Sequence clustering confounds AlphaFold2

Though typically associated with a single folded state, some globular proteins remodel their secondary and/or tertiary structures in response to cellular stimuli. AlphaFold21 (AF2) readily generates one dominant protein structure for these fold-switching (a.k.a. metamorphic) proteins2, but it often fails to predict their alternative experimentally observed structures3,4. Wayment-Steele, et al. steered AF2 to predict alternative structures of a few metamorphic proteins using a method they call AF-cluster5. However, their Paper lacks some essential controls needed to assess AF-cluster's reliability. We find that these controls show AF-cluster to be a poor predictor of metamorphic proteins. First, closer examination of the Paper's results reveals that random sequence sampling outperforms sequence clustering, challenging the claim that AF-cluster works by "deconvolving conflicting sets of couplings." Further, we observe that AF-cluster mistakes some single-folding KaiB homologs for fold switchers, a critical flaw bound to mislead users. Finally, proper error analysis reveals that AF-cluster predicts many correct structures with low confidence and some experimentally unobserved conformations with confidences similar to experimentally observed ones. For these reasons, we suggest using ColabFold6-based random sequence sampling7-augmented by other predictive approaches-as a more accurate and less computationally intense alternative to AF-cluster.

AlphaFold2 has more to learn about protein energy landscapes

Recent work suggests that AlphaFold2 (AF2)-a deep learning-based model that can accurately infer protein structure from sequence-may discern important features of folded protein energy landscapes, defined by the diversity and frequency of different conformations in the folded state. Here, we test the limits of its predictive power on fold-switching proteins, which assume two structures with regions of distinct secondary and/or tertiary structure. Using several implementations of AF2, including two published enhanced sampling approaches, we generated >280,000 models of 93 fold-switching proteins whose experimentally determined conformations were likely in AF2's training set. Combining all models, AF2 predicted fold switching with a modest success rate of ~25%, indicating that it does not readily sample both experimentally characterized conformations of most fold switchers. Further, AF2's confidence metrics selected against models consistent with experimentally determined fold-switching conformations in favor of inconsistent models. Accordingly, these confidence metrics-though suggested to evaluate protein energetics reliably-did not discriminate between low and high energy states of fold-switching proteins. We then evaluated AF2's performance on seven fold-switching proteins outside of its training set, generating >159,000 models in total. Fold switching was accurately predicted in one of seven targets with moderate confidence. Further, AF2 demonstrated no ability to predict alternative conformations of two newly discovered targets without homologs in the set of 93 fold switchers. These results indicate that AF2 has more to learn about the underlying energetics of protein ensembles and highlight the need for further developments of methods that readily predict multiple protein conformations.

ColabFold predicts alternative protein structures from single sequences, coevolution unnecessary for AF-cluster

Though typically associated with a single folded state, globular proteins are dynamic and often assume alternative or transient structures important for their functions1,2. Wayment-Steele, et al. steered ColabFold3 to predict alternative structures of several proteins using a method they call AF-cluster4. They propose that AF-cluster "enables ColabFold to sample alternate states of known metamorphic proteins with high confidence" by first clustering multiple sequence alignments (MSAs) in a way that "deconvolves" coevolutionary information specific to different conformations and then using these clusters as input for ColabFold. Contrary to this Coevolution Assumption, clustered MSAs are not needed to make these predictions. Rather, these alternative structures can be predicted from single sequences and/or sequence similarity, indicating that coevolutionary information is unnecessary for predictive success and may not be used at all. These results suggest that AF-cluster's predictive scope is likely limited to sequences with distinct-yet-homologous structures within ColabFold's training set.

Identification of a covert evolutionary pathway between two protein folds

Although homologous protein sequences are expected to adopt similar structures, some amino acid substitutions can interconvert α-helices and β-sheets. Such fold switching may have occurred over evolutionary history, but supporting evidence has been limited by the: (1) abundance and diversity of sequenced genes, (2) quantity of experimentally determined protein structures, and (3) assumptions underlying the statistical methods used to infer homology. Here, we overcome these barriers by applying multiple statistical methods to a family of ~600,000 bacterial response regulator proteins. We find that their homologous DNA-binding subunits assume divergent structures: helix-turn-helix versus α-helix + β-sheet (winged helix). Phylogenetic analyses, ancestral sequence reconstruction, and AlphaFold2 models indicate that amino acid substitutions facilitated a switch from helix-turn-helix into winged helix. This structural transformation likely expanded DNA-binding specificity. Our approach uncovers an evolutionary pathway between two protein folds and provides a methodology to identify secondary structure switching in other protein families.

Distinguishing features of fold-switching proteins

Though many folded proteins assume one stable structure that performs one function, a small-but-increasing number remodel their secondary and tertiary structures and change their functions in response to cellular stimuli. These fold-switching proteins regulate biological processes and are associated with autoimmune dysfunction, severe acute respiratory syndrome coronavirus-2 infection, and more. Despite their biological importance, it is difficult to computationally predict fold switching. With the aim of advancing computational prediction and experimental characterization of fold switchers, this review discusses several features that distinguish fold-switching proteins from their single-fold and intrinsically disordered counterparts. First, the isolated structures of fold switchers are less stable and more heterogeneous than single folders but more stable and less heterogeneous than intrinsically disordered proteins (IDPs). Second, the sequences of single fold, fold switching, and intrinsically disordered proteins can evolve at distinct rates. Third, proteins from these three classes are best predicted using different computational techniques. Finally, late-breaking results suggest that single folders, fold switchers, and IDPs have distinct patterns of residue-residue coevolution. The review closes by discussing high-throughput and medium-throughput experimental approaches that might be used to identify new fold-switching proteins.

The efficacy of intravenous tranexamic acid administration at induction in definitive hip fracture surgery: Is there a role?

Tranexamic acid (TXA) is a cheap and powerful drug that has several uses in surgery and is well established in elective orthopaedic surgery. At present, limited small studies have looked into its role in the acute hip fracture. Transfusion in the geriatric population presents risks and increased costs to healthcare systems around the world. Our retrospective study looks at the role of TXA administration at induction for both intracapsular fracture requiring hemiarthroplasty and our preferred method of fixation of extracapsular fracture by intramedullary nail (IM nail). We show a statistically significant reduction in the number of patients requiring transfusion as well as mean haemoglobin (Hb) drop in those undergoing hemiarthroplasty. This was not replicated in those undergoing IM nail fixation. Both groups showed no increase in 1-year mortality or thromboembolic events following TXA administration. These results support the use of TXA for hemiarthroplasty for intracapsular hip fractures over the age of 60.

OBJECTIVES

The aim of this pre and post interventional study looks at the effects of intravenous administration of tranexamic acid on induction for elderly patients undergoing hemiarthroplasty or intramedullary nail fixation for hip fractures.

