1.3 channel; when residue 33 (or 34) has negative electrostatic potential, the anti-parallel β-sheet domain of α-KTX-3 toxin peptide will keep away from the filter region of Kv1.3 channel, as BmKTX; when residue 33(or 34) has positive electrostatic potential, the anti-parallel β-sheet domain of α-KTX-3 toxin peptide will interact with the filter region of Kv1.3 channel, as BmKTX-D33H. Above all, electrostatic potential differences on toxin surfaces and correlations motions within the toxins will determine the toxin-potassium channel interaction model. In addition, the hydrogen bond interaction is the pivotal factor for the Kv1.3-Kaliotoxin association. Understanding the binding mechanism of toxin-potassium channel will facilitate the rational development of new toxin analogue.Communicated by Ramaswamy H. Sarma.

Performance of ZDOCK and IRAD in CAPRI rounds 39-45

We report docking performance on the six targets of Critical Assessment of PRedicted Interactions (CAPRI) rounds 39-45 that involved heteromeric protein-protein interactions and had the solved structures released since the rounds were held. Our general strategy involved protein-protein docking using ZDOCK, reranking using IRAD, and structural refinement using Rosetta. In addition, we made extensive use of experimental data to guide our docking runs. All the experimental information at the amino-acid level proved correct. However, for two targets, we also used protein-complex structures as templates for modeling interfaces. These resulted in incorrect predictions, presumably due to the low sequence identity between the targets and templates. Albeit a small number of targets, the performance described here compared somewhat less favorably with our previous CAPRI reports, which may be due to the CAPRI targets being increasingly challenging.

Combined transcriptomic and proteomic analysis reveals a diversity of venom-related and toxin-like peptides expressed in the mat anemone Zoanthus natalensis (Cnidaria, Hexacorallia)

Venoms from marine animals have been recognized as a new emerging source of peptide-based therapeutics. Several peptide toxins from sea anemone have been investigated as therapeutic leads or pharmacological tools. Venom complexity should be further highlighted using combined strategies of large-scale sequencing and data analysis which integrated transcriptomics and proteomics to elucidate new proteins or peptides to be compared among species. In this work, transcriptomic and proteomic analyses were combined to identify six groups of expressed peptide toxins in Zoanthus natalensis. These include neurotoxin, hemostatic and hemorrhagic toxin, protease inhibitor, mixed function enzymes, venom auxiliary proteins, allergen peptides, and peptides related to the innate immunity. Molecular docking analysis indicated that one expressed Zoanthus Kunitz-like peptide, ZoaKuz1, could be a voltage-gated potassium channels blocker and, hence, it was selected for functional studies. Functional bioassays revealed that ZoaKuz1 has an intrinsic neuroprotective activity in zebrafish model of Parkinson's disease. Since pharmacological blockade of K_V channels is known to induce neuroprotective effects, ZoaKuz1 holds the potential to be developed in a therapeutic tool to control neural dysfunction by slowing or even halting neurodegeneration mediated by ion-channel hyperactivity.

Molecular structure, expression, and bioactivity of B-cell-activating factor of the TNF family (BAFF) and its receptor BAFF-R in cats (Felis catus)

B-cell survival depends on signals induced by binding of B-cell activating factor (BAFF) to its receptor (BAFF-R). In this study, the full-length cDNAs of cat BAFF (cBAFF) and BAFF-R (cBAFF-R) were amplified from the spleen by reverse transcription PCR. The open reading frame of cBAFF cDNA encodes a protein of 285 amino acids containing a predicted transmembrane domain and a furin protease cleavage site, similar to mammalian, avian, and reptile BAFFs. The cBAFF-R gene encodes a 189 amino acid protein. Real-time quantitative PCR analyses revealed that the two genes are predominantly expressed in the spleen. csBAFF, EGFP/csBAFF, and cBAFF-R were efficiently expressed in Escherichia coli BL21 (DE3), as confirmed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and Western blotting analyses. After purification, the EGFP/csBAFF fusion protein showed a fluorescence spectrum similar to that of EGFP. Confocal laser scanning microscopy showed that EGFP/csBAFF bound to its receptor. In vitro, csBAFF promoted the survival of cat and mouse splenic B cells with/without a priming agent (Staphylococcus aureus Cowan 1, SAC) or anti-mouse IgM. Furthermore, it stimulated the survival of mouse B cells, similar to msBAFF. Recombinant cBAFF-R blocked the function of sBAFF in vitro. These findings indicate that csBAFF plays an important role in the survival of cat B cells and has functional cross reactivity between cats and other mammals, and suggest a role for the BAFF-BAFF-R system in regulating B-cell survival. Therefore, BAFF and BAFF-R show promise for enhancing the immune systems of animals.

Gutierrez L, Reyes AG, Absalón AE, Kelly S. Improving rifamycin production in Amycolatopsis mediterranei by expressing a Vitreoscilla hemoglobin (vhb) gene fused to a cytochrome P450 monooxygenase domain

Expression of the vhb gene encoding hemoglobin from Vitreoscilla stercoraria in several organisms, clearly enhances oxygen-dependent product formation. In a previous work, we expressed the vhb gene that encodes hemoglobin from V. stercoraria in Amycolatopsis mediterranei, resulting in an increase (oxygen-dependent formation) in rifamycin B production. In the present work, we first confirm; by heterologous expression in Escherichia coli, that rif-orf5 from the rifamycin biosynthetic gene cluster, really encodes a cytochrome P450 enzyme, which is the key step for oxygen incorporation in the final biosynthetic product. Likewise, we fused rif-orf5 to the vhb gene, as part of a genetic engineering strategy. The fused genes were used to generate an Amycolatopsis mediterranei transformant (Msb-HbCYP5). Interestingly, the fermentation of Msb-HbCYP5 manifested 1.5-fold higher rifamicin B production than the transformant with only the hemoglobin gene, and 2.2-fold higher than the parental strain.

