Impact of risk factors, early rehabilitation and management of lymphedema associated with breast cancer: a retrospective study of breast Cancer survivors over 5 years.

BACKGROUND: Breast cancer-related lymphedema (BCRL) is a potentially disabling and often irreversible consequence of breast cancer treatment, caused by the mechanical incompetence of the lymphatic system, resulting in reduced drainage capacity and functional overload due to an excessive volume of interstitial fluid surpassing the system's transport capacity in the arm. We wanted to determine the impact and explore the differences in independent risk factors for the occurrence of BCRL; incidence of BCRL over a five-year period at the Institute of Oncology Vojvodina in Sremska Kamenica and to answer the research question regarding the influence of the prehabilitation program on the overall incidence of BCRL during the observed five-year period. METHODS: From 2014 to 2018, a retrospective study was conducted at the Institute of Oncology of Vojvodina in Sremska Kamenica, analyzing female patients who had undergone breast cancer surgery. RESULTS: The study included 150 breast cancer patients who developed secondary lymphedema following surgery with the mean age of 59.2 ± 11.3 years. Fluctuations in hospitalization rates were observed over the five-year period, with the highest number of admissions in 2014 (24.0%) and a decline in 2018 (14.0%). The most common surgical procedure performed was left quadrantectomy (24.0%), followed by right quadrantectomy (20.0%) and left amputation (15.3%). The mean number of removed lymph nodes was 15.2 ± 6.1, with no statistically significant association between the number of removed lymph nodes and the manifestation of secondary lymphedema. The severity of secondary lymphedema varied based on patient age, with a higher incidence of moderate and severe lymphedema observed in patients aged 61 years and older. Patients who underwent radical surgery were more likely to experience severe lymphedema compared to those who had conservative surgery, although this difference was not statistically significant. CONCLUSION: In our study, the type of surgery, elapsed time since surgery, and the number of removed lymph nodes were not influencing factors for the occurrence of BCRL. However, concerning its severity, a greater number of systemic therapy modalities combined with radiotherapy were associated with a more frequent occurrence of mild and moderate BCRL. Also, the severity of BCRL varied among different age groups, with a higher incidence of moderate and severe lymphedema observed in patients aged 61 years and older. Ultimately, improving the quality of life for individuals affected by secondary lymphedema remains a crucial goal in the field of oncology.

Evaluation of the Structure-Function Relationship of SGNH Lipase from Streptomyces rimosus by Site-Directed Mutagenesis and Computational Approach.

Streptomyces rimosus extracellular lipase (SrL) is a multifunctional hydrolase belonging to the SGNH family. Here site-directed mutagenesis (SDM) was used for the first time to investigate the functional significance of the conserved amino acid residues Ser10, Gly54, Asn82, Asn213, and His216 in the active site of SrL. The hydrolytic activity of SrL variants was determined using para-nitrophenyl (pNP) esters with C4, C8, and C16 fatty acid chains. Mutation of Ser10, Asn82, or His216, but not Gly54, to Ala abolished lipase activity for all substrates. In contrast, the Asn213Ala variant showed increased enzymatic activity for C8 and C16 pNP esters. Molecular dynamics (MD) simulations showed that the interactions between the long alkyl chain substrate (C16) and Ser10 and Asn82 were strongest in Asn213Ala SrL. In addition to Asn82, Gly54, and Ser10, several new constituents of the substrate binding site were recognized (Lys28, Ser53, Thr89, and Glu212), as well as strong electrostatic interactions between Lys28 and Glu212. In addition to the H bonds Ser10-His216 and His216-Ser214, Tyr11 interacted strongly with Ser10 and His216 in all complexes with an active enzyme form. A previously unknown strong H bond between the catalytically important Asn82 and Gly54 was uncovered, which stabilizes the substrate in an orientation suitable for the enzyme reaction.

Effective Differences between 2D and 3D Planned Brachytherapy in Lung Cancer: An Institutional Retrospective Study.

