Fractal analysis of knee-joint vibroarthrographic signals via power spectral analysis

Parameters useful for the diagnosis of pathological processes leading to the deterioration of the articular cartilage surfaces of knee joints, such as osteoarthritis, may be derived from vibroarthrographic (VAG) signals. In the present work, we explore fractal analysis to parameterize the temporal and spectral variability of normal and abnormal VAG signals. The power spectrum analysis method was used with the 1/f model to derive estimates of the fractal dimension (FD). Classification accuracy of up to 0.74 was obtained with a single FD parameter, in terms of the area under the receiver operating characteristic curve (A_z), with a database of 89 VAG signals. Combinations of the features derived in the present work with other features we have reported upon recently, when used with several neural networks with radial basis functions, resulted in A_z values in the range [0.92, 0.96], with an exceptional case of perfect classification with A_z = 1.0. The proposed methods could help in the detection and monitoring of knee-joint pathology.     

Distinctive features of the two classes of eukaryotic peptide deformylases.

Peptide deformylases (PDFs) are essential enzymes of the N-terminal protein processing pathway of eubacteria. The recent discovery of two types of PDFs in higher plants, PDF1A and PDF1B, and the detection of PDF1A in humans, have raised questions concerning the importance of deformylation in eukaryotes. Here, we have characterized fully in vitro and compared the properties of the two classes of eukaryotic PDFs, PDF1A and PDF1B, using the PDFs from Arabidopsis thaliana and Lycopersicon esculentum. We have shown that the PDFs of a given class (1A or 1B) all display similar features, independently of their origin. We also observed similar specificity of all plant PDFs for natural substrate peptides, but identified a number of biochemical differences between the two classes (1A or 1B). The main difference lies at the level of the bound cofactor, iron for PDF1B-like bacterial PDFs, and zinc for PDF1A. The nature of the metal cation has important consequences concerning the relative sensitivity to oxygen of the two plant PDFs. Investigation of the specificity of these enzymes with unusual substrates revealed additional differences between the two types of PDFs, enabling us to identify specific inhibitors with a lower affinity against PDF1As. However, the two plant PDFs were inhibited equally strongly in vitro by actinonin, an antibiotic that specifically acts on bacterial PDFs. Uptake of actinonin by A. thaliana seedlings was used to investigate the function of PDFs in the plant. Because it induces an albino phenotype, we conclude that deformylation is likely to play an essential role in the chloroplast.     

Peptide deformylases from Vibrio parahaemolyticus phage and bacteria display similar deformylase activity and inhibitor binding clefts

Unexpected peptide deformylase (PDF) genes were recently retrieved in numerous marine phage genomes. While various hypotheses dealing with the occurrence of these intriguing sequences have been made, no further characterization and functional studies have been described thus far. In this study, we characterize the bacteriophage Vp16 PDF enzyme, as representative member of the newly identified C-terminally truncated viral PDFs. We show here that conditions classically used for bacterial PDFs lead to an enzyme exhibiting weak activity. Nonetheless, our integrated biophysical and biochemical approaches reveal specific effects of pH and metals on Vp16 PDF stability and activity. A novel purification protocol taking in account these data allowed strong improvement of Vp16 PDF specific activity to values similar to those of bacterial PDFs. We next show that Vp16 PDF is as sensitive to the natural inhibitor compound of PDFs, actinonin, as bacterial PDFs. Comparison of the 3D structures of Vp16 and E. coli PDFs bound to actinonin also reveals that both PDFs display identical substrate binding mode. We conclude that bacteriophage Vp16 PDF protein has functional peptide deformylase activity and we suggest that encoded phage PDFs might be important for viral fitness.     

Normal versus gamma: stochastic models of copepod molting rate

Molting rate is a key life history parameter in copepods. Sincecopepod population growth is an inherently exponential process,accurate formulation of molting rate is of critical importance.Many experiments have been conducted to culture different copepodspecies under varying temperatures and food concentrations.Probability density functions (PDFs) then were used to estimatethe median development time (MDT) of different copepod stagesfrom the experimental data. These MDTs are used in copepod populationmodels. Asymmetrical PDFs are widely used to model molting rate,because the shapes of these curves are similar to laboratorydata on cohort development. In this paper, we developed an individualstochastic model (ISM) to simulate the molting rate with differentPDFs. We showed that there was no connection between the asymmetryof cohorts and the asymmetry of the molting PDF. Although age-within-stagemodels have been widely used to simulate copepod populationdynamics, we found that none had used the correct formulationof molting rate. The population model requires the probabilityof molting at each time step, whereas the laboratory-derivedPDF is the frequency distribution of stage duration. Therefore,the PDF cannot be applied directly to the population model.We present here a corrected formula based on the PDF for usein copepod population models, termed the probability of moltingfor remaining individuals (PMR). Despite emphasis on use ofthe gamma function for copepod molting, we found simpler functionswork equally well, but that prior use of incorrect molting ratefunctions in copepod models can seriously overestimate generationtime.     