ClusPro PeptiDock: efficient global docking of peptide recognition motifs using FFT

Summary

We present an approach for the efficient docking of peptide motifs to their free receptor structures. Using a motif based search, we can retrieve structural fragments from the Protein Data Bank (PDB) that are very similar to the peptide’s final, bound conformation. We use a Fast Fourier Transform (FFT) based docking method to quickly perform global rigid body docking of these fragments to the receptor. According to CAPRI peptide docking criteria, an acceptable conformation can often be found among the top-ranking predictions.

Availability and Implementation

The method is available as part of the protein-protein docking server ClusPro at https://peptidock.cluspro.org/nousername.php.

Supplementary information

Supplementary data are available at Bioinformatics online.

A Novel ShK-Like Toxic Peptide from the Transcriptome of the Cnidarian Palythoa caribaeorum Displays Neuroprotection and Cardioprotection in Zebrafish

Palythoa caribaeorum (class Anthozoa) is a zoantharian which, together with other cnidarians, like jellyfishes, hydra, and sea anemones, possesses specialized structures in its tissues, the cnidocytes, which deliver an array of toxins in order to capture prey and deter predators. The whole transcriptome of P. caribaeroum was deep sequenced, and a diversity of toxin-related peptide sequences were identified, and some retrieved for functional analysis. In this work, a peptide precursor containing a ShK domain, named PcShK3, was analyzed by means of computational processing, comprising structural phylogenetic analysis, model prediction, and dynamics simulation of peptide-receptor interaction. The combined data indicated that PcShK3 is a distinct peptide which is homologous to a cluster of peptides belonging to the ShK toxin family. In vivo, PcShK3 distributed across the vitelline membrane and accumulated in the yolk sac stripe of zebrafish larvae. Notably, it displayed a significant cardio-protective effect in zebrafish in concentrations inferior to the IC₅₀ (<43.53 ± 6.45 &micro;M), while in high concentrations (>IC₅₀), it accumulated in the blood and caused pericardial edema, being cardiotoxic to zebrafish larvae. Remarkably, PcShK3 suppressed the 6-OHDA-induced neurotoxicity on the locomotive behavior of zebrafish. The present results indicated that PcShK3 is a novel member of ShK toxin family, and has the intrinsic ability to induce neuro- and cardio-protective effects or cause cardiac toxicity, according to its effective concentration.

An alternative conformation of human TrpRS suggests a role of zinc in activating non-enzymatic function

Tryptophanyl-tRNA synthetase (TrpRS) in vertebrates contains a N-terminal extension in front of the catalytic core. Proteolytic removal of the N-terminal 93 amino acids gives rise to T2-TrpRS, which has potent anti-angiogenic activity mediated through its extracellular interaction with VE-cadherin. Zinc has been shown to have anti-angiogenic effects and can bind to human TrpRS. However, the connection between zinc and the anti-angiogenic function of TrpRS has not been explored. Here we report that zinc binding can induce structural relaxation in human TrpRS to facilitate the proteolytic generation of a T2-TrpRS-like fragment. The zinc-binding site is likely to be contained within T2-TrpRS, and the zinc-bound conformation of T2-TrpRS is mimicked by mutation H130R. We determined the crystal structure of H130R T2-TrpRS at 2.8 Å resolution, which reveals drastically different conformation from that of wild-type (WT) T2-TrpRS. The conformational change creates larger binding surfaces for VE-cadherin as suggested by molecular dynamic simulations. Surface plasmon resonance analysis indicates more than 50-fold increase in binding affinity of H130R T2-TrpRS for VE-cadherin, compared to WT T2-TrpRS. The enhanced interaction is also confirmed by a cell-based binding analysis. These results suggest that zinc plays an important role in activating TrpRS for angiogenesis regulation.

The antitumor activity and preliminary modeling on the potential mechanism of action of human peroxiredoxin-5

Goat peroxiredoxin-5 (gPRDX5) was verified as a good anti-cancer bioactive peptide (ACBP) against different tumor cell lines. Considering the immunogenicity between species for further therapeutic application, it is necessary to similarly investigate the antitumor activity of human peroxiredoxin-5 (hPRDX5) with 89% similarity in sequence to gPRDX5. In order to evaluate its antitumor activity, the potential anti-neoplastic effect of hPRDX5 on a mouse model was observed directly. The results of its in vivo antitumor activity suggested that hPRDX5 could resist immunosuppression by promoting lymphocyte proliferation and up-regulating the levels of serum cytokines. Meanwhile, PD-L1 was speculated as one of the targets of hPRDX5 to inhibit tumor by enhancing the immune activity according to a preliminary molecular docking study on the interactions between hPRDX5 and PD-L1. The modeling provides a basis for structural modification on hPRDX5/PD-L1 for further biological and biochemical study on the pathway blocking mechanism of hPRDX5. In this work, the results demonstrate that hPRDX5 displays efficient antitumor and immunoregulatory properties in the colon cancer C26/BALB/c and melanoma B16/C57Bl/6 mice tumor models, and suggest the potential of developing peptides from hPRDX5 as low molecular weight drug candidates for corresponding cancer immunotherapy.

Molecular Docking at a Glance

The current chapter introduces different aspects of molecular docking technique in order to give an overview to the readers about the topics which will be dealt with throughout this volume. Like many other fields of science, molecular docking studies has experienced a lagging period of slow and steady increase in terms of acquiring attention of scientific community as well as its frequency of application, followed by a pronounced era of exponential expansion in theory, methodology, areas of application and performance due to developments in related technologies such as computational resources and theoretical as well as experimental biophysical methods. In the following sections the evolution of molecular docking will be reviewed and its different components including methods, search algorithms, scoring functions, validation of the methods, and area of applications plus few case studies will be touched briefly.

Performance of ZDOCK and IRAD in CAPRI rounds 28-34

We report the performance of our protein-protein docking pipeline, including the ZDOCK rigid-body docking algorithm, on 19 targets in CAPRI rounds 28-34. Following the docking step, we reranked the ZDOCK predictions using the IRAD scoring function, pruned redundant predictions, performed energy landscape analysis, and utilized our interface prediction approach RCF. In addition, we applied constraints to the search space based on biological information that we culled from the literature, which increased the chance of making a correct prediction. For all but two targets we were able to find and apply biological information and we found the information to be highly accurate, indicating that effective incorporation of biological information is an important component for protein-protein docking. Proteins 2017; 85:408-416. © 2016 Wiley Periodicals, Inc.