Background and Objectives: Advanced lung cancer is usually manifested by endoluminal tumor propagation, resulting in central airway obstruction. The objective of this study is to compare the high dose rate brachytherapy treatment outcomes in non-small-cell lung cancer (NSCLC) depending on the treatment planning pattern-two-dimension (2D) or three-dimension (3D) treatment planning. Materials and Methods: The study was retrospective and two groups of patients were compared in it (a group of 101 patients who underwent 2D planned high-dose-rate endobronchial brachytherapy (HDR-EBBT) in 2017/18 and a group of 83 patients who underwent 3D planned HDR-EBBT between January 2021 and June 2023). Results: In the group of 3D planned brachytherapy patients, there was a significant improvement in terms of loss of symptoms of bronchial obstruction (p = 0.038), but no improvement in terms of ECOG PS (European Cooperative Oncology Group Performance Status) of the patient (p = 0.847) and loss of lung atelectasis (if there was any at the beginning of the disease) (p = 0.781). Two-year overall survival and time-to-progression periods were similar for both groups of patients (p = 0.110 and 0.154). Fewer treatment complications were observed, and 91.4% were in 3D planned brachytherapy (BT) patients. Conclusions: Three-dimensionally planned HDR-EBBT is a suggestive, effective palliative method for the disobstruction of large airways caused by endobronchial lung tumor growth. Independent or more often combined with other types of specific oncological treatment, it certainly leads to the loss of symptoms caused by bronchial obstruction and the improvement of the quality of life of patients with advanced NSCLC. Complications of the procedure with 3D planning are less compared to 2D planned HDR-EBBT.

Assessment and Application of the Hear Score in Remote Emergency Medicine Outposts in Bosnia and Herzegovina.

Background and Objectives. In emergency departments, chest pain is a common concern, highlighting the critical importance of distinguishing between acute coronary syndrome and other potential causes. Our research aimed to introduce and implement the HEAR score, specifically, in remote emergency outposts in Bosnia and Herzegovina. Materials and Methods. This follow-up study conducted a retrospective analysis of a prospective cohort consisting of patients who were admitted to the remote emergency medicine outposts in Canton Sarajevo and Zenica from 1 November to 31 December 2023. Results. This study comprised 103 (12.9%) patients with low-risk HEAR scores and 338 (83.8%) with high-risk HEAR scores, primarily female (221, 56.9%), with a mean age of 63.5 ± 11.2). Patients with low-risk HEAR scores were significantly younger (50.5 ± 15.6 vs. 65.9 ± 12.1), had fewer smokers (p < 0.05), and exhibited a lower incidence of cardiovascular risk factors compared to those with high-risk HEAR scores. Low-risk HEAR score for prediction of AMI had a sensitivity of 97.1% (95% CI 89.9-99.6%); specificity of 27.3% (95% CI 22.8-32.1%); PPV of 19.82% (95% CI 18.67-21.03%), and NPV of 98.08% (95% CI 92.80-99.51%). Within 30 days of the admission to the emergency department outpost, out of all 441 patients, 100 (22.7%) were diagnosed with MACE, with AMI 69 (15.6%), 3 deaths (0.7%), 6 (1.4%) had a CABG, and 22 (4.9%) underwent PCI. A low-risk HEAR score had a sensitivity of 97.0% (95% CI 91.7-99.4%) and specificity of 27.3% (95% CI 22.8-32.1%); PPV of 25.5% (95% CI 25.59-28.37%); NPV of 97.14% (95% CI 91.68-99.06%) for 30-day MACE. Conclusions. In conclusion, the outcomes of this study align with existing research, underscoring the effectiveness of the HEAR score in risk stratification for patients with chest pain. In practical terms, the implementation of the HEAR score in clinical decision-making processes holds significant promise.

Identification of an Additional Metal-Binding Site in Human Dipeptidyl Peptidase III.