Expression, purification, and activity assay of peptide deformylase from Escherichia coli and Staphylococcus aureus

Peptide deformylase (PDF) is considered an attractive target for screening novel antibiotics. The PDF from Escherichia coli and Staphylococcus aureus are representative of the gram-negative species type of PDF (type I PDF) and the gram-positive species type of PDF (type II PDF), respectively. They could be used for screening broad-spectrum antibiotics. Herein, we cloned the def gene by PCR, inserted it into plasmid pET-22b-def, and transformed the plasmid into E. coli BL21 (DE3) cells, then the cells were induced by IPTG to express PDF. E. coli Ni(2+)-PDF was extracted and purified by ion-exchange chromatography and gel filtration chromatography. S. aureus PDFs were extracted and purified using the MagExtractor kit. The nickel form of S. aureus PDF was obtained by adding NiCl(2) to all reagents used for purification. Iron-enriched S. aureus PDF was obtained by adding FeCl(3) to the growth medium for E. coli BL21 (DE3) cells and adding FeCl(3) and catalase to all reagents used for purification. The activities of PDFs were analyzed, compared, and grouped according to the experimental conditions that produced optimal activity, and we used actinonin as an inhibitor of PDF and calculated the IC(50) value. We obtained high expression of E. coli and S. aureus PDF with high activity and stability. The function of PDFs was inhibited by actinonin in a dose-dependent manner. Results may be helpful for future mechanistic investigations of PDF as well as high-throughput screening for other PDF inhibitors.     

Multi-scale AM–FM analysis for the classification of surface electromyographic signals

In this work, multi-scale amplitude modulation–frequency modulation (AM–FM) features are extracted from surface electromyographic (SEMG) signals and they are used for the classification of neuromuscular disorders. The method is validated on SEMG signals recorded from a total of 40 subjects: 20 normal and 20 abnormal cases (11 myopathy, and 9 neuropathy cases), at 10%, 30%, 50%, 70% and 100% of maximum voluntary contraction (MVC), from the biceps brachii muscle. For the classification, three classifiers are used: (i) the statistical K-nearest neighbor (KNN), (ii) the self-organizing map (SOM) and (iii) the support vector machine (SVM). For all classifiers, the leave-one-out methodology is used to validate the classification of the SEMG signals into normal or abnormal (myopathy or neuropathy). A classification success rate of 78% for the AM–FM features and SVM models was achieved. These results also show that SEMG can be used as a non-invasive alternative to needle EMG for differentiating between normal and abnormal (myopathy, or neuropathy) cases.     

The crystal structure of mitochondrial (Type 1A) peptide deformylase provides clear guidelines for the design of inhibitors specific for the bacterial forms

Peptide deformylase (PDF) inhibitors have a strong potential to be used as a new class of antibiotics. However, recent studies have shown that the mitochondria of most eukaryotes, including humans, contain an essential PDF, PDF1A. The crystal structure of the Arabidopsis thaliana PDF1A (AtPDF1A), considered representative of PDF1As in general, has been determined. This structure displays several similarities to that of known bacterial PDFs. AtPDF1A behaves as a dimer, with the C-terminal residues responsible for linking the two subunits. This arrangement is similar to that of Leptospira interrogans PDF, the only other dimeric PDF identified to date. AtPDF1A is the first PDF for which zinc has been identified as the catalytic ion. However, the zinc binding pocket does not differ from the binding pockets of PDFs with iron rather than zinc. The crystal structure of AtPDF1A in complex with a substrate analog revealed that the substrate binding pocket of PDF1A displays strong modifications. The S1' binding pocket is significantly narrower, due to the creation of a floor from residues present in all PDF1As but not in bacterial PDFs. A true S3' pocket is created by the residues of a helical CD-loop, which is very long in PDF1As. Finally, these modified substrate binding pockets modify the position of the substrate in the active site. These differences provide guidelines for the design of bacterial PDF inhibitors that will not target mitochondrial PDFs.     