G-actin guides p53 nuclear transport: potential contribution of monomeric actin in altered localization of mutant p53

p53 preserves genomic integrity by restricting anomaly at the gene level. Till date, limited information is available for cytosol to nuclear shuttling of p53; except microtubule-based trafficking route, which utilizes minus-end directed motor dynein. The present study suggests that monomeric actin (G-actin) guides p53 traffic towards the nucleus. Histidine-tag pull-down assay using purified p53(1–393)-His and G-actin confirms direct physical association between p53 and monomeric G-actin. Co-immunoprecipitation data supports the same. Confocal imaging explores intense perinuclear colocalization between p53 and G-actin. To address atomistic details of the complex, constraint-based docked model of p53:G-actin complex was generated based on crystal structures. MD simulation reveals that p53 DNA-binding domain arrests very well the G-actin protein. Docking benchmark studies have been carried out for a known crystal structure, 1YCS (complex between p53DBD and BP2), which validates the docking protocol we adopted. Co-immunoprecipitation study using “hot-spot” p53 mutants suggested reduced G-actin association with cancer-associated p53 conformational mutants (R175H and R249S). Considering these findings, we hypothesized that point mutation in p53 structure, which diminishes p53:G-actin complexation results in mutant p53 altered subcellular localization. Our model suggests p53Arg249 form polar-contact with Arg357 of G-actin, which upon mutation, destabilizes p53:G-actin interaction and results in cytoplasmic retention of p53R249S.

A rational design for improving the trypsin resistance of aflatoxin-detoxifizyme (ADTZ) based on molecular structure evaluation

The resistance of feed enzymes against proteases is crucial in livestock farming. In this study, the trypsin resistance of aflatoxin-detoxifizyme (ADTZ) is improved. ADTZ possesses 72 lys/arg residue sites, 45 of which are scattered on the outermost layers of the molecule (RSA≧25%). These 45 lys/arg sites could be target sites for trypsin hydrolysis. By considering shape-matching (including physical and secondary bond interactions) and the "induced fit-effect", we hypothesized that some of these lys/arg sites are vulnerable to trypsin. A protein-protein docking simulation method was used to avoid the massive computational requirements and to address the intricacy of selecting candidate sites, as candidate site selection is affected by space displacement. Optimal mutants (K244Q/K213C/K270T and R356E/K357T/R623C) were predicted by computational design with protein folding energy analysis and molecular dynamics simulations. A trypsin digestion assay was performed, and the mutants displayed much higher stability against trypsin hydrolysis compared to the native enzyme. Moreover, temperature- and pH-activity profiles revealed that the designed mutations did not affect the catalytic activity of the enzyme.

A human monoclonal antibody against HPV16 recognizes an immunodominant and neutralizing epitope partially overlapping with that of H16.V5

The presence of neutralizing epitopes in human papillomavirus (HPV) L1 virus-like particles (VLPs) is the structural basis of prophylactic vaccines. An anti-HPV16 neutralizing monoclonal antibody (N-mAb) 26D1 was isolated from a memory B cell of a human vaccinee. The pre-binding of heparan sulfate to VLPs inhibited the binding of both N-mAbs to the antigen, indicating that the epitopes are critical for viral cell attachment/entry. Hybrid VLP binding with surface loop swapping between types indicated the essential roles of the DE and FG loops for both 26D1 (DEa in particular) and H16.V5 binding. Specifically, Tyr(135) and Val(141) on the DEa loop were shown to be critical residues for 26D1 binding via site-directed mutagenesis. Partially overlap between the epitopes between 26D1 and H16.V5 was shown using pairwise epitope mapping, and their binding difference is demonstrated to be predominantly in DE loop region. In addition, 26D1 epitope is immunodominant epitope recognized by both antibodies elicited by the authentic virus from infected individuals and polyclonal antibodies from vaccinees. Overall, a partially overlapping but distinct neutralizing epitope from that of H16.V5 was identified using a human N-mAb, shedding lights to the antibody arrays as part of human immune response to vaccination and infection.

Predicted binding site information improves model ranking in protein docking using experimental and computer-generated target structures

Background

Protein-protein interactions (PPIs) mediate the vast majority of biological processes, therefore, significant efforts have been directed to investigate PPIs to fully comprehend cellular functions. Predicting complex structures is critical to reveal molecular mechanisms by which proteins operate. Despite recent advances in the development of new methods to model macromolecular assemblies, most current methodologies are designed to work with experimentally determined protein structures. However, because only computer-generated models are available for a large number of proteins in a given genome, computational tools should tolerate structural inaccuracies in order to perform the genome-wide modeling of PPIs.

Results

To address this problem, we developed eRank^PPI, an algorithm for the identification of near-native conformations generated by protein docking using experimental structures as well as protein models. The scoring function implemented in eRank^PPI employs multiple features including interface probability estimates calculated by eFindSite^PPI and a novel contact-based symmetry score. In comparative benchmarks using representative datasets of homo- and hetero-complexes, we show that eRank^PPI consistently outperforms state-of-the-art algorithms improving the success rate by ~10 %.

Conclusions

eRank^PPI was designed to bridge the gap between the volume of sequence data, the evidence of binary interactions, and the atomic details of pharmacologically relevant protein complexes. Tolerating structure imperfections in computer-generated models opens up a possibility to conduct the exhaustive structure-based reconstruction of PPI networks across proteomes. The methods and datasets used in this study are available at www.brylinski.org/erankppi.