Dipeptidyl peptidase III (DPP III, EC 3.4.14.4) is a monozinc metalloexopeptidase that hydrolyzes dipeptides from the N-terminus of peptides consisting of three or more amino acids. Recently, DPP III has attracted great interest from scientists, and numerous studies have been conducted showing that it is involved in the regulation of various physiological processes. Since it is the only metalloenzyme among the dipeptidyl peptidases, we considered it important to study the process of binding and exchange of physiologically relevant metal dications in DPP III. Using fluorimetry, we measured the Kd values for the binding of Zn2+, Cu2+, and Co2+ to the catalytic site, and using isothermal titration calorimetry (ITC), we measured the Kd values for the binding of these metals to an additional binding site. The structure of the catalytic metal's binding site is known from previous studies, and in this work, the affinities for this site were calculated for Zn2+, Cu2+, Co2+, and Mn2+ using the QM approach. The structures of the additional binding sites for the Zn2+ and Cu2+ were also identified, and MD simulations showed that two Cu2+ ions bound to the catalytic and inhibitory sites exchanged less frequently than the Zn2+ ions bound to these sites.

Identification of SH2 Domain-Containing Protein 3C as a Novel, Putative Interactor of Dipeptidyl Peptidase 3.

Dipeptidyl peptidase 3 (DPP3) is a zinc-dependent exopeptidase with broad specificity for four to eight amino acid residue substrates. It has a role in the regulation of oxidative stress response NRF2-KEAP1 pathway through the interaction with KEAP1. We have conducted stable isotope labeling by amino acids in a cell culture coupled to mass spectrometry (SILAC-MS) interactome analysis of TRex HEK293T cells using DPP3 as bait and identified SH2 Domain-Containing Protein 3C (SH2D3C) as prey. SH2D3C is one of three members of a family of proteins that contain both the SH2 domain and a domain similar to guanine nucleotide exchange factor domains of Ras family GTPases (Ras GEF-like domain), named novel SH2-containing proteins (NSP). NSPs, including SH2D3C (NSP3), are adaptor proteins involved in the regulation of adhesion, migration, tissue organization, and immune response. We have shown that SH2D3C binds to DPP3 through its C-terminal Ras GEF-like domain, detected the colocalization of the proteins in living cells, and confirmed direct interaction in the cytosol and membrane ruffles. Computational analysis also confirmed the binding of the C-terminal domain of SH2D3C to DPP3, but the exact model could not be discerned. This is the first indication that DPP3 and SH2D3C are interacting partners, and further studies to elucidate the physiological significance of this interaction are on the way.

Influence of Mutations of Conserved Arginines on Neuropeptide Binding in the DPP III Active Site.

Dipeptidyl peptidase III (DPP III), a zinc exopeptidase, is involved in the final steps of intercellular protein degradation and has a marked affinity for opioid peptides such as enkephalins and endomorphins. Recently, we characterized a number of neuropeptides as potential substrates and inhibitors of human DPP III and provided an explanation for their differential behavior. These studies prompted us to investigate the influence of the conserved R399 and R669 on neuropeptides binding to DPP III. Measuring kinetic parameters in inhibitory assays, we found that mutation of R669 to Ala or Met significantly reduced the inhibitory properties of the slow substrates tynorphin and valorphin, whereas the effects on binding of the good substrates Arg2-2NA and Leu-enkephalin were small. Molecular dynamics simulations of wild-type (WT) and mutant DPP III complexes with Leu-enkephalin, tynorphin, valorphin, and Arg2-2NA in conjunction with calculations of binding free energies revealed that the lower inhibitory potency of slow substrates in the R669A mutant can be explained by the lower binding affinity of tynorphin and the higher propensity of valorphin to hydrolyze in the mutant than in WT. The R399A mutation was shown to affect the binding and/or hydrolysis of both good and slow substrates, with the effects on Leu-enkephalin being the most pronounced.

Demystifying DPP III Catalyzed Peptide Hydrolysis-Computational Study of the Complete Catalytic Cycle of Human DPP III Catalyzed Tynorphin Hydrolysis.

