Harald Lanig

• PD Dr. rer. nat.
• Friedrich-Alexander-University Erlangen-Nürnberg

Enzymes capable of processing a variety of compounds enable plants to adapt to diverse environmental conditions. PRISEs (progesterone-5β-reductase/iridoid synthase-like enzymes), examples of such substrate-promiscuous enzymes, are involved in iridoid and cardenolide pathways and demonstrate notable substrate promiscuity by reducing the activated C=...

An automated pipeline for comprehensive calculation of intermolecular interaction energies based on molecular force-fields using the Tinker molecular modelling package is presented. Starting with non-optimized chemically intuitive monomer structures, the pipeline allows the approximation of global minimum energy monomers and dimers, configuration s...

An automated pipeline for comprehensive calculation of intermolecular interaction energies based on molecular force-fields using the Tinker molecular modelling package is presented. Starting with non-optimized chemically intuitive monomer structures, the pipeline allows the approximation of global minimum energy monomers and dimers, configuration s...

3β-hydroxy-Δ5-steroid dehydrogenases (3βHSDs) are supposed to be involved in 5β-cardenolide biosynthesis. Here, a novel 3βHSD (Dl3βHSD2) was isolated from Digitalis lanata shoot cultures and expressed in E. coli. Recombinant Dl3βHSD1 and Dl3βHSD2 shared 70% amino acid identity, reduced various 3-oxopregnanes and oxidised 3-hydroxypregnanes, but onl...

Bottom-up variants of Dissipative Particle Dynamics (DPD), where particles can be defined as small molecules with a molecular weight in the order of 100 Daltons, allow the study of large (bio)molecular systems and supramolecular phenomena on the nanometre length and microsecond time scale. The conservative interaction between two DPD particles i an...

Objectives Rheumatoid arthritis (RA) is an autoimmune disease strongly associated with the major histocompatibility complex (MHC) class II allele DRB1*04:01, which encodes a protein that binds self-peptides for presentation to T cells. This study characterises the autoantigen-presenting function of DRB1*04:01 (HLA-DRA*01:01/HLA-DRB1*04:01) at a mol...

Three putative 21-hydroxypregnane 21-O-malonyltransferases (21MaT) from Digitalis lanata were partially purified. Two of them were supposed to be BAHD-type enzymes. We were unable to purify them in quantities necessary for reliable sequencing. We identified two genes in A. thaliana coding for substrate-promiscuous BAHD-type phenolic glucoside malon...

Targeted structural modifications have led to a novel type of buprenorphine‐derived opioid receptor ligand displaying an improved selectivity profile for the μ‐OR subtype. On this basis, it is shown that phenylazocarboxamides may serve as useful bioisosteric replacements for the widely occurring cinnamide units, without loss of OR binding affinity...

Particle-based mesoscopic simulation with Dissipative Particle Dynamics (DPD) enables the study of supramolecular phenomena at the nanometer length and microsecond time scale for large interacting chemical ensembles representing millions of atoms. The conservative interaction between two DPD particles i and j is characterized by an isotropic repuls...

Fibulin-4 is a 50 kDa glycoprotein of elastic fibers and plays an important role in development and function of elastic tissues. Fibulin-4 consists of a tandem array of five calcium-binding epidermal growth factor-like modules flanked by N- and C-terminal domains. Mutations in the human fibulin-4 gene EFEMP2 have been identified in patients affecte...

Molecular mechanics methods are often used because they are fast and can be applied to a large number of molecules with many atoms. Performing molecular mechanics in its literally sense, molecules and molecular assemblies are abstracted by cumulative forces acting between atoms. Two different force fields may share the same functional form but use...

This chapter outlines a typical molecular dynamics (MD) scenario. The movement of each atom influences the motion of every other atom within the molecule, resulting in a complex mathematical problem of coupled differential equations. The development of methods for describing the motion of atoms in molecules accurately started by using Newton's equa...

Fibulin-4 is a 60kDa calcium binding glycoprotein that has an important role in development and integrity of extracellular matrices. It interacts with elastin, fibrillin-1 and collagen IV as well as with lysyl oxidases and is involved in elastogenesis and cross-link formation. To date, several mutations in the fibulin-4 gene (FBLN4/EFEMP2) are know...