Performance of ZDOCK in CAPRI rounds 20-26

We report the performance of our approaches for protein-protein docking and interface analysis in CAPRI rounds 20-26. At the core of our pipeline was the ZDOCK program for rigid-body protein-protein docking. We then reranked the ZDOCK predictions using the ZRANK or IRAD scoring functions, pruned and analyzed energy landscapes using clustering, and analyzed the docking results using our interface prediction approach RCF. When possible, we used biological information from the literature to apply constraints to the search space during or after the ZDOCK runs. For approximately half of the standard docking challenges we made at least one prediction that was acceptable or better. For the scoring challenges we made acceptable or better predictions for all but one target. This indicates that our scoring functions are generally able to select the correct binding mode.

In vitro affinity maturation and characterization of anti-P24 antibody for HIV diagnostic assay

P24 antigen is the main structural protein of HIV-1, its detection provide a means to aid the early diagnosis of HIV-1 infection. The aim of this study was to improve the selectivity and sensitivity of the HIV P24 diagnostic assay by developing a cohort of 9E8 affinity-matured antibodies through in vitro phage affinity maturation which was performed by complementarity determining region (CDR)-hot spot mutagenesis strategy. Antibody 9E8-491 had an affinity constant of 5.64 × 10(-11) M, which was 5.7-fold higher than that of the parent antibody (9E8). Furthermore, the affinity, sensitivity and specificity of 9E8-491 were higher than those of 9E8, which indicate that 9E8-491 is a good candidate detection antibody for HIV P24 assay. Structure analysis of matured variants revealed that most hydrogen bonds resided in HCDR3. Among the antibody-antigen predicted binding residues, Tyr(100A/100B) was the original conserved residue that was commonly present in HCDR3 of 9E8 and variants. Arg(100)/Asp(100C) was the major variant substitution that most likely influenced the binding differences among variants and 9E8 monoclonal antibody. Both efficient library panning and predicted structural data were in agreement that the binding residues were mostly located in HCDR3 and enabled identification of key residues that influence antibody affinity.

Toxin acidic residue evolutionary function-guided design of de novo peptide drugs for the immunotherapeutic target, the Kv1.3 channel

During the long-term evolution of animal toxins acting on potassium channels, the acidic residues can orientate the toxin binding interfaces by adjusting the molecular polarity. Based on the evolutionary function of toxin acidic residues, de novo peptide drugs with distinct binding interfaces were designed for the immunotherapeutic target, the Kv1.3 channel. Using a natural basic toxin, BmKTX, as a template, which contains 2 acidic residues (Asp19 and Asp33), we engineered two new peptides BmKTX-19 with 1 acidic residue (Asp33), and BmKTX-196 with 2 acidic residues (Asp6 and Asp33) through only adjusting acidic residue distribution for reorientation of BmKTX binding interface. Pharmacological experiments indicated that BmKTX-19 and BmKTX-196 peptides were specific inhibitors of the Kv1.3 channel and effectively suppressed cytokine secretion. In addition to the structural similarity between the designed and native peptides, both experimental alanine-scanning mutagenesis and computational simulation further indicated that the binding interface of wild-type BmKTX was successfully reoriented in BmKTX-19 and BmKTX-196, which adopted distinct toxin surfaces as binding interfaces. Together, these findings indicate not only the promising prospect of BmKTX-19 and BmKTX-196 as drug candidates but also the desirable feasibility of the evolution-guided peptide drug design for discovering numerous peptide drugs for the Kv1.3 channel.

Binding site and inhibitory mechanism of the mambalgin-2 pain-relieving peptide on acid-sensing ion channel 1a

Acid-sensing ion channels (ASICs) are neuronal proton-gated cation channels associated with nociception, fear, depression, seizure, and neuronal degeneration, suggesting roles in pain and neurological and psychiatric disorders. We have recently discovered black mamba venom peptides called mambalgin-1 and mambalgin-2, which are new three-finger toxins that specifically inhibit with the same pharmacological profile ASIC channels to exert strong analgesic effects in vivo. We now combined bioinformatics and functional approaches to uncover the molecular mechanism of channel inhibition by the mambalgin-2 pain-relieving peptide. Mambalgin-2 binds mainly in a region of ASIC1a involving the upper part of the thumb domain (residues Asp-349 and Phe-350), the palm domain of an adjacent subunit, and the β-ball domain (residues Arg-190, Asp-258, and Gln-259). This region overlaps with the acidic pocket (pH sensor) of the channel. The peptide exerts both stimulatory and inhibitory effects on ASIC1a, and we propose a model where mambalgin-2 traps the channel in a closed conformation by precluding the conformational change of the palm and β-ball domains that follows proton activation. These data help to understand inhibition by mambalgins and provide clues for the development of new optimized blockers of ASIC channels.

Association between WDR21A polymorphisms and airway responsiveness to inhaled corticosteroids in asthmatic patients

OBJECTIVE

Genetic polymorphism is partially responsible for the wide variation in the response of moderate-to-severe asthmatic patients to inhaled corticosteroids. The goal of the study was to examine polymorphisms in WDR21A, which encodes a putative glucocorticoid receptor (GR)-interacting protein, for their possible association with corticosteroid responsiveness.

METHODS

The change in forced expiratory volume in 1 s [FEV(1) (ΔFEV(1))] induced by 4 weeks of inhaled treatment with fluticasone propionate (1000 µg daily) was measured in 230 asthmatic patients. Fifteen single nucleotide polymorphisms (SNPs) of WDR21A were genotyped using a TaqMan assay, and 11 SNPs were used for further analysis. WDR21A transcripts were analyzed for variant splicing using reverse transcriptase-PCR. The WDR21A protein structure was predicted using a template-based modeling method and docked to a GR using Zdock.

RESULTS

Of the 11 SNPs and three haplotypes of WDR21A analyzed, only the intronic SNP -10073G>C appeared to affect ΔFEV(1). The ΔFEV(1) of the -10073C/C homozygous genotype was twice that of the -10073G/G and -10073C/G genotypes (P(corr)=0.04 in recessive model). No splicing variant of WDR21A was observed, regardless of genotype. The predicted WDR21A protein structure was similar to the Gβ(1) protein structure (template modeling-score=0.93).

CONCLUSION

The minor allele -10073C of WDR21A may induce a good response to inhaled corticosteroids possibly through competition with the Gβ(1) proteins for binding to GRs.