Dipeptidyl peptides III (DPP III) is a dual-domain zinc exopeptidase that hydrolyzes peptides of varying sequence and size. Despite attempts to elucidate and narrow down the broad substrate-specificity of DPP III, there is no explanation as to why some of them, such as tynorphin (VVYPW), the truncated form of the endogenous heptapeptide spinorphin, are the slow-reacting substrates of DPP III compared to others, such as Leu-enkephalin. Using quantum molecular mechanics calculations followed by various molecular dynamics techniques, we describe for the first time the entire catalytic cycle of human DPP III, providing theoretical insight into the inhibitory mechanism of tynorphin. The chemical step of peptide bond hydrolysis and the substrate binding to the active site of the enzyme and release of the product were described for DPP III in complex with tynorphin and Leu-enkephalin and their products. We found that tynorphin is cleaved by the same reaction mechanism determined for Leu-enkephalin. More importantly, we showed that the product stabilization and regeneration of the enzyme, but not the nucleophilic attack of the catalytic water molecule and inversion at the nitrogen atom of the cleavable peptide bond, correspond to the rate-determining steps of the overall catalytic cycle of the enzyme.

Interdisciplinary Study of the Effects of Dipeptidyl-Peptidase III Cancer Mutations on the KEAP1-NRF2 Signaling Pathway.

Dipeptidyl peptidase III (DPP III) is associated with cancer progression via interaction with KEAP1, leading to upregulation of the KEAP1-NRF2 oxidative stress pathway. Numerous DPP III mutations have been found in human tumor genomes, and it is suggested that some of them may alter affinity for KEAP1. One such example is the DPP III-R623W variant, which in our previous study showed much higher affinity for the Kelch domain of KEAP1 than the wild-type protein. In this work, we have investigated the effects of this mutation in cultured cells and the effects of several other DPP III mutations on the stability of KEAP1-DPP III complex using an interdisciplinary approach combining biochemical, biophysical and molecular biology methods with computational studies. We determined the affinity of the DPP III variants for the Kelch domain experimentally and by molecular modeling, as well as the effects of the R623W on the expression of several NRF2-controlled genes. We confirmed that the R623W variant upregulates NQO1 expression at the transcriptional level. This supports the hypothesis from our previous study that the increased affinity of the R623W variant for KEAP1 leads to upregulation of the KEAP1-NRF2 pathway. These results provide a new perspective on the involvement of DPP III in cancer progression and prognosis.

Bis(phenylethynyl)arene Linkers in Tetracationic Bis-triarylborane Chromophores Control Fluorimetric and Raman Sensing of Various DNAs and RNAs.

We report four new luminescent tetracationic bis-triarylborane DNA and RNA sensors that show high binding affinities, in several cases even in the nanomolar range. Three of the compounds contain substituted, highly emissive and structurally flexible bis(2,6-dimethylphenyl-4-ethynyl)arene linkers (3: arene=5,5'-2,2'-bithiophene; 4: arene=1,4-benzene; 5: arene=9,10-anthracene) between the two boryl moieties and serve as efficient dual Raman and fluorescence chromophores. The shorter analogue 6 employs 9,10-anthracene as the linker and demonstrates the importance of an adequate linker length with a certain level of flexibility by exhibiting generally lower binding affinities than 3-5. Pronounced aggregation-deaggregation processes are observed in fluorimetric titration experiments with DNA for compounds 3 and 5. Molecular modelling of complexes of 5 with AT-DNA, suggest the minor groove as the dominant binding site for monomeric 5, but demonstrate that dimers of 5 can also be accommodated. Strong SERS responses for 3-5 versus a very weak response for 6, particularly the strong signals from anthracene itself observed for 5 but not for 6, demonstrate the importance of triple bonds for strong Raman activity in molecules of this compound class. The energy of the characteristic stretching vibration of the C≡C bonds is significantly dependent on the aromatic moiety between the triple bonds. The insertion of aromatic moieties between two C≡C bonds thus offers an alternative design for dual Raman and fluorescence chromophores, applicable in multiplex biological Raman imaging.