Knowledge-based interaction potentials for proteins.

We discuss the derivation of atomic-level potentials of mean force from the known protein structures and their applicability for structural evaluation applications. In the derivation process, rigorous density estimation methodology is used to estimate the probability density functions (PDFs) for the distributions of interatomic distances in the protein structures. Potentials of mean force are then derived from these density functions using simple Boltzmann's relation. We also test the potentials against pairs of current and superseded protein structures in the Protein Data Bank. Using PDF potentials to evaluate each structure pair, we are able to identify, with high accuracy, which of the two structures is of higher resolution or better quality. This result shows that the PDF potentials are sensitive to details in protein structures as the current and superseded atomic coordinates generally do not differ by more than 1 A in root-mean-square deviation, and that the PDF potentials could potentially be used for X-ray structure refinement and protein structure prediction.     

Crustacean Pigmentary-Effector Hormones: Chemistry and Functions of RPCH, PDH, and Related Peptides

Integumental color changes and eye pigment movements in crustaceansare regulated by pigmentary-effector hormones. The identifiedhormones include: an octapeptide RPCH (red pigment-concentratinghormone) and several forms of octadecapeptide PDH (pigment-dispersinghormone: -PDH, ß-PDH). RPCH-related peptides (AKHs,adipokinetic hormones) and PDH-related peptides (PDFs, pigment-dispersingfactors) occur in insects, and are recognized as members ofAKH/RPCH and PDH/PDF peptide families. The domain for maturepeptide is located between the signal peptide and precursor-relatedpeptide in AKH/RPCH precursors, and at the C-terminal end inthe PDH/PDF precursors. The precursor-related (associated) peptidesin RPCH and PDH precursors in Crustacea show little or no similarityto corresponding domains of AKH and PDF precursors in insects.Although the functions of precursor-related peptides are unknown,the mature peptides are shown to serve diverse functions. RPCH'sactions in crustaceans include: pigment concentration in oneor more types of chromatophores, dark-adaptational screeningpigment movement in distal eye pigment cells, increase of retinalsensitivity, and neuromodulation. The related AKHs largely influencemetabolism in insects, although they serve additional functions.PDHs trigger pigment dispersion in chromatophores and inducelight-adaptational screening pigment movements in extraretinulareye pigment cells. The related PDFs appear to serve as a transmitterof circadian signals in the regulation of biological rhythmsin insects. Evolutionary relationships among the PDH/PDF peptidesand directions for future research are discussed.     

Epileptic Seizure Detection Based on New Hybrid Models with Electroencephalogram Signals

Objectives: Epileptic seizures are one of the most common diseases in society and difficult to detect. In this study, a new method was proposed to automatically detect and classify epileptic seizures from EEG (Electroencephalography) signals.Methods: In the proposed method, EEG signals classification five-classes including the cases of eyes open, eyes closed, healthy, from the tumor region, an epileptic seizure, has been carried out by using the support vector machine (SVM) and the normalization methods comprising the z-score, minimum-maximum, and MAD normalizations. To classify the EEG signals, the support vector machine classifiers having different kernel functions, including Linear, Cubic, and Medium Gaussian, have been used. In order to evaluate the performance of the proposed hybrid models, the confusion matrix, ROC curves, and classification accuracy have been used. The used SVM models are Linear SVM, Cubic SVM, and Medium Gaussian SVM.Results: Without the normalizations, the obtained classification accuracies are 76.90%, 82.40%, and 81.70% using Linear SVM, Cubic SVM, and Medium Gaussian SVM, respectively. After applying the z-score normalization to the multi-class EEG signals dataset, the obtained classification accuracies are 77.10%, 82.30%, and 81.70% using Linear SVM, Cubic SVM, and Medium Gaussian SVM, respectively. With the minimum-maximum normalization, the obtained classification accuracies are 77.20%, 82.40%, and 81.50% using Linear SVM, Cubic SVM, and Medium Gaussian SVM, respectively. Moreover, finally, after applying the MAD normalization to the multi-class EEG signals dataset, the obtained classification accuracies are 76.70%, 82.50%, and 81.40% using Linear SVM, Cubic SVM, and Medium Gaussian SVM, respectively.Conclusion: The obtained results have shown that the best hybrid model is the combination of cubic SVM and MAD normalization in the classification of EEG signals classification five-classes.     

cDNA cloning of the housefly pigment-dispersing factor (PDF) precursor protein and its peptide comparison among the insect circadian neuropeptides.