Engineering protein therapeutics: predictive performances of a structure-based virtual affinity maturation protocol

The implementation of a structure based virtual affinity maturation protocol and evaluation of its predictivity are presented. The in silico protocol is based on conformational sampling of the interface residues (using the Dead End Elimination/A* algorithm), followed by the estimation of the change of free energy of binding due to a point mutation, applying MM/PBSA calculations. Several implementations of the protocol have been evaluated for 173 mutations in 7 different protein complexes for which experimental data were available: the use of the Boltzamnn averaged predictor based on the free energy of binding (ΔΔG(*)) combined with the one based on its polar component only (ΔΔE(pol*)) led to the proposal of a subset of mutations out of which 45% would have successfully enhanced the binding. When focusing on those mutations that are less likely to be introduced by natural in vivo maturation methods (99 mutations with at least two base changes in the codon), the success rate is increased to 63%. In another evaluation, focusing on 56 alanine scanning mutations, the in silico protocol was able to detect 89% of the hot-spots.

Structure and function of ameloblastin as an extracellular matrix protein: adhesion, calcium binding, and CD63 interaction in human and mouse

The functional significance of extracellular matrix proteins in the life of vertebrates is underscored by a high level of sequence variability in tandem with a substantial degree of conservation in terms of cell-cell and cell-matrix adhesion interactions. Many extracellular matrix proteins feature multiple adhesion domains for successful attachment to substrates, such as integrin, CD63, and heparin. Here we have used homology and ab initio modeling algorithms to compare mouse ameloblastin (mAMBN) and human ameloblastin (hABMN) isoforms and to analyze their potential for cell adhesion and interaction with other matrix molecules as well as calcium binding. Sequence comparison between mAMBN and hAMBN revealed a 26-amino-acid deletion in mAMBN, corresponding to a helix-loop-helix frameshift. The human AMBN domain (174Q-201G), homologous to the mAMBN 157E-178I helix-loop-helix region, formed a helix-loop motif with an extended loop, suggesting a higher degree of flexibility of hAMBN compared with mAMBN, as confirmed by molecular dynamics simulation. Heparin-binding domains, CD63-interaction domains, and calcium-binding sites in both hAMBN and mAMBN support the concept of AMBN as an extracellular matrix protein. The high level of conservation between AMBN functional domains related to adhesion and differentiation was remarkable when compared with only 61% amino acid sequence homology.

Prediction of protein-protein binding free energies

We present an energy function for predicting binding free energies of protein-protein complexes, using the three-dimensional structures of the complex and unbound proteins as input. Our function is a linear combination of nine terms and achieves a correlation coefficient of 0.63 with experimental measurements when tested on a benchmark of 144 complexes using leave-one-out cross validation. Although we systematically tested both atomic and residue-based scoring functions, the selected function is dominated by residue-based terms. Our function is stable for subsets of the benchmark stratified by experimental pH and extent of conformational change upon complex formation, with correlation coefficients ranging from 0.61 to 0.66.

DEVELOPMENT OF AN AFFINITY EVALUATION AND PREDICTION SYSTEM BY USING THE SHAPE COMPLEMENTARITY CHARACTERISTIC BETWEEN PROTEINS

A system was developed to evaluate and predict the interaction between protein pairs by using the widely used shape complementarity search method as the algorithm for docking simulations between the proteins. This system, which we call the affinity evaluation and prediction (AEP) system, was used to evaluate the interaction between 20 protein pairs. The system first executes a "round robin" shape complementarity search of the target protein group, and evaluates the interaction of the complex structures obtained by shape complementarity search. These complex structures are selected by using a statistical procedure that we developed called "grouping". At a low prevalence of 5.0%, our AEP system predicted protein–protein interaction with 65.0% recall, 15.1% precision, 80.0% accuracy, and had an area under the curve (AUC) of 0.74. By optimizing the grouping process, our AEP system successfully predicted 13 protein pairs (among 20 pairs) that were biologically significant combinations. Our ultimate goal is to construct an affinity database that will provide crucial information obtained using our AEP system to cell biologists and drug designers.

Integrating atom-based and residue-based scoring functions for protein-protein docking

Most scoring functions for protein-protein docking algorithms are either atom-based or residue-based, with the former being able to produce higher quality structures and latter more tolerant to conformational changes upon binding. Earlier, we developed the ZRANK algorithm for reranking docking predictions, with a scoring function that contained only atom-based terms. Here we combine ZRANK's atom-based potentials with five residue-based potentials published by other labs, as well as an atom-based potential IFACE that we published after ZRANK. We simultaneously optimized the weights for selected combinations of terms in the scoring function, using decoys generated with the protein-protein docking algorithm ZDOCK. We performed rigorous cross validation of the combinations using 96 test cases from a docking benchmark. Judged by the integrative success rate of making 1000 predictions per complex, addition of IFACE and the best residue-based pair potential reduced the number of cases without a correct prediction by 38 and 27% relative to ZDOCK and ZRANK, respectively. Thus combination of residue-based and atom-based potentials into a scoring function can improve performance for protein-protein docking. The resulting scoring function is called IRAD (integration of residue- and atom-based potentials for docking) and is available at http://zlab.umassmed.edu.

Trifluoperazine regulation of calmodulin binding to Fas: a computational study

Death-inducing signaling complex (DISC) formation is a critical step in Fas-mediated signaling for apoptosis. Previous experiments have demonstrated that the calmodulin (CaM) antagonist, trifluoperazine (TFP) regulates CaM-Fas binding and affects Fas-mediated DISC formation. In this study, we investigated the anti-cooperative characteristics of TFP binding to CaM and the effect of TFP on the CaM-Fas interaction from both structural and thermodynamic perspectives using combined molecular dynamics simulations and binding free energy analyses. We studied the interactions of different numbers of TFP molecules with CaM and explored the effects of the resulting conformational changes in CaM on CaM-Fas binding. Results from these analyses showed that the number of TFP molecules bound to CaM directly influenced α-helix formation and hydrogen bond occupancy within the α-helices of CaM, contributing to the conformational and motion changes in CaM. These changes affected CaM binding to Fas, resulting in secondary structural changes in Fas and conformational and motion changes of Fas in CaM-Fas complexes, potentially perturbing the recruitment of Fas-associated death domain for DISC formation. The computational results from this study reveal the structural and molecular mechanisms that underlie the role of the CaM antagonist, TFP, in regulation of CaM-Fas binding and Fas-mediated DISC formation in a concentration-dependent manner.