DESIGN

Pre and post interventional, randomised observational study SETTING: Large hip fracture unit, Level 2 Trauma Centre, single centre PATIENTS: Two arms of the study looking at those aged above the age of 60 undergoing hemiarthroplasty and intramedullary nail fixation without and with tranexamic acid on induction.

RESULTS

12.1% of hemiarthroplasties required post-operative transfusion without tranexamic acid compared to 2.6% of those with tranexamic acid (n=15 vs n=3 respectively, p=0.006). Equally, the mean Hb drop in g/L is reduced in those with tranexamic acid compared to those without (mean Hb = 14.6 vs 17.7 respectively, p=0.034). This was not replicated in the IM nail group between those without and those with tranexamic acid (n=31 vs n=20 respectively, p= 0.16). The mean Hb drop in g/L was not statistically significant in the tranexamic acid arm compared to without (mean Hb = 19.2 vs mean Hb = 21.9, p=0.11). Gross reporting of thromboembolic events did not demonstrate an increase in the number of those with DVT, PE, MI or stroke. 1-year mortality was not statistically significant in either hemiarthroplasty or IM nail fixation following tranexamic acid administration.

CONCLUSIONS

Tranexamic acid both statistically significantly reduces the number of patients requiring transfusion post hemiarthroplasty and also the value of mean Hb drop without appearing to increase in thromboembolic events or 1 year mortality rates. This does not appear to be emulated in the IM nail fixation although both thrombotic events and 1-year mortality rates are also not affected by administration of TXA. We propose that TXA has a role in hemiarthroplasty surgery in reducing post-operative transfusions.

LEVEL OF EVIDENCE

Level 3 - retrospective cohort study.

Plausible blockers of Spike RBD in SARS-CoV2-molecular design and underlying interaction dynamics from high-level structural descriptors

Abstract

COVID-19 is characterized by an unprecedented abrupt increase in the viral transmission rate (SARS-CoV-2) relative to its pandemic evolutionary ancestor, SARS-CoV (2003). The complex molecular cascade of events related to the viral pathogenicity is triggered by the Spike protein upon interacting with the ACE2 receptor on human lung cells through its receptor binding domain (RBD_Spike). One potential therapeutic strategy to combat COVID-19 could thus be limiting the infection by blocking this key interaction. In this current study, we adopt a protein design approach to predict and propose non-virulent structural mimics of the RBD_Spike which can potentially serve as its competitive inhibitors in binding to ACE2. The RBD_Spike is an independently foldable protein domain, resilient to conformational changes upon mutations and therefore an attractive target for strategic re-design. Interestingly, in spite of displaying an optimal shape fit between their interacting surfaces (attributed to a consequently high mutual affinity), the RBD_Spike–ACE2 interaction appears to have a quasi-stable character due to a poor electrostatic match at their interface. Structural analyses of homologous protein complexes reveal that the ACE2 binding site of RBD_Spike has an unusually high degree of solvent-exposed hydrophobic residues, attributed to key evolutionary changes, making it inherently “reaction-prone.” The designed mimics aimed to block the viral entry by occupying the available binding sites on ACE2, are tested to have signatures of stable high-affinity binding with ACE2 (cross-validated by appropriate free energy estimates), overriding the native quasi-stable feature. The results show the apt of directly adapting natural examples in rational protein design, wherein, homology-based threading coupled with strategic “hydrophobic ↔ polar” mutations serve as a potential breakthrough.

Graphical Abstract

Supplementary Information

The online version contains supplementary material available at 10.1007/s00894-021-04779-0.

Structural motifs in protein cores and at protein-protein interfaces are different

Structures of proteins and protein-protein complexes are determined by the same physical principles and thus share a number of similarities. At the same time, there could be differences because in order to function, proteins interact with other molecules, undergo conformations changes, and so forth, which might impose different restraints on the tertiary versus quaternary structures. This study focuses on structural properties of protein-protein interfaces in comparison with the protein core, based on the wealth of currently available structural data and new structure-based approaches. The results showed that physicochemical characteristics, such as amino acid composition, residue-residue contact preferences, and hydrophilicity/hydrophobicity distributions, are similar in protein core and protein-protein interfaces. On the other hand, characteristics that reflect the evolutionary pressure, such as structural composition and packing, are largely different. The results provide important insight into fundamental properties of protein structure and function. At the same time, the results contribute to better understanding of the ways to dock proteins. Recent progress in predicting structures of individual proteins follows the advancement of deep learning techniques and new approaches to residue coevolution data. Protein core could potentially provide large amounts of data for application of the deep learning to docking. However, our results showed that the core motifs are significantly different from those at protein-protein interfaces, and thus may not be directly useful for docking. At the same time, such difference may help to overcome a major obstacle in application of the coevolutionary data to docking-discrimination of the intramolecular information not directly relevant to docking.

How to choose templates for modeling of protein complexes: Insights from benchmarking template-based docking

Comparative docking is based on experimentally determined structures of protein-protein complexes (templates), following the paradigm that proteins with similar sequences and/or structures form similar complexes. Modeling utilizing structure similarity of target monomers to template complexes significantly expands structural coverage of the interactome. Template-based docking by structure alignment can be performed for the entire structures or by aligning targets to the bound interfaces of the experimentally determined complexes. Systematic benchmarking of docking protocols based on full and interface structure alignment showed that both protocols perform similarly, with top 1 docking success rate 26%. However, in terms of the models' quality, the interface-based docking performed marginally better. The interface-based docking is preferable when one would suspect a significant conformational change in the full protein structure upon binding, for example, a rearrangement of the domains in multidomain proteins. Importantly, if the same structure is selected as the top template by both full and interface alignment, the docking success rate increases 2-fold for both top 1 and top 10 predictions. Matching structural annotations of the target and template proteins for template detection, as a computationally less expensive alternative to structural alignment, did not improve the docking performance. Sophisticated remote sequence homology detection added templates to the pool of those identified by structure-based alignment, suggesting that for practical docking, the combination of the structure alignment protocols and the remote sequence homology detection may be useful in order to avoid potential flaws in generation of the structural templates library.

A framework to rank genomic alterations as targets for cancer precision medicine: the ESMO Scale for Clinical Actionability of molecular Targets (ESCAT)

Background

In order to facilitate implementation of precision medicine in clinical management of cancer, there is a need to harmonise and standardise the reporting and interpretation of clinically relevant genomics data.

Methods

The European Society for Medical Oncology (ESMO) Translational Research and Precision Medicine Working Group (TR and PM WG) launched a collaborative project to propose a classification system for molecular aberrations based on the evidence available supporting their value as clinical targets. A group of experts from several institutions was assembled to review available evidence, reach a consensus on grading criteria and present a classification system. This was then reviewed, amended and finally approved by the ESMO TR and PM WG and the ESMO leadership.