Unravelling the inhibitory zinc ion binding site and the metal exchange mechanism in human DPP III.

Dipeptidyl peptidase III (DPP III), a zinc-dependent exopeptidase, is widely distributed in organisms and present in almost all human tissues. In addition to its involvement in protein catabolism, it plays a role in oxidative stress and blood pressure regulation, and there is evidence of its involvement in pain modulation. Excess zinc ions have been found to inhibit its hydrolytic activity, but the binding affinity, binding site geometry, and mechanism of inhibitory activity have been unknown. Using several different computational approaches, we determined the inhibitory zinc ion binding site, its coordination and relative binding affinity. During some simulations the translocation of the zinc ion from the inhibitory to the catalytic binding site was observed, accompanied by movement of the catalytic zinc ion toward the exit of the substrate binding site. The traced behavior suggests an associative type of metal ion exchange, in which the formation of the ternary complex between enzyme and two metal ions precedes the exit of the catalytic metal ion. Differently from our previous findings that binding of a peptide induces partial opening of hDPP III, the globularity of the protein did not change in MD simulations of the hermorphin-like peptide bound to hDPP III with two zinc ions. However, the entrance to the interdomain cleft widens during Zn diffusion into the protein and was found to be the highest energy barrier in the process of metal translocation from the solvent to the active site. Finally, we discuss why excess zinc reduces enzyme activity.

Triarylborane Dyes as a Novel Non-Covalent and Non-Inhibitive Fluorimetric Markers for DPP III Enzyme.

Novel dyes were prepared by simple "click CuAAC" attachment of a triarylborane-alkyne to the azide side chain of an amino acid yielding triarylborane dye 1 which was conjugated with pyrene (dye 2) forming a triarylborane-pyrene FRET pair. In contrast to previous cationic triarylboranes, the novel neutral dyes interact only with proteins, while their affinity to DNA/RNA is completely abolished. Both the reference triarylborane amino acid and triarylborane-pyrene conjugate bind to BSA and the hDPP III enzyme with high affinities, exhibiting a strong (up to 100-fold) fluorescence increase, whereby the triarylborane-pyrene conjugate additionally retained FRET upon binding to the protein. Furthermore, the triarylborane dyes, upon binding to the hDPP III enzyme, did not impair its enzymatic activity under a wide range of experimental conditions, thus being the first non-covalent fluorimetric markers for hDPP III, also applicable during enzymatic reactions with hDPP III substrates.

A Quadrupolar Bis-Triarylborane Chromophore as a Fluorimetric and Chirooptic Probe for Simultaneous and Selective Sensing of DNA, RNA and Proteins.

A water-soluble tetracationic quadrupolar bis-triarylborane chromophore showed strong binding to ds-DNA, ds-RNA, ss-RNA, as well as to the naturally most abundant protein, BSA. The novel dye can distinguish between DNA/RNA and BSA by fluorescence emission separated by Δ ν ˜ =3600 cm-1 , allowing for the simultaneous quantification of DNA/RNA and protein (BSA) in a mixture. The applicability of such fluorimetric differentiation in vitro was demonstrated, strongly supporting a protein-like target as a dominant binding site of 1 in cells. Moreover, our dye also bound strongly to ss-RNA, with the unusual rod-like structure of the dye, decorated by four positive charges at its termini and having a hydrophobic core, acting as a spindle for wrapping A, C and U ss-RNAs, but not poly G, the latter preserving its secondary structure. To the best of our knowledge, such unmatched, multifaceted binding activity of a small molecule toward DNA, RNA, and proteins and the selectivity of its fluorimetric and chirooptic response makes the quadrupolar bis-triarylborane a novel chromophore/fluorophore moiety for biochemical applications.

A Quadrupolar Bis-Triarylborane Chromophore as a Fluorimetric and Chirooptic Probe for Simultaneous and Selective Sensing of DNA, RNA and Proteins.