Performance of ZDOCK and ZRANK in CAPRI rounds 13-19

We report the performance of the ZDOCK and ZRANK algorithms in CAPRI rounds 13-19 and introduce a novel measure atom contact frequency (ACF). To compute ACF, we identify the residues that most often make contact with the binding partner in the complete set of ZDOCK predictions for each target. We used ACF to predict the interface of the proteins, which, in combination with the biological data available in the literature, is a valuable addition to our docking pipeline. Furthermore, we incorporated a straightforward and efficient clustering algorithm with two purposes: (1) to determine clusters of similar docking poses (corresponding to energy funnels) and (2) to remove redundancies from the final set of predictions. With these new developments, we achieved at least one acceptable prediction for targets 29 and 36, at least one medium-quality prediction for targets 41 and 42, and at least one high-quality prediction for targets 37 and 40; thus, we succeeded for six out of a total of 12 targets.

A comprehensive model of the spectrin divalent tetramer binding region deduced using homology modeling and chemical cross-linking of a mini-spectrin

Spectrin dimer-tetramer interconversion is a critical contributor to red cell membrane stability, but some properties of spectrin tetramer formation cannot be studied effectively using monomeric recombinant domains. To address these limitations, a fused αβ mini-spectrin was produced that forms wild-type divalent tetramer complexes. Using this mini-spectrin, a medium-resolution structure of a seven-repeat bivalent tetramer was produced using homology modeling coupled with chemical cross-linking. Inter- and intramolecular cross-links provided critical distance constraints for evaluating and optimizing the best conformational model and appropriate docking interfaces. The two strands twist around each other to form a super-coiled, rope-like structure with the AB helix face of one strand associating with the opposing AC helix face. Interestingly, two tetramer site hereditary anemia mutations that exhibit wild-type binding in univalent head-to-head assays are located in the interstrand region. This suggests that perturbations of the interstrand region can destabilize spectrin tetramers and the membrane skeleton. The α subunit N-terminal cross-links to multiple sites on both strands, demonstrating that this non-homologous tail remains flexible and forms heterogeneous structures in the tetramer complex. Although no cross-links were observed involving the β subunit non-homologous C-terminal tail, several cross-links were observed only when this domain was present, suggesting it induces subtle conformational changes to the tetramer site region. This medium-resolution model provides a basis for further studies of the bivalent spectrin tetramer site, including analysis of functional consequences of interstrand interactions and mutations located at substantial molecular distances from the tetramer site.

The flexible C-terminal arm of the Lassa arenavirus Z-protein mediates interactions with multiple binding partners

The arenavirus genome encodes for a Z-protein, which contains a RING domain that coordinates two zinc ions, and has been identified as having several functional roles at various stages of the virus life cycle. Z-protein binds to multiple host proteins and has been directly implicated in the promotion of viral budding, repression of mRNA translation, and apoptosis of infected cells. Using homology models of the Z-protein from Lassa strain arenavirus, replica exchange molecular dynamics (MD) was used to refine the structures, which were then subsequently clustered. Population-weighted ensembles of low-energy cluster representatives were predicted based upon optimal agreement of the chemical shifts computed with the SPARTA program with the experimental NMR chemical shifts. A member of the refined ensemble was identified to be a potential binder of budding factor Tsg101 based on its correspondence to the structure of the HIV-1 Gag late domain when bound to Tsg101. Members of these ensembles were docked against the crystal structure of human eIF4E translation initiation factor. Two plausible binding modes emerged based upon their agreement with experimental observation, favorable interaction energies and stability during MD trajectories. Mutations to Z are proposed that would either inhibit both binding mechanisms or selectively inhibit only one mode. The C-terminal domain conformation of the most populated member of the representative ensemble shielded protein-binding recognition motifs for Tsg101 and eIF4E and represents the most populated state free in solution. We propose that C-terminal flexibility is key for mediating the different functional states of the Z-protein.

Homology model and potential virus-capsid binding site of a putative HEV receptor Grp78

P239, a truncated construct of the hepatitis E virus (HEV) ORF2 protein, has been proven able to bind with a chaperone, Grp78, in both an in vitro co-immune precipitation test and an in vivo cell model. We previously solved the crystal structure of E2s--the C-terminal domain of p239 involved in host interactions. In the present study, we built a 3D structure of Grp78 using homology modeling methods, and docked this molecule with E2s using the Zdockpro module of the InsightII software package. The modeled Grp78 structure was deemed feasible by profile 3D evaluation and molecular dynamic simulations. The docking result consists of six clusters of distinct complexes and C035 was selected as the most reasonable. The interacting interface of the predicted complex is comprised of the Grp78 linker region and nucleotide binding domain along with the E2s groove region and surrounding loops. Using energy, hydrogen bond and solvent accessible surface analyses, we identified a series of key residues that may be involved in the Grp78:E2s interaction. By comparing with the known structure of the Hsp70:J complex, we further concluded that the interaction of Grp78 and E2s could interrupt binding of Grp78 with the J domain, and in turn diminish or even eliminate the binding ability of the Grp78 substrate binding domain. The predicted series of key residues also provides clues for further research that should improve our understanding of the fundamental molecular mechanisms of HEV infection.