Results

This first version of the ESMO Scale of Clinical Actionability for molecular Targets (ESCAT) defines six levels of clinical evidence for molecular targets according to the implications for patient management: tier I, targets ready for implementation in routine clinical decisions; tier II, investigational targets that likely define a patient population that benefits from a targeted drug but additional data are needed; tier III, clinical benefit previously demonstrated in other tumour types or for similar molecular targets; tier IV, preclinical evidence of actionability; tier V, evidence supporting co-targeting approaches; and tier X, lack of evidence for actionability.

Conclusions

The ESCAT defines clinical evidence-based criteria to prioritise genomic alterations as markers to select patients for targeted therapies. This classification system aims to offer a common language for all the relevant stakeholders in cancer medicine and drug development.

Blind prediction of homo- and hetero-protein complexes: The CASP13-CAPRI experiment

We present the results for CAPRI Round 46, the third joint CASP-CAPRI protein assembly prediction challenge. The Round comprised a total of 20 targets including 14 homo-oligomers and 6 heterocomplexes. Eight of the homo-oligomer targets and one heterodimer comprised proteins that could be readily modeled using templates from the Protein Data Bank, often available for the full assembly. The remaining 11 targets comprised 5 homodimers, 3 heterodimers, and two higher-order assemblies. These were more difficult to model, as their prediction mainly involved "ab-initio" docking of subunit models derived from distantly related templates. A total of ~30 CAPRI groups, including 9 automatic servers, submitted on average ~2000 models per target. About 17 groups participated in the CAPRI scoring rounds, offered for most targets, submitting ~170 models per target. The prediction performance, measured by the fraction of models of acceptable quality or higher submitted across all predictors groups, was very good to excellent for the nine easy targets. Poorer performance was achieved by predictors for the 11 difficult targets, with medium and high quality models submitted for only 3 of these targets. A similar performance "gap" was displayed by scorer groups, highlighting yet again the unmet challenge of modeling the conformational changes of the protein components that occur upon binding or that must be accounted for in template-based modeling. Our analysis also indicates that residues in binding interfaces were less well predicted in this set of targets than in previous Rounds, providing useful insights for directions of future improvements.

Structural changes in DNA-binding proteins on complexation

Characterization and prediction of the DNA-biding regions in proteins are essential for our understanding of how proteins recognize/bind DNA. We analyze the unbound (U) and the bound (B) forms of proteins from the protein–DNA docking benchmark that contains 66 binary protein–DNA complexes along with their unbound counterparts. Proteins binding DNA undergo greater structural changes on complexation (in particular, those in the enzyme category) than those involved in protein–protein interactions (PPI). While interface atoms involved in PPI exhibit an increase in their solvent-accessible surface area (ASA) in the bound form in the majority of the cases compared to the unbound interface, protein–DNA interactions indicate increase and decrease in equal measure. In 25% structures, the U form has missing residues which are located in the interface in the B form. The missing atoms contribute more toward the buried surface area compared to other interface atoms. Lys, Gly and Arg are prominent in disordered segments that get ordered in the interface on complexation. In going from U to B, there may be an increase in coil and helical content at the expense of turns and strands. Consideration of flexibility cannot distinguish the interface residues from the surface residues in the U form.

Clinical and molecular characterization of patients with cancer of unknown primary in the modern era

Background

On the basis of historical data, patients with cancer of unknown primary (CUP) are generally assumed to have a dismal prognosis with overall survival of less than 1 year. Treatment is typically cytotoxic chemotherapy guided by histologic features and the pattern of metastatic spread. The purpose of this study was to provide a clinical and pathologic description of patients with CUP in the modern era, to define the frequency of clinically actionable molecular alterations in this population, to determine how molecular testing can alter therapeutic decisions, and to investigate novel uses of next-generation sequencing in the evaluation and treatment of patients with CUP.

Patients and methods

Under Institutional Review Board approval, we identified all CUP patients evaluated at our institution over a recent 2-year period. We documented demographic information, clinical outcomes, pathologic evaluations, next-generation sequencing of available tumor tissue, use of targeted therapies, and clinical trial enrollment.

Results

We identified 333 patients with a diagnosis of CUP evaluated at our institution from 1 January 2014 through 30 June 2016. Of these patients, 150 had targeted next-generation sequencing carried out on available tissue. Median overall survival in this cohort was 13 months. Forty-five of 150 (30%) patients had potentially targetable genomic alterations identified by tumor molecular profiling, and 15 of 150 (10%) received targeted therapies. Dominant mutation signatures were identified in 21 of 150 (14%), largely implicating exogenous mutagen exposures such as ultraviolet radiation and tobacco.

Conclusions

Patients with CUP represent a heterogeneous population, harboring a variety of potentially targetable alterations. Next-generation sequencing may provide an opportunity for CUP patients to benefit from novel personalized therapies.

Oncologist use and perception of large panel next-generation tumor sequencing

BACKGROUND

Genomic profiling is increasingly incorporated into oncology research and the clinical care of cancer patients. We sought to determine physician perception and use of enterprise-scale clinical sequencing at our center, including whether testing changed management and the reasoning behind this decision-making.

PATIENTS AND METHODS

All physicians who consented patients to MSK-IMPACT, a next-generation hybridization capture assay, in tumor types where molecular profiling is not routinely performed were asked to complete a questionnaire for each patient. Physician determination of genomic 'actionability' was compared to an expertly curated knowledgebase of somatic variants. Reported management decisions were compared to chart review.

RESULTS

Responses were received from 146 physicians pertaining to 1932 patients diagnosed with 1 of 49 cancer types. Physicians indicated that sequencing altered management in 21% (331/1593) of patients in need of a treatment change. Among those in whom treatment was not altered, physicians indicated the presence of an actionable alteration in 55% (805/1474), however, only 45% (362/805) of these cases had a genomic variant annotated as actionable by expert curators. Further evaluation of these patients revealed that 66% (291/443) had a variant in a gene associated with biologic but not clinical evidence of actionability or a variant of unknown significance in a gene with at least one known actionable alteration. Of the cases annotated as actionable by experts, physicians identified an actionable alteration in 81% (362/445). In total, 13% (245/1932) of patients were enrolled to a genomically matched trial.

CONCLUSION

Although physician and expert assessment differed, clinicians demonstrate substantial awareness of the genes associated with potential actionability and report using this knowledge to inform management in one in five patients.

CLINICAL TRIAL NUMBER

NCT01775072.