Invited for the cover of this issue are the groups of Todd B. Marder at the Julius-Maximilians-Universität Würzburg and Ivo Piantanida at the Ruder Boskovic Institute. The image depicts the molecular structure of a bis-triarylborane-based chromophore that is simultaneously detecting ds-DNA and proteins. Read the full text of the article at 10.1002/chem.201903936.

Oxidase or peptidase? A computational insight into a putative aflatoxin oxidase from Armillariella tabescens.

Aflatoxin oxidase (AFO), an enzyme isolated from Armillariella tabescens, has been reported to degrade aflatoxin B1 (AFB1). However, recent studies reported sequence and structure similarities with the dipeptidyl peptidase III (DPP III) family of enzymes and confirmed peptidase activity toward DPP III substrates. In light of these investigations, an extensive computational study was performed in order to improve understanding of the AFO functions. Steered MD simulations revealed long-range domain motions described as protein opening, characteristic for DPPs III and necessary for substrate binding. Newly identified open and partially open forms of the enzyme closely resemble those of the human DPP III orthologue. Docking of a synthetic DPP III substrate Arg2 -2-naphthylamide revealed a binding mode similar to the one found in crystal structures of human DPP III complexes with peptides with the S1 and S2 subsites' amino acid residues conserved. On the other hand, no energetically favorable AFB1 binding mode was detected, suggesting that aflatoxins are not good substrates of AFO. High plasticity of the zinc ion coordination sphere within the active site, consistent with that of up to date studied DPPs III, was observed as well. A detailed electrostatic analysis of the active site revealed a predominance of negatively charged regions, unsuitable for the binding of the neutral AFB1. The present study is in line with the most recent experimental study on this enzyme, both suggesting that AFO is a typical member of the DPP III family.

New Zinc Ion Parameters Suitable for Classical MD Simulations of Zinc Metallopeptidases.

The main aim of this work was to find parameters for the zinc ion in human dipeptidyl peptidase III (DPP III) active site that would enable its reliable modeling. Since the parameters publicly available failed to reproduce the zinc ion coordination in the enzyme, we developed a new set of the hybrid bonded/nonbonded parameters for the zinc ion suitable for molecular modeling of the human DPP III, dynamics, and ligand binding. The parameters allowed exchange of the water molecules coordinating the zinc ion and proved to be robust enough to enable reliable modeling not only of human DPP III and its orthologues but also of the other zinc-dependent peptidases with the zinc ion coordination similar to that in dipeptidyl peptidases III, i.e., peptidases with the zinc ion coordinated with two histidines and one glutamate. The new parameters were tested on a set of 21 different systems comprising 8 different peptidases, 5 DPP III orthologues, thermolysin, neprilysin, and aminopeptidase N, and the results are summarized in the second part of the article.

The role of conserved Cys residues in Brassica rapa auxin amidohydrolase: Cys139 is crucial for the enzyme activity and Cys320 regulates enzyme stability.

Brassica rapa auxin amidohydrolase (BrILL2) participates in the homeostasis of the plant hormones auxins by hydrolyzing the amino acid conjugates of auxins, thereby releasing the free active form of hormones. Herein, the potential role of the two conserved Cys residues of BrILL2 (at sequence positions 139 and 320) has been investigated by using interdisciplinary approaches and methods of molecular biology, biochemistry, biophysics and molecular modelling. The obtained results show that both Cys residues participate in the regulation of enzyme activity. Cys320 located in the satellite domain of the enzyme is mainly responsible for protein stability and regulation of enzyme activity through polymer formation, as has been revealed by enzyme kinetics and differential scanning calorimetry analysis of the BrILL2 wild type and mutants C320S and C139S. Cys139 positioned in the active site of the catalytic domain is involved in the coordination of one Mn(2+) ion of the bimetal center and is crucial for the enzymatic activity. Although the point mutation Cys139 to Ser causes the loss of enzyme activity, it does not affect the metal binding to the BrILL2 enzyme, as has been shown by isothermal titration calorimetry, circular dichroism spectropolarimetry and differential scanning calorimetry data. MD simulations (200 ns) revealed a different active site architecture of the BrILL2C139S mutant in comparison to the wild type enzyme. Additional possible reasons for the inactivity of the BrILL2C139S mutant have been discussed based on MD simulations and MM-PBSA free energy calculations of BrILL2 enzyme complexes (wt and C139S mutant) with IPA-Ala as a substrate.