Structural insight into the role of thrombospondin-1 binding to calreticulin in calreticulin-induced focal adhesion disassembly

Thrombospondin-1 (TSP1) binding to calreticulin (CRT) on the cell surface stimulates association of CRT with LDL receptor-related protein (LRP1) to signal focal adhesion disassembly and engagement of cellular activities. The structural basis for this phenomenon is unknown. We studied the binding thermodynamics of the TSP1-CRT complex and the conformational changes in CRT induced by binding to TSP1 with combined binding free energy analysis, molecular dynamics simulation, and anisotropic network model restrained molecular dynamics simulation. Results showed that mutations of Lys 24 and Lys 32 in TSP1 to Ala and of amino acids 24-26 and 32-34 in CRT to Ala significantly weakened the binding of TSP1 and CRT, which is consistent with experimental results. Upon validation of the calculated binding affinity changes of the TSP1-CRT complex by mutations in key residues in TSP1 and CRT with the experimental results, we performed conformational analyses to understand the role of TSP1 binding to CRT in the induction of conformational changes in CRT. Conformational analyses showed that TSP1 binding to CRT resulted in a more "open" conformation and a significant rotational change for the CRT N-domain with respect to the CRT P-domain, which could expose the potential binding site(s) in CRT for binding to LRP1 to signal focal adhesion disassembly. Results offer structural insight into the role of TSP1 binding to CRT in CRT-induced focal adhesion disassembly.

Iron-sulfur cluster biosynthesis: characterization of IscU-IscS complex formation and a structural model for sulfide delivery to the [2Fe-2S] assembly site

Recent work on the bacterial iron-sulfur cluster (isc) family of gene products, and eukaryotic homologs, has advanced the molecular understanding of cellular mechanisms of iron-sulfur cluster biosynthesis. Members of the IscS family are pyridoxyl-5'-phosophate dependent proteins that deliver inorganic sulfide during assembly of the [2Fe-2S] cluster on the IscU scaffold protein. Herein it is demonstrated through calorimetry, fluorescence, and protein stability measurements that Thermotoga maritima IscS forms a 1:1 complex with IscU in a concentration-dependent manner (K(D) varying from 6 to 34 microM, over an IscS concentration range of approximately 2-50 microM). Docking simulations of representative IscU and IscS proteins reveal critical contact surfaces at the N-terminal helix of IscU and a C-terminal loop comprising a chaperone binding domain. Consistent with the isothermal titration calorimetry results described here, an overall dominant contribution of charged surfaces with a change in the molar heat capacity of binding, DeltaC(p) approximately 199.8 kcal K(-1) mol(-1), is observed that accounts for approximately 10% of the total accessible surface area at the binding interface. Both apo and holo IscUs and homologs were found to bind to IscS in an enthalpically driven reaction with comparable K(D) values. Both helix and loop regions are highly conserved among phylogenetically diverse organisms from a pool of archael, bacterial, fungal, and mammalian representatives.

Heterotrimeric G-proteins interact directly with cytoskeletal components to modify microtubule-dependent cellular processes

A large percentage of current drugs target G-protein-coupled receptors, which couple to well-known signaling pathways involving cAMP or calcium. G-proteins themselves may subserve a second messenger function. Here, we review the role of tubulin and microtubules in directly mediating effects of heterotrimeric G-proteins on neuronal outgrowth, shape and differentiation. G-protein-tubulin interactions appear to be regulated by neurotransmitter activity, and, in turn, regulate the location of Galpha in membrane microdomains (such as lipid rafts) or the cytosol. Tubulin binds with nanomolar affinity to Gsalpha, Gialpha1 and Gqalpha (but not other Galpha subunits) as well as Gbeta(1)gamma(2) subunits. Galpha subunits destabilize microtubules by stimulating tubulin's GTPase, while Gbetagamma subunits promote microtubule stability. The same region on Gsalpha that binds adenylyl cyclase and Gbetagamma also interacts with tubulin, suggesting that cytoskeletal proteins are novel Galpha effectors. Additionally, intracellular Gialpha-GDP, in concert with other GTPase proteins and Gbetagamma, regulates the position of the mitotic spindle in mitosis. Thus, G-protein activation modulates cell growth and differentiation by directly altering microtubule stability. Further studies are needed to fully establish a structural mechanism of this interaction and its role in synaptic plasticity.

The development of an affinity evaluation and prediction system by using protein-protein docking simulations and parameter tuning

A system was developed to evaluate and predict the interaction between protein pairs by using the widely used shape complementarity search method as the algorithm for docking simulations between the proteins. We used this system, which we call the affinity evaluation and prediction (AEP) system, to evaluate the interaction between 20 protein pairs. The system first executes a “round robin” shape complementarity search of the target protein group, and evaluates the interaction between the complex structures obtained by the search. These complex structures are selected by using a statistical procedure that we developed called ‘grouping’. At a prevalence of 5.0%, our AEP system predicted protein–protein interactions with a 50.0% recall, 55.6% precision, 95.5% accuracy, and an F-measure of 0.526. By optimizing the grouping process, our AEP system successfully predicted 10 protein pairs (among 20 pairs) that were biologically relevant combinations. Our ultimate goal is to construct an affinity database that will provide cell biologists and drug designers with crucial information obtained using our AEP system.

Conformation and free energy analyses of the complex of calcium-bound calmodulin and the Fas death domain

Previous studies have demonstrated a calcium-dependent interaction of calmodulin (CaM) and Fas that is regulated during Fas-induced apoptosis in several cell lines, including cholangiocarcinoma, Jurkat cells, and osteoclasts. The binding of CaM and Fas has been identified on residues 231-254 of Fas; the V254N point mutation decreases the CaM/Fas binding, and the C-terminal deletion mutation increases the CaM/Fas binding. Recent studies have shown that CaM is recruited into the Fas-mediated death-inducing signaling complex (DISC) in a calcium-dependent manner. However, the molecular mechanisms whereby Fas mutations and CaM/Fas binding might regulate Fas-mediated DISC formation are unknown. In this study we investigated the binding thermodynamics and conformation of the CaM/Fas complexes with combined explicit solvent molecular-dynamics simulations and implicit solvent binding free-energy calculations. The binding free-energy analysis demonstrated that the Fas V254N point mutation reduced its binding affinity with CaM. In contrast, the Fas mutant with the deletion of the 15 amino acid at the C-terminus increased its binding to CaM. These observations are consistent with previous findings from biochemical studies. Conformational analyses further showed that the Fas V254N mutation resulted in an unstable conformation, whereas the C-terminal deletion mutation stabilized the Fas conformation, and both mutations resulted in changes of the degree of correlation between the motions of the residues in Fas. Analysis of the CaM/Fas complex revealed that CaM/Fas binding stabilized the conformation of both CaM and Fas and changed the degree of correlated motion of the residues of CaM and Fas. The results presented here provide structural evidence for the roles of Fas mutations and CaM/Fas binding in Fas-induced DISC formation. Understanding the molecular mechanisms of CaM/Fas binding in Fas-mediated DISC formation should provide important insights into the function of Fas mutations and CaM in regulating Fas-mediated apoptosis.