Changes in protein structure at the interface accompanying complex formation

Protein interactions are essential in all biological processes. The changes brought about in the structure when a free component forms a complex with another molecule need to be characterized for a proper understanding of molecular recognition as well as for the successful implementation of docking algorithms. Here, unbound (U) and bound (B) forms of protein structures from the Protein-Protein Interaction Affinity Database are compared in order to enumerate the changes that occur at the interface atoms/residues in terms of the solvent-accessible surface area (ASA), secondary structure, temperature factors (B factors) and disorder-to-order transitions. It is found that the interface atoms optimize contacts with the atoms in the partner protein, which leads to an increase in their ASA in the bound interface in the majority (69%) of the proteins when compared with the unbound interface, and this is independent of the root-mean-square deviation between the U and B forms. Changes in secondary structure during the transition indicate a likely extension of helices and strands at the expense of turns and coils. A reduction in flexibility during complex formation is reflected in the decrease in B factors of the interface residues on going from the U form to the B form. There is, however, no distinction in flexibility between the interface and the surface in the monomeric structure, thereby highlighting the potential problem of using B factors for the prediction of binding sites in the unbound form for docking another protein. 16% of the proteins have missing (disordered) residues in the U form which are observed (ordered) in the B form, mostly with an irregular conformation; the data set also shows differences in the composition of interface and non-interface residues in the disordered polypeptide segments as well as differences in their surface burial.

Proline substitutions in a Mip-like peptidyl-prolyl cis-trans isomerase severely affect its structure, stability, shape and activity

FKBP22, an Escherichia coli-specific peptidyl-prolyl cis-trans isomerase, shows substantial homology with the Mip-like virulence factors. Mip-like proteins are homodimeric and possess a V-shaped conformation. Their N-terminal domains form dimers, whereas their C-terminal domains bind protein/peptide substrates and distinct inhibitors such as rapamycin and FK506. Interestingly, the two domains of the Mip-like proteins are separated by a lengthy, protease-susceptible α-helix. To delineate the structural requirement of this domain-connecting region in Mip-like proteins, we have investigated a recombinant FKBP22 (rFKBP22) and its three point mutants I65P, V72P and A82P using different probes. Each mutant harbors a Pro substitution mutation at a distinct location in the hinge region. We report that the three mutants are not only different from each other but also different from rFKBP22 in structure and activity. Unlike rFKBP22, the three mutants were unfolded by a non-two state mechanism in the presence of urea. In addition, the stabilities of the mutants, particularly I65P and V72P, differed considerably from that of rFKBP22. Conversely, the rapamycin binding affinity of no mutant was different from that of rFKBP22. Of the mutants, I65P showed the highest levels of structural/functional loss and dissociated partly in solution. Our computational study indicated a severe collapse of the V-shape in I65P due to the anomalous movement of its C-terminal domains. The α-helical nature of the domain-connecting region is, therefore, critical for the Mip-like proteins.

Flexibility in the N-terminal actin-binding domain: clues from in silico mutations and molecular dynamics

Dystrophin is a long, rod-shaped cytoskeleton protein implicated in muscular dystrophy (MDys). Utrophin is the closest autosomal homolog of dystrophin. Both proteins have N-terminal actin-binding domain (N-ABD), a central rod domain and C-terminal region. N-ABD, composed of two calponin homology (CH) subdomains joined by a helical linker, harbors a few disease causing missense mutations. Although the two proteins share considerable homology (>72%) in N-ABD, recent structural and biochemical studies have shown that there are significant differences (including stability, mode of actin-binding) and their functions are not completely interchangeable. In this investigation, we have used extensive molecular dynamics simulations to understand the differences and the similarities of these two proteins, along with another actin-binding protein, fimbrin. In silico mutations were performed to identify two key residues that might be responsible for the dynamical difference between the molecules. Simulation points to the inherent flexibility of the linker region, which adapts different conformations in the wild type dystrophin. Mutations T220V and G130D in dystrophin constrain the flexibility of the central helical region, while in the two known disease-causing mutants, K18N and L54R, the helicity of the region is compromised. Phylogenetic tree and sequence analysis revealed that dystrophin and utrophin genes have probably originated from the same ancestor. The investigation would provide insight into the functional diversity of two closely related proteins and fimbrin, and contribute to our understanding of the mechanism of MDys.

Identification of the target DNA sequence and characterization of DNA binding features of HlyU, and suggestion of a redox switch for hlyA expression in the human pathogen Vibrio cholerae from in silico studies

HlyU, a transcriptional regulator common in many Vibrio species, activates the hemolysin gene hlyA in Vibrio cholerae, the rtxA1 operon in Vibrio vulnificus and the genes of plp-vah1 and rtxACHBDE gene clusters in Vibrio anguillarum. The protein is also proposed to be a potential global virulence regulator for V. cholerae and V. vulnificus. Mechanisms of gene control by HlyU in V. vulnificus and V. anguillarum are reported. However, detailed elucidation of the interaction of HlyU in V. cholerae with its target DNA at the molecular level is not available. Here we report a 17-bp imperfect palindrome sequence, 5′-TAATTCAGACTAAATTA-3′, 173 bp upstream of hlyA promoter, as the binding site of HlyU. This winged helix-turn-helix protein binds necessarily as a dimer with the recognition helices contacting the major grooves and the β-sheet wings, the minor grooves. Such interactions enhance hlyA promoter activity in vivo. Mutations affecting dimerization as well as those in the DNA–protein interface hamper DNA binding and transcription regulation. Molecular dynamic simulations show hydrogen bonding patterns involving residues at the mutation sites and confirmed their importance in DNA binding. On binding to HlyU, DNA deviates by ∼68º from linearity. Dynamics also suggest a possible redox control in HlyU.

Reassessing buried surface areas in protein-protein complexes

The buried surface area (BSA), which measures the size of the interface in a protein-protein complex may differ from the accessible surface area (ASA) lost upon association (which we call DSA), if conformation changes take place. To evaluate the DSA, we measure the ASA of the interface atoms in the bound and unbound states of the components of 144 protein-protein complexes taken from the Protein-Protein Interaction Affinity Database of Kastritis et al. (2011). We observe differences exceeding 20%, and a systematic bias in the distribution. On average, the ASA calculated in the bound state of the components is 3.3% greater than in their unbound state, and the BSA, 7% greater than the DSA. The bias is observed even in complexes where the conformation changes are small. An examination of the bound and unbound structures points to a possible origin: local movements optimize contacts with the other component at the cost of internal contacts, and presumably also the binding free energy.