Pigment-dispersing factor (PDF), an 18-amino acid neuropeptide, is a principal circadian neurotransmitter for the circadian rhythms of the locomotor activity in flies. Recently, two completely different types of PDF precursor were clarified; that of the cricket Gryllus bimaculatus and that of the last-summer cicada Meimuna opalifera. The G. bimaculatus PDF precursor is extraordinarily short and comprises a nuclear localization signal (NLS), while the M. opalifera PDF precursor is of ordinary length, comparable to that seen for the precursors of crustacean beta-PDH homologues. Although their PDF peptide regions were exactly the same, the regions containing a signal peptide combined with a PDF-associated peptide (PAP) were remarkably different from each other. Such a grouping suggested a fundamental role for the PAP peptide in the circadian clock, perhaps associated with PDF function. In the present study, the cDNA cloning of PDF from the adult brains of the housefly Musca domestica was carried out and it was found that an isolated clone (527 bp) encodes a PDF precursor protein of ordinary length. The PDF peptide shows a high sequence identity (78%-94%) and similarity (89%-100%) to insect PDFs and also to the crustacean beta-PDH peptides. In particular, there is only a single amino acid difference between the PDFs of Musca and Drosophila; at position 14 Ser for Musca PDF and Asn for Drosophila PDF. A characteristic Ser10 in Drosophila was retained in Musca, indicating the presence of a structural profile unique to these PDFs. The results of sequence analyses suggest that Musca and Drosophila PDFs are to be considered members of a single group that has evolved structurally. When the primary structure of the PAP regions was compared, the Musca PDF precursor also belonged to the same group as that to which the Drosophila PDF precursor belongs.     

Sleep staging with movement-related signals

Body movement related signals (i.e., activity due to postural changes and the ballistocardiac effort) were recorded from six normal volunteers using the static-charge-sensitive bed (SCSB). Visual sleep staging was performed on the basis of simultaneously recorded EEG, EMG and EOG signals. A statistical classification technique was used to determine if reliable sleep staging could be performed using only the SCSB signal. A classification rate of between 52% and 75% was obtained for sleep staging in the five conventional sleep stages and the awake state. These rates improved from 78% to 89% for classification between awake, REM and non-REM sleep and from 86% to 98% for awake versus asleep classification.     

Evaluation of contextual analysis for computer classification of cervical smears

A procedure for automated analysis of cervical smears has been implemented in an image cytometry system. Smears are described exclusively in terms of global and contextual information extracted by pattern-recognition algorithms and represented by a vector of proportions of cellular object types. Linear discriminant functions, based on a Fisher criterion, are derived to classify smears with a cross-section of diagnoses into two broad categories, normal and abnormal. Results obtained from 83 smears indicate 78% correct classification. In contrast to most automated systems, good classification results were obtained in normal smears with benign changes caused by inflammation and with postmenopausal atrophia and in abnormals with mild dysplasia. These findings suggest that contextual analysis may be sensitive to subtle changes in cellular morphology and to progressive patterns of dysplasia. When used with standard isolated cell analysis, contextual analysis may provide additional complementary information for automated cervical prescreening.     

Type 3 peptide deformylases are required for oxidative phosphorylation in Trypanosoma brucei

Peptide deformylase (PDF) catalyses the removal of the formyl group from the first methionine of nascent proteins. Type 1 PDFs are found in bacteria and have orthologues in most eukaryotes. Type 2 PDFs are restricted to bacteria. Type 3 enzymes are found in Archaea and trypanosomatids and have not been studied experimentally yet. Thus, TbPDF1 and TbPDF2, the two PDF orthologues of the parasitic protozoa Trypanosoma brucei, are of type 3. An experimental analysis of these enzymes shows that both are mitochondrially localized, but that only TbPDF1 is essential for normal growth. Recombinant TbPDF1 exhibits PDF activity with a substrate specificity identical to that of bacterial enzymes. Consistent with these results, TbPDF1 is required for oxidative but not for mitochondrial substrate-level phosphorylation. Ablation of TbPDF2, in contrast, does neither affect growth on standard medium nor oxidative phosphorylation. However, a reduced level of TbPDF2 slows down growth in a medium that selects for highly efficient oxidative phosphorylation. Furthermore, combined ablation of TbPDF1 and TbPDF2 results in an earlier growth arrest than is observed by downregulation of TbPDF1 alone. These results suggest that TbPDF2 is functionally linked to TbPDF1, and that it can influence the efficiency of oxidative phosphorylation.     