Sensing of Double-Stranded DNA/RNA Secondary Structures by Water Soluble Homochiral Perylene Bisimide Dyes.

A broad series of homochiral perylene bisimide (PBI) dyes were synthesized that are appended with amino acids and cationic side chains at the imide positions. Self-assembly behavior of these ionic PBIs has been studied in aqueous media by UV/Vis spectroscopy, revealing formation of excitonically coupled H-type aggregates. The interactions of these ionic PBIs with different ds-DNA and ds-RNA have been explored by thermal denaturation, fluorimetric titration and circular dichroism (CD) experiments. These PBIs strongly stabilized ds-DNA/RNA against thermal denaturation as revealed by high melting temperatures of the formed PBI/polynucleotide complexes. Fluorimetric titrations showed that these PBIs bind to ds-DNA/RNA with high binding constants depending on the number of the positive charges in the side chains. Thus, spermine-containing PBIs with six positive charges each showed higher binding constants (logKs =9.2-9.8) than their dioxa analogues (logKs =6.5-7.9) having two positive charges each. Induced circular dichroism (ICD) of PBI assemblies created within DNA/RNA grooves was observed. These ICD profiles are strongly dependent on the steric demand of the chiral substituents of the amino acid units and the secondary structure of the DNA or RNA. The observed ICD effects can be explained by non-covalent binding of excitonically coupled PBI dimer aggregates into the minor groove of DNA and major groove of RNA which is further supported by molecular modeling studies.

Aryl-bis-(scorpiand)-aza receptors differentiate between nucleotide monophosphates by a combination of aromatic, hydrogen bond and electrostatic interactions.

Bis-polyaza pyridinophane scorpiands bind nucleotides in aqueous medium with 10-100 micromolar affinity, predominantly by electrostatic interactions between nucleotide phosphates and protonated aliphatic amines and assisted by aromatic stacking interactions. The pyridine-scorpiand receptor showed rare selectivity toward CMP with respect to other nucleotides, whereby two orders of magnitude affinity difference between CMP and UMP was the most appealing. The phenanthroline-scorpiand receptor revealed at pH 5 strong selectivity toward AMP with respect to other NMPs, based on the protonation of adenine heterocyclic N1. The results stress that the efficient recognition of small biomolecules within scorpiand-like receptors relies mostly on the electrostatic and H-bonding interactions despite the competitive interactions in the bulk solvent, thus supporting further optimisation of this versatile artificial moiety.

BioMe: biologically relevant metals.

In this article, we introduce BioMe (biologically relevant metals), a web-based platform for calculation of various statistical properties of metal-binding sites. Users can obtain the following statistical properties: presence of selected ligands in metal coordination sphere, distribution of coordination numbers, percentage of metal ions coordinated by the combination of selected ligands, distribution of monodentate and bidentate metal-carboxyl, bindings for ASP and GLU, percentage of particular binuclear metal centers, distribution of coordination geometry, descriptive statistics for a metal ion-donor distance and percentage of the selected metal ions coordinated by each of the selected ligands. Statistics is presented in numerical and graphical forms. The underlying database contains information about all contacts within the range of 3 Å from a metal ion found in the asymmetric crystal unit. The stored information for each metal ion includes Protein Data Bank code, structure determination method, types of metal-binding chains [protein, ribonucleic acid (RNA), deoxyribonucleic acid (DNA), water and other] and names of the bounded ligands (amino acid residue, RNA nucleotide, DNA nucleotide, water and other) and the coordination number, the coordination geometry and, if applicable, another metal(s). BioMe is on a regular weekly update schedule. It is accessible at http://metals.zesoi.fer.hr.