Protein l-isoaspartyl-O-methyltransferase of Vibrio cholerae: interaction with cofactors and effect of osmolytes on unfolding

Protein l-isoaspartyl-O-methyltransferase (PIMT) is an ubiquitous enzyme widely distributed in cells and plays a role in the repair of deamidated and isomerized proteins. In this study, we show that this enzyme is present in cytosolic extract of Vibrio cholerae, an enteric pathogenic Gram-negative bacterium and is enzymatically active. Additionally, we focus on the detailed biophysical characterization of the recombinant PIMT from V. cholerae to gain insight into its structure, stability and the cofactor binding. The equilibrium denaturation of PIMT has been studied using tryptophan fluorescence and CD spectroscopy. The far- and near-UV CD, as well as fluorescence experiments reveal the presence of a non-native intermediate in the folding pathway. Binding of the hydrophobic fluorescent probe, bis-ANS, to the intermediate occurs with high affinity because of the exposure of the hydrophobic clusters during the unfolding process. The existence of the probable intermediate has also been confirmed from limited tryptic digestion and DLS experiments. The protein shows higher binding affinity for AdoHcy, in comparison to AdoMet, and the binding increases the midpoint of thermal unfolding by 6 and 5 °C, respectively. Modeling and molecular dynamics simulations also support the higher stability of the protein in presence of AdoHcy.

Abstract P1-05-10: Targeting breast cancer metastasis through disruption of novel PELP1-G9a complex

Although there are several therapies available for the treatment of breast cancer, many patients have tumor recurrences that ultimately metastasize. There are several oncogenic estrogen receptor alpha (ERα) coregulators that promote breast cancer metastasis and targeting these coregulators could be a promising cancer therapeutic. One coactivator of ERα that is known to be upregulated in breast cancer and promote metastasis is proline-, glutamic acid-, and leucine-rich protein 1 (PELP1). PELP1 affects the migratory and invasive potential of breast cancer cells both in vitro and in vivo and modulates the expression of several genes involved in the epithelial to mesenchymal transition (EMT) including Snail, Twist and Zeb1. To elucidate the mechanism by which PELP1 promotes metastasis, we studied the proteins that interact with PELP1 and promote cancer metastasis. We identified a novel PELP1-interacting protein G9a (Bat8/KMT1C/EHMT2), a histone lysine methyltransferase known to overexpressed in aggressive breast cancer and promote invasion and metastasis. G9a contributes to the epigenetic silencing of tumor suppressor genes, interacts with Snail to promote EMT and its knockdown inhibits cell migration and invasion as well as lung metastasis. The objective of this study is to characterize the interaction of PELP1 and G9a in the promotion of breast cancer metastasis. The complex formation of PELP1 and G9a was confirmed by an in vivo immunoprecipitation and an in vitro binding assay. The region of PELP1 that binds to G9a was mapped further by PELP-GST deletions. To determine whether formation of the complex is necessary for PELP1's oncogenic functions including the promotion of metastasis, we developed a peptide to disrupt the complex formation. The sequence of the peptide has homology to both PELP1 and G9a with a TAT-sequence to enable cellular uptake. Cellular uptake was confirmed by fluorescent microscopy while biotin-avidin peptide pull-down assays confirmed PELP1-peptide binding. A peptide competition assay confirmed that the peptide could interrupt PELP1-G9a interaction. Treatment of two ER-positive, PELP1-overexpressing breast cancer cells (MCF7-PELP and ZR75-PELP) with the peptide significantly inhibited the PELP-1 mediated proliferation. Peptide treatment also substantially inhibited PELP1-mediated cell migration in Boyden chamber assays as well as decreased anchorage independence as seen by soft agar assay. Interestingly, disrupting PELP1-G9a interaction with the peptide also sensitized tamoxifen and letrozole resistant cells to the respective hormonal therapy. Mechanistic studies revealed that PELP1-G9a interactions play a critical role in epigenetic changes in therapy resistant cells. In conclusion, our studies identified a novel complex involved in breast cancer metastasis. The interaction of PELP1 and G9a is required for PELP1-mediated oncogenic properties and disruption of the complex by peptide treatment results in decreased metastatic potential and changes in epigenetic modifications. The novel peptide could be used for therapeutic targeting of breast cancer metastasis and therapy resistance. This work was supported by the NIH grant CA095681 and CPRIT pre-doctoral fellowship RP101491.

Citation Information: Cancer Res 2012;72(24 Suppl):Abstract nr P1-05-10.

Discrimination of ligands with different flexibilities resulting from the plasticity of the binding site in tubulin

Tubulin, an α,β heterodimer, has four distinct ligand binding sites (for paclitaxel, peloruside/laulimalide, vinca, and colchicine). The site where colchicine binds is a promising drug target for arresting cell division and has been observed to accommodate compounds that are structurally diverse but possess comparable affinity. This investigation, using two such structurally different ligands as probes (one being colchicine itself and another, TN16), aims to provide insight into the origin of this diverse acceptability to provide a better perspective for the design of novel therapeutic molecules. Thermodynamic measurements reveal interesting interplay between entropy and enthalpy. Although both these parameters are favourable for TN16 binding (ΔH < 0, ΔS > 0), but the magnitude of entropy has the determining role for colchicine binding as its enthalpic component is destabilizing (ΔH > 0, ΔS > 0). Molecular dynamics simulation provides atomistic insight into the mechanism, pointing to the inherent flexibility of the binding pocket that can drastically change its shape depending on the ligand that it accepts. Simulation shows that in the complexed states both the ligands have freedom to move within the binding pocket; colchicine can switch its interactions like a "flying trapeze", whereas TN16 rocks like a "swing cradle", both benefiting entropically, although in two different ways. Additionally, the experimental results with respect to the role of solvation entropy correlate well with the computed difference in the hydration: water molecules associated with the ligands are released upon complexation. The complementary role of van der Waals packing versus flexibility controls the entropy-enthalpy modulations. This analysis provides lessons for the design of new ligands that should balance between the "better fit" and "flexibility"', instead of focusing only on the receptor-ligand interactions.

Interaction of polyethyleneimine-functionalized ZnO nanoparticles with bovine serum albumin

In biological fluids, nanoparticles are always surrounded by proteins. As the protein is adsorbed on the surface, the extent of adsorption and the effect on the protein conformation and stability are dependent on the chemical nature, shape, and size of the nanoparticle (NP). We have carried out a detailed investigation on the interaction of bovine serum albumin (BSA) with polyethyleneimine-functionalized ZnO nanoparticles (ZnO-PEI). ZnO-PEI was synthesized using a wet chemical method with a core size of ~3-7 nm (from transmission electron microscopy). The interaction of BSA with ZnO-PEI was examined using a combination of calorimetric, spectroscopic, and computational techniques. The binding was studied by ITC (isothermal titration calorimetry), and the result revealed that the complexation is enthalpy-driven, indicating the possible involvement of electrostatic interaction. To investigate the nature of the interaction and the location of the binding site, a detailed domain-wise surface electrostatic potential calculation was performed using adaptive Poisson-Boltzmann software (APBS). The result shows that the protein surface can bind the nanoparticle. On binding ZnO-PEI, the protein gets destabilized to some extent, as displayed by CD (circular dichroism) and FTIR (Fourier transform infrared) spectroscopy. Chemical and thermal denaturation of BSA, when carried out in the presence of ZnO-PEI, also indicated a small perturbation in the protein structure. A comparison of the enthalpy and entropy components of binding with those derived for the interaction of BSA with ZnO nanoparticles explains the effect of hydrophilic cationic species attached on the NP surface. The effect of the NP surface modification on the structure and stability of BSA would find useful applications in nanobiotechnology.