An unusual peptide deformylase features in the human mitochondrial N-terminal methionine excision pathway

Dedicated machinery for N-terminal methionine excision (NME) was recently identified in plant organelles and shown to be essential in plastids. We report here the existence of mitochondrial NME in mammals, as shown by the identification of cDNAs encoding specific peptide deformylases (PDFs) and new methionine aminopeptidases (MAP1D). We cloned the two full-length human cDNAs and showed that the N-terminal domains of the encoded enzymes were specifically involved in targeting to mitochondria. In contrast to mitochondrial MAP1D, the human PDF sequence differed from that of known PDFs in several key features. We characterized the human PDF fully in vivo and in vitro. Comparison of the processed human enzyme with the plant mitochondrial PDF1A, to which it is phylogenetically related, showed that the human enzyme had an extra N-terminal domain involved in both mitochondrial targeting and enzyme stability. Mammalian PDFs also display non-random substitutions in the conserved motifs important for activity. Human PDF site-directed mutagenesis variants were studied and compared with the corresponding plant PDF1A variants. We found that amino acid substitutions in human PDF specifically altered its catalytic site, resulting in an enzyme intermediate between bacterial PDF1Bs and plant PDF1As. Because (i) human PDF was found to be active both in vitro and in vivo, (ii) the entire machinery is conserved and expressed in most animals, (iii) the mitochondrial genome expresses substrates for these enzymes, and (iv) mRNA synthesis is regulated, we conclude that animal mitochondria have a functional NME machinery that can be regulated.     

Phylogenomic and biochemical characterization of three Legionella pneumophila polypeptide deformylases

Legionella pneumophila is a gram-negative facultative intracellular human pathogen that can cause fatal Legionnaires' disease. Polypeptide deformylase (PDF) is a novel broad-spectrum antibacterial target, and reports of inhibitors of PDF with potent activities against L. pneumophila have been published previously. Here, we report the identification of not one but three putative pdf genes, pdfA, pdfB, and pdfC, in the complete genome sequences of three strains of L. pneumophila. Phylogenetic analysis showed that L. pneumophila PdfA is most closely related to the commonly known gamma-proteobacterial PDFs encoded by the gene def. PdfB and PdfC are more divergent and do not cluster with any specific bacterial or eukaryotic PDF. All three putative pdf genes from L. pneumophila strain Philadelphia 1 have been cloned, and their encoded products have been overexpressed in Escherichia coli and purified. Enzymatic characterization shows that the purified PDFs with Ni2+ substituted are catalytically active and able to remove the N-formyl group from several synthetic polypeptides, although they appear to have different substrate specificities. Surprisingly, while PdfA and PdfB with Zn2+ substituted are much less active than the Ni2+ forms of each enzyme, PdfC with Zn2+ substituted was as active as the Ni2+ form for the fMA substrate and exhibited substrate specificity different from that of Ni2+ PdfC. Furthermore, the catalytic activities of these enzymes are potently inhibited by a known small-molecule PDF inhibitor, BB-3497, which also inhibits the extracellular growth of L. pneumophila. These results indicate that even though L. pneumophila has three PDFs, they can be effectively inhibited by PDF inhibitors which can, therefore, have potent anti-L. pneumophila activity.     

Palaeontology in the third dimension: a comprehensive guide for the integration of three-dimensional content in publications

During the last decade, three-dimensional, digital models have become increasingly important in geosciences and in particular in palaeontological research. Although significant advances in hard- and software technology have facilitated the acquisition and creation of such models, the presentation of three-dimensional data is still greatly handicapped by the traditionally two-dimensional means of publication. The ability to integrate three-dimensional (3D) models, which can be interactively manipulated, into portable document format (PDF) documents not only considerably improves their accessibility, but also represents an innovative, but so far neglected, approach for the presentation and communication of digital data. This article introduces and illustrates a comprehensive workflow for the creation of 3D PDFs, incorporating different techniques and methodological steps, and using both commercial and freely available software resources. Advantages and disadvantages of each method are discussed, and are accompanied by selected examples of digital models. These examples encompass different methods of data acquisition (computed tomography, synchrotron radiation X-ray tomographic microscopy, photogrammetry) and span a wide range of sizes and taxonomic groups. To the best of the author’s knowledge, this article represents the first application of 3D PDF technology fully integrated into a scientific publication in palaeontology or even geosciences, and not restricted to supplementary material. It provides the reader with extended visual information and facilitates the dissemination of data. As both authors and readers benefit greatly from their usage, it is argued that 3D PDFs should become an accepted standard in palaeontological publications of three-dimensional models.     