Vein Patterning 1 (VEP1)-encoded progesterone 5β-reductases/iridoid synthases (PRISE) belong to the short-chain dehydrogenase/reductase superfamily of proteins. They are characterized by a set of highly conserved amino acids in the substrate-binding pocket. All PRISEs are capable of reducing the activated C=C double bond of various enones enantiose...

A 4.1μs molecular dynamics simulation of the NR4A1 (hNur77) apo-protein has been undertaken and a previously undetected druggable pocket has become apparent that is located remotely from the ‘traditional’ nuclear receptor ligand-binding site. A NR4A1/bisindole ligand complex at this novel site has been found to be stable over 1 μs of simulation and...

As a scientist, you are used to facing a wide range of tricky situations, related and sometimes not directly related to science. Many unforeseen circumstances can cross your way. Your precisely adjusted experiments are not working as desired, your carefully arranged simulations give inconsistent results, your manuscript unexpectedly is rejected by...

Partial agonists exhibit a submaximal capacity to enhance the coupling of one receptor to an intracellular binding partner. Although a multitude of studies have reported different ligand-specific conformations for a given receptor, little is known about the mechanism by which different receptor conformations are connected to the capacity to activat...

Based on the recently described crystal structure of the β2 adrenergic receptor - Gs-protein complex, we report the first molecular-dynamics simulations of ternary GPCR complexes designed to identify the selectivity determinants for receptor-G-protein binding. Long-term molecular dynamics simulations of agonist-bound β2AR-Gαs and D2R-Gαi complexes...

RMS-deviations within the MD simulations. (A) The RMS-deviations for the individual components of the β2AR-Gαs system are shown. Values for the ligand BI167107, β2AR and Gαs are given in yellow, dark-blue and light-blue, respectively. (B) The RMS-deviations for the individual components of the D2DownR-Gαi system are shown. Values for the ligand dop...

Density profiles of the simulation systems. The partial density profiles of individual components of the simulation systems are shown for the simulation time steps 0–100 ns (first 100 ns) and 900–1000 ns (last 100 ns). (TIFF)

Equilibration of the simulation systems. (A) The β2AR-system (blue ribbons) is shown from the top after insertion into the DOPC-bilayer (grey sticks), but before equilibration steps were performed. (B) After equilibration, the gaps between the receptor and the membrane appeared to be perfectly closed. (C) A side view on the β2AR-Gαs simulation syst...

Conformational changes of Gαi within the D2Down/UpR-Gαi-simulations. (A, B) The D2DownR- and the D2UpR-Gαi-complexes are shown as green and red ribbons, respectively. Residues R227 and D315 are represented as sticks. (C) The distance between the atoms CZ of R227 and CG of D315 is depicted throughout the MD simulations (green: D2DownR-Gαi, red: D2Up...

Alignment of contact areas of chosen Gα-subunits. Amino acids within the Gαs and Gαi sequences forming stable contacts to receptor residues are highlighted with a blue and green background, respectively (according to Figure 4). Red backgrounds point to sequence differences between Gαi and Gαo subunits. Red letters indicate residues involved in ioni...

Conformational changes in the active-state models of the D2R-Gαi-complex. The backbone atoms of GPCRs and G-proteins are shown as ribbons, whereas residue R380 and the nucleotides of the G-proteins are represented as sticks and spheres, respectively. Red arrows denote major helical movements upon receptor activation. (A) Intracellular view of the s...

Atomic fluctuations within the MD simulations. The atomic fluctuations for the Cα-atoms of the β2AR-Gαs-complex (A), the D2DownR-Gαi-complex (B) and the D2UpR-Gαi-complex (C) are given in blue, green and red, respectively. The thickness of the lines indicate different fitting procedures (on Cα-atoms): the thick lines for receptors and G-proteins po...

Free energies of binding for the ternary complexes. The free energies of binding for the β2AR-Gαs system (A), for the D2DownR-Gαi system (B) and for the D2UpR-Gαi system (C) are shown. Here, the free energy of binding consists of a molecular mechanics energy term (internal energy of bonds, angles and dihedrals), the polar contribution and the nonpo...