Abstract P4-06-01: Significance and Therapeutic Potential of PELP1 in ER-Negative Breast Cancers

Background: During the past 20 years, studies have extensively focused on the role of estrogen receptor (ER) and progesterone receptor (PR) in breast cancer. Even through ER and PR explain the biology of ER-positive tumors, it remain unknown as to what drives ER-negative metastatic tumors. Recent advances implicated potential importance of several additional nuclear receptor (NRs) including ERRα, AR, GR, and PPAR in breast cancer. NR action is complex, requires functional interactions with coregulators, and deregulation of coregulators occur during cancer progression. As a modulator of multiple NR functions, coregulators are likely to play a role in breast cancer progression to metastasis. Recent studies indicated that metastatic tumors have increased expression of corgulators. Proline glutamic acid rich protein (PELP1) is a NR coregulator, and its expression is upregulated during breast cancer progression. The objective of this study is to examine whether proto-oncogene PELP1 contributes to metastatic potential of ER-negative breast cancer cells and to test whether blocking of PELP1 signaling axis will have therapeutic effect.

Methods: We have used two ER-negative model cells; (1) MDA-MB231 cells that facilitate study of bone and lungs metastasis of breast cancer cells using Nude mice models, (2) 4T1 cells, a clinically relevant model of spontaneous breast cancer metastasis that facilitate tumor growth studies using syngenic mice. To establish the significance of PELP1 axis, we have established clones stably expressing PELP1-shRNA (MDA-MB231- PELP1 shRNA, 4T1-PELP1 shRNA). Proliferation was measured using CellTiter-Glo assays. Role of PELP1 on metastasis was studied using Boyden chamber, wound healing, invasion and MMP assays. Epithelial to Mesenchymal Transition (EMT) real time qPCR Array (Super array) was used to identify PELP1 target genes and targets were validated using ChIP assays. Nude mice based assays were performed to study the role of PELP1 on in vivo metastasis.

Results: MDA-MB231 and 4T1 cells expressing PELP1-shRNA showed decreased PELP1 expression (∼75% of endogenous levels) and exhibited decreased propensity to proliferate in in vitro growth assays. Boyden chamber and wound healing assays showed PELP1 down regulation substantially affect migratory potential of MDA-MB231 and 4T1 cells. PELP1 shRNA model cells showed alterations in the expression of the EMT markers. EMT array studies identified eight genes involved in the EMT (including MMPs, E-cadherin, MTA1) as PELP1 potential target genes and ChIP studies showed PELP1 recruitment to these gene promoters. Overexpression of PELP1 in nonmetastatic cells increases their propensity for metastasis in vivo, while, PELP1 knockdown in metastatic model cells decreased their metastatic potential. Nanopartiles delivering PELP1-siRNA significantly affected the growth and metastatic potential of ER-ve cells.

Conclusions: These results suggest that PELP1 play a role in ER-ve breast cancer metastasis by promoting cell motility and EMTand blockage of PELP1 axis reduces metastasis potential of ER-negative breast cancer cells. Understanding how NR coregulator PELP1play a role in metastasis will be useful in maximizing treatment opportunities for metastatic breast cancer. This study is funded by Komen grant KG091267.

Citation Information: Cancer Res 2010;70(24 Suppl):Abstract nr P4-06-01.

Abstract P4-02-10: Significance of ER-Coregulator-Src Axis in Hormonal Resistance

Background: The estrogen receptor (ER) is implicated in the progression of breast cancer. Endocrine therapy using Tamoxifen, a selective estrogen receptor modulator (SERM), improves disease-free survival in postmenopausal women. Despite positive effects, initial or acquired resistance to endocrine therapies frequently occurs. Recent studies suggested the presence of alternative signaling pathways (including HER2 and c-Src kinase) that contribute to ER activation in the absence of estrogen. ER-coregulators play an essential role in hormonal responsiveness and coregulators such as PELP1 couples Src axis to ER thus representing a new pathway for targeted drug therapy. In this study, we examined the therapeutic efficacy of targeting the PELP-Src axis in blocking therapy resistance.

Methods: Three breast cancer model cell lines with resistance to Tamoxifen were used in this study: (1) MCF7-PELP1 (2) MCF7-HER2/neu and (3) MCF7-Tam. To establish the significance of ER-PELP1 coregulator-Src axis, we have generated additional model cells that stably express Src-ShRNA (MCF7-PELP1 -Src-shRNA and MCF7-HER2-SrcshRNA). Model cells were tested for proliferation using CellTiter-Glo assays, anchorage dependence and ER-extranuclear signaling by Western analysis using phospho-antibodies. Orally soluble Src inhibitor Dasatinib (SPRYCEL)was used to test whether it (a) blocks of ER-coactivator-Src signaling and (b) sensitizes the resistant breast cancer cells to endocrine therapy. Pre-clinical nude mice xenograft based studies were performed to validate the effect of Dasatinib alone or in combination with tamoxifen in vivo. IHC analysis of the tumors was performed to examine the effect of Dasatinib on ER signaling components.

Results: Src knock down or Dasatinib (100 nM) treatment substantially inhibited the growth of MCF7-PELP1, MCF7-HER2/neu and MCF7- Tam model cells in proliferation assays. Depletion of Src using siRNA substantially reduced E2 mediated activation of Src, MAPK and AKT in resistant model cells. In post-menopausal xenograft based studies, treatment with Dasatinib significantly inhibited the growth of therapy resistant cells. IHC analysis revealed that the tumors are ER positive, and Dasatinib (15 mg/kg/d) treated tumors exhibited alterations in Src and AKT pathways. Combinatorial therapy of Tamoxifen (100 μg/mouse/day) with Dasatinib showed better therapeutic effect compared to single agent therapy on the growth of therapy resistant tumors.

Conclusions: The results from this study showed that ER-PELP1 coregulator-Src axis play an important role in promoting hormonal resistance and blocking this axis prevents the development of hormonal independence in vivo. ER coregulator PELP1 and Src kinase are commonly deregulated in breast cancers therefore combination therapies using both endocrine agents and Dasatinib may have better therapeutic effect by delaying the development of hormonal resistance This study is supported by DOD grant W81XWH-08-1-0604.

Citation Information: Cancer Res 2010;70(24 Suppl):Abstract nr P4-02-10.