Identification and rational redesign of peptide ligands to CRIP1, a novel biomarker for cancers

Cysteine-rich intestinal protein 1 (CRIP1) has been identified as a novel marker for early detection of cancers. Here we report on the use of phage display in combination with molecular modeling to identify a high-affinity ligand for CRIP1. Panning experiments using a circularized C7C phage library yielded several consensus sequences with modest binding affinities to purified CRIP1. Two sequence motifs, A1 and B5, having the highest affinities for CRIP1, were chosen for further study. With peptide structure information and the NMR structure of CRIP1, the higher-affinity A1 peptide was computationally redesigned, yielding a novel peptide, A1M, whose affinity was predicted to be much improved. Synthesis of the peptide and saturation and competitive binding studies demonstrated approximately a 10–28-fold improvement in the affinity of A1M compared to that of either A1 or B5 peptide. These techniques have broad application to the design of novel ligand peptides.

Breast cancer is one of the most frequently diagnosed malignancies in American females and is the second leading cause of cancer deaths in women. Several improvements in diagnostic protocols have enhanced our ability for earlier detection of breast cancer, resulting in improvement of therapeutic outcome and an increased survival rate for breast cancer patients. However, current early screening techniques are neither comprehensive nor infallible. Imaging techniques that improve breast cancer detection, localization, and evaluation of therapy are essential in combating the disease. Cysteine-rich intestinal protein 1 (CRIP1) has been identified as a novel marker for early detection of breast cancers. Here, we report the use of phage display and computational molecular modeling to identify a high-affinity ligand for CRIP1. Phage display panning experiments initially identified consensus peptide sequences with modest binding affinity to purified CRIP1. Using ab initio modeling of binding peptide structures, computational docking, and recently developed free energy estimation protocols, we redesigned the peptides to increase their affinity for CRIP1. Synthesis of the redesigned peptide and binding studies demonstrated approximately a 10–28-fold improvement in the binding affinity. The combination of computational and experimental techniques in this study demonstrates a potentially powerful tool in modulating protein–protein interactions.

Structural model of a complex between the heterotrimeric G protein, Gsalpha, and tubulin

A number of studies have demonstrated interplay between the cytoskeleton and G protein signaling. Many of these studies have determined a specific interaction between tubulin, the building block of microtubules, and G proteins. The alpha subunits of some heterotrimeric G proteins, including Gsalpha, have been shown to interact strongly with tubulin. Binding of Galpha to tubulin results in increased dynamicity of microtubules due to activation of GTPase of tubulin. Tubulin also activates Gsalpha via a direct transfer of GTP between these molecules. Structural insight into the interaction between tubulin and Gsalpha was required, and was determined, in this report, through biochemical and molecular docking techniques. Solid phase peptide arrays suggested that a portion of the amino terminus, alpha2-beta4 (the region between switch II and switch III) and alpha3-beta5 (just distal to the switch III region) domains of Gsalpha are important for interaction with tubulin. Molecular docking studies revealed the best-fit models based on the biochemical data, showing an interface between the two molecules that includes the adenylyl cyclase/Gbetagamma interaction regions of Gsalpha and the exchangeable nucleotide-binding site of tubulin. These structural models explain the ability of tubulin to facilitate GTP exchange on Galpha and the ability of Galpha to activate tubulin GTPase.

The performance of ZDOCK and ZRANK in rounds 6-11 of CAPRI

We present an evaluation of our protein-protein docking approach using the ZDOCK and ZRANK algorithms, in combination with structural clustering and filtering, utilizing biological data in Rounds 6-11 of the CAPRI docking experiment. We achieved at least one prediction of acceptable accuracy for five of six targets submitted. In addition, two targets resulted in medium-accuracy predictions. In the new scoring portion of the CAPRI exercise, we were able to attain at least one acceptable prediction for the three targets submitted and achieved three medium-accuracy predictions for Target 26. Scoring was performed using ZRANK, a new algorithm for reranking initial-stage docking predictions using a weighted energy function and no structural refinement. Here we outline a practical and successful docking strategy, given limited prior biological knowledge of the complex to be predicted.

Autoantibody-catalyzed hydrolysis of amyloid beta peptide

We describe IgM class human autoantibodies that hydrolyze amyloid beta peptide 1-40 (Abeta40). A monoclonal IgM from a patient with Waldenström's macroglobulinemia hydrolyzed Abeta40 at the Lys-28-Gly-29 bond and Lys-16-Ala-17 bonds. The catalytic activity was inhibited stoichiometrically by an electrophilic serine protease inhibitor. Treatment with the catalytic IgM blocked the aggregation and toxicity of Abeta40 in neuronal cell cultures. IgMs purified from the sera of patients with Alzheimer disease (AD) hydrolyzed Abeta40 at rates superior to IgMs from age-matched humans without dementia. IgMs from non-elderly humans expressed the least catalytic activity. The reaction rate was sufficient to afford appreciable degradation at physiological Abeta and IgM concentrations found in peripheral circulation. Increased Abeta concentrations in the AD brain are thought to induce neurodegenerative effects. Peripheral administration of Abeta binding antibodies has been suggested as a potential treatment of AD. Our results suggest that catalytic IgM autoantibodies can help clear Abeta, and they open the possibility of using catalytic Abs for AD immunotherapy.