Results of the computational alanine scanning for the receptors and the G-proteins. aa refers to the amino acids mutated to alanine. ΔΔG-values are provided in the format ‘value ± standard deviation’. The left column shows the regions within the GPCRs and the G-proteins, to which the mutated amino acids belong. (DOC)

Amino-acid contacts within the D2DownR-Gαi-simulation. The occurrence for each amino-acid contact throughout the MD simulation is shown in the grey columns. (DOC)

Distances between receptors and G-proteins within the MD simulations. (A) The distances between the centers of mass of β2AR and the whole Gαs and β2AR and the C-terminus of Gα are shown in dark-blue and light-blue, respectively. (B) The distances between the centers of mass of D2DownR and the whole Gαi and D2DownR and the C-terminus of Gα are shown...

Amino-acid contacts within the β2AR-Gαs-simulation. The occurrence for each amino-acid contact throughout the MD simulation is shown in the grey columns. (DOC)

Amino-acid contacts within the D2UpR-Gαi-simulation. The occurrence for each amino-acid contact throughout the MD simulation is shown in the grey columns. (DOC)

We describe computational studies of the mode of action of the prolyl hydroxylase domain containing protein (PHD2). Long-term molecular dynamics (MD) simulations were performed to investigate the rigidity of the crystallographically observed conformations of PHD2 in solution. We also describe the influence of the C-terminal oxygen-dependent degrada...

G-protein-coupled receptors have extraordinary therapeutic potential as targets for a broad spectrum of diseases. Understanding their function at the molecular level is therefore essential. A variety of crystal structures have made the investigation of the inactive receptor state possible. Recently released X-ray structures of opsin and the β(2)-ad...

Interleukin-21 (IL-21) has been shown to restore immunoglobulin production together with Interleukin-4 (IL-4) in common variable immunodeficiency syndrome (CVID). Here, we elucidate the functional and structural properties of the corresponding IL-21R : IL-4R system. An in vitro cell culture system was established to study the molecular effects of I...

CAChe ist keinesfalls nur ein weiteres Molecular Modelling-Paket, sondern präsentiert sich als eine integrierte Arbeitsumgebung zur Planung, Durchführung, Auswertung und Dokumentation/Archivierung vollständiger Projekte.

Single-chain Fv triplebodies (sctb), consisting of a single polypeptide chain with 3 single-chain antibody variable fragments connected in tandem, were generated as antileukemic agents. A CD19-specific sctb of this format has previously been shown to be superior to a bispecific single-chain Fv antibody fragment (bsscFv) for the elimination of leuke...

Die Modellierung von biologischen Makromolekülen sowie deren Wechselwirkungen mit der Umgebung und/oder Liganden stellt einen wichtigen Teilbereich der Computer-Chemie dar, besonders in der pharmazeutischen Industrie. Das sehr umfangreiche Programmpaket AMBER ist speziell an Proteinchemiker adressiert. Es wurde kürzlich in der Version 5.0 freigegeb...

Extensive molecular-dynamics simulations show that the distance between the centers of gravity of the two equivalent helices 3 in the DNA-binding heads of the dimer of the tetracycline-repressor protein (TetR) can be used as a reliable diagnostic of induction. This is not, however, true for X-ray structures, but only for molecular-dynamics simulati...

Synthesis, biological investigations and molecular docking studies of nonantibiotic and nontetracyclic inducers that feature a minimal key motif of the natural lead tetracycline are presented. The diarylpropane-1,3-dione motif was identified as the minimal substructure responsible for TetR induction by tetracyclines. The first nontetracyclic surrog...

Assembling phenylpiperazines with 7a-azaindole via different spacer elements, we developed subtype selective dopamine receptor ligands of types 1a,c, 2a, and 3a preferentially interacting with D4, D2, and D3, respectively. To complete this set, the methylthio analogues 2b and 3b exceeding the affinity of 2a and 3a by one order of magnitude and the...

In recent years, the earlier view of proteins as relatively rigid structures has been replaced by a dynamic model in which the internal motions and resulting conformational changes play an essential role in their function. In this context, molecular dynamics (MD) simulations have become an important computational tool for understanding the physical...