Potential role of estrogen receptor coregulator in mitosis

Abstract #5036

Background: Estrogen stimulates breast tissue to increase cell divisions (mitosis) and is implicated in breast cancer progression. ER action is complex and requires functional interactions with coregulators. Proline-, glutamic acid-, and leucine-rich protein (PELP)-1, also known as modulator of nongenomic actions of estrogen receptor (MNAR), is a novel nuclear receptor (ER) coregulator with multitude of functions. Emerging evidence suggest that PELP1 expression is deregulated in breast cancer and serves as a scaffolding protein that couples various signaling complexes with estrogen receptor. In this study we found that ER coregulator PELP1 plays a novel role in mitosis.&#x2028; Material and Methods: To understand the mechanism by which ER coregulator PELP1 contribute to breast cancer progression, we have utilized small RNA interference methodology and established breast cancer model cells that stably express PELP1-shRNA (MCF7-PELP1shRNA). FACS analysis was used to determine the cell cycle status of the model cells. Using confocal microscopy, immunoprecipitation, in vitro kinase assays, site directed mutagenesis and Western analysis using phospho-antibodies we studied the mechanism and significance of PELP1 signaling in mitotic progression. We also developed PELP1 siRNA nanoparticles and used them as well as CDK1 inhibitors in cell proliferation studies.&#x2028; Results: Down regulation of PELP1 expression resulted in decreased estrogen mediated cell proliferation, delayed mitotic progression and induced accumulation of mitotic cells. Interestingly, PELP1 depleted cells also exhibited multinucleation. Western analysis of various markers of mitotic progression revealed a delay in the kinetics of G2M initiation and progression. Confocal analysis revealed colocalization of CDK1 and PELP1 in G2M. Immunoprecipitation assays demonstrate that endogenous CDK1 form functional complex with PELP1 and Src kinase during mitosis. Using deletion and mutagenesis approach, we have mapped the putative CDK1 phosphorylation sites on PELP1. Down regulation of PELP1 or overexpression of PELP1 mutants (that cannot be phosphorylated by CDK1), reduces the magnitude of Src activation, which is an essential driving force for timely progression of M phase. PELP1 siRNA nanoparticles alone or in combination with CDK1 inhibitors have shown to significantly reduce the proliferation of breast cancer cells and showed increased response in tamoxifen resistant breast cancer cells.&#x2028; Discussion: These results suggest that ER coregulator PELP1 play a novel role in G2M progression. Since PELP1 expression is deregulated in breast cancer, PELP1 ability to regulate mitosis could contribute to the progression of cancer by causing genomic instability through the deregulation of mitosis. Taken together our findings suggest that estrogen can promote neoplasia using coregulators by two distinct mechanisms (1) Coregulator induction of target genes and (2) Coregulator mediated actions in mitosis. ER coregulator PELP1 play multiple roles in Estrogen mediated neoplasia, and thus represent a target for novel therapeutic breast cancer strategies by forming the “next generation” of antimitotic drugs.

Citation Information: Cancer Res 2009;69(2 Suppl):Abstract nr 5036.

The assessment of osteoporosis risk factors in Iranian women compared with Indian women

BACKGROUND

Osteoporosis is an important public health problem in older adults. It is more common in postmenopausal women and not only gives rise to morbidity but also markedly diminishes the quality of life in this population. There is lack of information about the risk factor of osteoporosis in developing countries. In this study we aimed to assess the risk factors for osteoporosis in postmenopausal women from selected BMD centers of two developing Asian countries (Iran and India).

METHODS

This study is a multicenter interview-based study conducted in selected hospitals and health centers from urban areas in Iran and India. The case group included postmenopausal osteoporotic women who were identified as patients with bone density higher than 2.5 SD below average of young normal bone density (in L1-L4) spine region interest and/or total femoral region) by using DEXA method. The controls were chosen from postmenopausal women with normal bone density (in L1-L4 spine and total femoral regions using DEXA method) matching in age groups was strategy of choice.The sample sizes included from Iran a total of 363 subjects (178 osteoporotic and 185 normal) and from India a total of 354 subjects (203 osteoporotic and 151 normal).

RESULTS

The significant (p < 0.05) risk factors in present study population with their Odds Ratios (in parenthesis, respectively in Iran and India) were as follow:Lower education defined as less than class 12 or nil college (2.1) (2.7), duration of menopause greater than 5 years: (2.2) (1.4), Menarche age (after 14 years): (1.9) (1.6), Menopause age (before 45 years): (1.1) (2), Parity more than 3: (1.1) (1), Bone and joint problem (2.3) (2.2). Calcium supplementation (0.6) and HRT (0.4) were shown as protective factors and steroid therapy (3.3) was found as a risk factor in Iran. Calcium supplementation more than 1 year (0.3) was shown as a protective factor in India.Pure vegetarianism: (2.2) and Red meat consumption more than 4 times per week (1.4) was shown as a risk factor in Indian and Iranian subjects respectively. Regular consumption of Soya (0.3), almond (0.5), fish (0.5), fruits (0.4) and milk tea 4 cups per day and more (0.4) appeared to be significant protective factors in India. Regular consumption of cheese (0.5), milk (0.5), chicken (0.4), egg (0.6), fruit (0.4), tea 7 cups per day and more (0.3) were found to be significant protective factors in Iran. Exercises were shown as protective factor in Iran (0.4) and India (0.4). There were no significant differences in association of risk factors and osteoporosis between Iranian and Indian subjects.

CONCLUSION

Osteoporosis in Iranian and Indian subjects also appears to be associated with several known risk factors that well described in the literature. There were no significant differences in association of risk factors and osteoporosis between Iranian and Indian subjects. It was shown a protective role of certain nutritional dietary components and also exercises in both populations and can be exploited in preventive educational strategies on osteoporosis in these populations.

Estrogen receptor ?1 and the ?2/?cx isoforms in nonneoplastic endometrium and in endometrioid carcinoma

Estrogen receptor beta (ERbeta) has five carboxyl-terminal (C-terminal) isoforms derived from alternative splicing. ERbeta1 is the wild-type receptor whereas ERbeta2/betacx lacks the activation function (AF)-2 core essential for ligand-dependent transcriptional activation and so behaves as a dominant-negative receptor affecting the function of ERalpha. The objective of this study was to analyze the expression of ERbeta1 and ERbeta2/betacx isoforms in nonneoplastic endometrium and endometrioid carcinoma. The study was conducted on samples of 22 proliferative endometrium, 15 secretory endometrium, 20 simple hyperplasia (without atypia), and 26 endometrioid carcinomas. The transcript and protein levels were determined by semiquantitative reverse transcriptase-polymerase chain reaction and immunohistochemistry, respectively. For the detection of ERbeta2/betacx protein, a polyclonal antibody was raised to its unique C-terminus, characterized, and used in immunohistochemistry. The two ERbeta isoforms are expressed in the proliferative and secretory phase endometrium with no significant change in their relative levels. The levels of the ERbeta1 isoform were lower as compared to the levels of ERbeta2 in all the groups studied. Expression of ERbeta2/betacx was decreased in endometrioid carcinoma as compared to proliferative endometrium (P < 0.01). A significant decrease of the ERbeta2/ERbetacx transcript was observed with higher grade tumors (P = 0.041). Progesterone receptor (PR) expression was not influenced by either of the ERbeta isoforms which was observed by logistic regression analysis in all the groups. The coexpression of ERbeta2/betacx with ERalpha did not affect PR levels (logistic regression analysis). Thus, we conclude in the human endometrium, there is significant ERbeta2/betacx isoform expression and alterations in its levels could be involved in endometrial cancer progression.