cDNA cloning and nuclear localization of the circadian neuropeptide designated as pigment-dispersing factor PDF in the cricket Gryllus bimaculatus

Pigment-dispersing factor (PDF) was recently reported to be a principal circadian neuromodulator involved in transmitting circadian rhythms of daily locomotion in insects. In Drosophila, PDF functions in some of the neurons expressing the clock genes period, timeless, Clock, and cycle, and those clock genes in turn regulate pdf gene expression. In the present study, we cloned a cDNA encoding PDF in the brain of a nocturnal insect, the cricket Gryllus bimaculatus, and found that an isolated clone (310 bp) codes for an extraordinarily short precursor protein with no definite signal sequence, but a nuclear localization signal (NLS)-like sequence instead. The cricket PDF exhibits high sequence identity (78-94%) and similarity (89-100%) to insect PDFs and also to crustacean beta-PDH peptides. In the optic lobes of G. bimaculatus there are PDF-immunoreactive neurons in both the medulla and lamina neuropiles. Among the strongly immunoreactive lamina PDF neurons, on electron microscopy we identified cells exhibiting distinct staining that is not only cytoplasmic but also nuclear. When GFP-fused PDF precursor proteins were expressed in COS-7 cells, distinct translocation of the fusion protein into the nucleus was observed. This is the first finding of PDF peptide in the nucleus, which suggests a fundamental role of PDF peptide per se in the circadian clock system.     

A biomechanical model for fibril recruitment: Evaluation in tendons and arteries

Simulations of soft tissue mechanobiological behaviour are increasingly important for clinical prediction of aneurysm, tendinopathy and other disorders. Mechanical behaviour at low stretches is governed by fibril straightening, transitioning into load-bearing at recruitment stretch, resulting in a tissue stiffening effect. Previous investigations have suggested theoretical relationships between stress-stretch measurements and recruitment probability density function (PDF) but not derived these rigorously nor evaluated these experimentally. Other work has proposed image-based methods for measurement of recruitment but made use of arbitrary fibril critical straightness parameters. The aim of this work was to provide a sound theoretical basis for estimating recruitment PDF from stress-stretch measurements and to evaluate this relationship using image-based methods, clearly motivating the choice of fibril critical straightness parameter in rat tail tendon and porcine artery. Rigorous derivation showed that the recruitment PDF may be estimated from the second stretch derivative of the first Piola-Kirchoff tissue stress. Image-based fibril recruitment identified the fibril straightness parameter that maximised Pearson correlation coefficients (PCC) with estimated PDFs. Using these critical straightness parameters the new method for estimating recruitment PDF showed a PCC with image-based measures of 0.915 and 0.933 for tendons and arteries respectively. This method may be used for accurate estimation of fibril recruitment PDF in mechanobiological simulation where fibril-level mechanical parameters are important for predicting cell behaviour.     

Unique structural characteristics of peptide deformylase from pathogenic bacterium Leptospira interrogans

Peptide deformylase (PDF), which is essential for normal growth of bacteria but not for higher organisms, is explored as an attractive target for developing novel antibiotics. Here, we present the crystal structure of Leptospira interrogans PDF (LiPDF) at 2.2A resolution. To our knowledge, this is the first crystal structure of PDF associating in a stable dimer. The key loop (named the CD-loop: amino acid residues 66-76) near the active-site pocket adopts "closed" or "open" conformations in the two monomers forming the dimer. In the closed subunit, the CD-loop and residue Arg109 block the entry of the substrate-binding pocket, while the active-site pocket of the open subunit is occupied by the C-terminal tail from the neighbouring molecule. Moreover, a formate group, as one product of deformylisation, is observed bound with the active-site zinc ion. LiPDF displays significant structural differences in the C-terminal region compared to both type-I and type-II PDFs, suggesting a new family of PDFs.