Is perioperative blood transfusion a risk factor for mortality or infection after hip fracture?

OBJECTIVES

To assess whether allogeneic blood transfusion in the perioperative period is associated with changes in mortality or complication rates in patients undergoing surgical treatment for hip fracture (proximal femoral fracture).

DESIGN

Retrospective case-control series, all patients followed up for 1 year or until death.

SETTING

District General Hospital in Peterborough, UK. PATIENTS PARTICIPANTS: Three thousand six hundred twenty-five consecutive patients admitted and operated for hip fracture (proximal femoral fracture) during July 1989 to January 2002 (151 months); 1068 (29.9%) received a perioperative allogeneic blood transfusion.

MAIN OUTCOME MEASURES

Thirty- 120-, and 365-day mortality, deep and superficial wound infection rates.

RESULTS

Overall mortality for all patients at 1 year post fracture was 28.2% (1007 patients). Transfusion was associated with a statistically significant increase in mortality from 120 days onward after hip fracture. However, when this was adjusted with a statistical regression model for baseline characteristics and confounding variables, this difference became statistically insignificant (P = 0.17). Infection rates in the transfusion group were 2.0% for superficial infection and 0.9% for deep infection compared with 1.9% and 0.6%, respectively, in the nontransfusion group. These figures were not statistically significantly different. Other complications of deep venous thrombosis, chest infection, and congestive cardiac failure showed no statistically significant increase in those patients who received transfusion.

CONCLUSIONS

Our data suggest that transfusion is not associated with a change in mortality or infection rates in the hip-fracture patient.

Maintenance of genomic integrity in mammalian kidney cells exposed to hyperosmotic stress

Changes in environmental salinity/osmolality impose an osmotic stress upon cells because, if left uncompensated, such changes will alter the conserved intracellular ionic milieu and macromolecular density, for which cell metabolism in most extant cells has been optimized. Cell responses to osmotic stress include rapid posttranslational and slower transcriptional events for the compensatory regulation of cell volume, intracellular electrolyte concentrations, and protein stability/activity. Changes in external osmolality are perceived by osmosensors that control the activation of signal transduction pathways giving rise to the above responses. We have recently shown that the targets of such pathways include cell cycle-regulatory and DNA damage-inducible genes (reviewed in Kültz, D., 2000. Environmental stressors and gene responses, Elsevier, Amsterdam. pp 157-179). Moreover, recent evidence suggests that hyperosmotic stress causes chromosomal aberrations and DNA double-strand breaks in mammalian cells. We propose that the modulation of cell cycle checkpoints and the preservation of genomic integrity are important aspects of cellular osmoprotection and as essential for cellular osmotic stress resistance as the capacity for cell volume regulation and maintaining inorganic ion homeostasis and protein stability/activity.

A novel 14-3-3 gene is osmoregulated in gill epithelium of the euryhaline teleost Fundulus heteroclitus

We have cloned and analyzed the full-length coding sequence and 3′ untranslated region (UTR) of a unique 14-3-3 gene of the euryhaline teleost Fundulus heteroclitus, which we named 14-3-3.a. Phylogenetic analysis of the deduced amino acid sequence revealed that the 14-3-3.a gene product is most similar to vertebrate 14-3-3ζ and β, yet it displays considerable divergence to known classes of vertebrate 14-3-3 isoforms. The N and C termini of 14-3-3.a are the most unique regions, whereas the amino acid residues forming the amphipathic ligand-binding groove are highly conserved. F. heteroclitus 14-3-3.a mRNA expression is high in gill epithelium, moderate in intestine and brain, and low in gonads, white muscle and heart. Because 14-3-3 proteins are important molecular scaffolds and cofactors for phosphoproteins and signaling complexes, the high level of 14-3-3.a expression in gill epithelium of the euryhaline teleost F. heteroclitus suggests that it is crucial for signal transduction in gill epithelial cells. We provide evidence that 14-3-3.a is involved in osmosensory signal transduction by showing that its mRNA and protein levels in gill epithelium, but not in any other tissue analyzed, increase two- to fourfold within 24h of salinity transfer of fish from sea water to fresh water. These data are clear evidence for an important role of 14-3-3.a in the remodeling of gill epithelium during transition of euryhaline fish between plasma-hyperosmotic and plasma-hyposmotic environments.

Hyperosmolality in the form of elevated NaCl but not urea causes DNA damage in murine kidney cells

This study demonstrates, by using neutral comet assay and pulsed field gel electrophoresis, that hyperosmotic stress causes DNA damage in the form of double strand breaks (dsb). Different solutes increase the rate of DNA dsb to different degrees at identical strengths of hyperosmolality. Hyperosmolality in the form of elevated NaCl (HNa) is most potent in this regard, whereas hyperosmolality in the form of elevated urea (HU) does not cause DNA dsb. The amount of DNA dsb increases significantly as early as 15 min after the onset of HNa. By using neutral comet and DNA ladder assays, we show that this rapid induction of DNA damage is not attributable to apoptosis. We demonstrate that renal inner medullary cells are able to efficiently repair hyperosmotic DNA damage within 48 h after exposure to hyperosmolality. DNA repair correlates with cell survival and is repressed by 25 microM LY294002, an inhibitor of DNA-activated protein kinases. These results strongly suggest that the hyperosmotic stress resistance of renal inner medullary cells is based not only on adaptations that protect cellular proteins from osmotic damage but, in addition, on adaptations that compensate DNA damage and maintain genomic integrity.

Mutational replacement of molybdenum by vanadium in assimilation of N2 or NO3- as nitrogen source in the cyanobacterium Nostoc muscorum

Tungsten resistant (Wr) mutants of Het+Nif+Nia+, Het+Nif-Nia+ and Het+Nif+Nia- strains of Nostoc muscorum were isolated with severely defective molybdate transport activity. All such mutants showed vanadium (V)-dependent nitrogenase activity and/or nitrate reductase activity and V-dependent growth on N2-nitrogen and/or NO3(-)-nitrogen and V-dependent NO3(-)-repression of heterocyst formation and nitrogenase activity. None of them grew with molybdenum (Mo) under parallel growth condition. Results strongly suggest the ability of V to replace Mo in N2-assimilation or NO3(-)-assimilation under Mo-deficiency.