Collagen type II (CII) is a cartilage-specific target of pathologic humoral autoimmune responses in rheumatoid arthritis as well as in the collagen-induced arthritis model. The aim of the present study is to investigate the critical amino acid residues conferring CII epitope specificity of the prototypic arthritogenic murine mAb CIIC1. A homology m...

Molecular mechanics (MM) rests on a view of molecules as balls held together by springs. The potential energy of a molecule can be written as the sum of terms involving bond stretching, angle bending, dihedral angles and nonbonded interactions. Giving these terms explicit mathematical forms constitutes devising a forcefield, and giving actual numbe...

In recent decades, new less-invasive, nonlinear optical methods have been proposed and optimized for monitoring fast physiological processes in biological cells. One of these methods allows the action potential (AP) in cardiomyocytes or neurons to be monitored by means of second-harmonic generation (SHG). We now present the first, to our knowledge,...

Proline-derived peptide mimetics have become an area of paramount importance in peptide and protein chemistry. Since protein crystal structures frequently display Psi angles of 140-170 degrees for prolyl moieties, our intention was to design a completely novel series of 2,3-fused-proline-derived lactams covering this particular conformational space...

The binding specificity of alpha7beta1 integrins for different laminin isoforms is defined by the X1 and X2 splice domains located in the beta-propeller domain of the alpha7 subunit. In order to gain insight into the mechanism of specific laminin-integrin interactions, we defined laminin-binding epitopes of the alpha7X1 and -X2 domains by single am...

Molecular-dynamics simulations have been used to investigate the mechanism of induction of a mutant (revTetR) of the tetracycline repressor protein (TetR) that shows the reverse phenotype (i.e., it is induced in the absence of tetracyclines and not in their presence). Low-frequency, normal-mode analyses demonstrate that the reverse phenotype is rep...

A combination of structures, energies, and spectral data calculated using density functional theory (DFT) with experimental NMR data has been used to assign conformational equilibria for tetracycline and 5a,6-anhydrotetracycline in water at pH 1, 7, and 10 and in chloroform (5a,6-anhydrotetracycline) and methanol (tetracycline). The results suggest...

A series of novel 2,4-diaminopyrimido[4,5-b]indol-6-ols has been synthesized and the in vitro cytotoxic activities were evaluated against four human cancer cell lines originating from solid tumors. An increase in activity was observed when a heteroaromatic ring was annulated on side g of the pyrimido[4,5-b]indole system to give compounds with activ...

Semiempirical molecular orbital theory has been used for a systematic scan of the binding positions for a Mg2+ ion with 5a,6–anhydrotetracycline taking both conformational flexibility and possible different tautomeric forms into account. The magnesium ion has been calculated alone and with four or five complexed water molecules in order to simulate...

“GeometricData.zip” with the coordinates of the minima for each cluster/protonation pattern/water complexation sphere. The name tag indicates the protonation pattern, the conformation and the amount of water molecules in the complexation sphere

The binding motif (pharmacophore) for induction and the changes in the structure of the binding site that accompany induction have been determined from molecular-dynamics simulations on the tetracycline-repressor signal-transduction protein. The changes and the induction mechanism are discussed and compared with conclusions drawn from earlier X-ray...

Molecular dynamics simulations on the tetracycline-repressor (TetR) protein, both in the absence of an inducer and complexed with the inducers tetracycline and 5a,6-anhydrotetracycline, show significant differences in the structures and dynamics of the induced and non-induced forms of the protein. Calpha-density-difference plots, low-frequency norm...

We present a computational model study designed to simulate the results of time-resolved fluorescence spectra of tryptophan in proteins. In such measurements, the occurrence of more than one fluorescence lifetime is generally attributed to the existence of several tryptophan rotamers and/or structural conformations of the protein structure. The pro...

We report a consistent set of AMBER force-field parameters for the most common phosphorylated amino acids, phosphoserine, phosphothreonine, phosphotyrosine, and phosphohistidine in different protonation states. The calculation of atomic charges followed the original restrained electrostatic potential fitting procedure used to determine the charges...

A review. The mol.-modeling software Chimera is presented for visualization and anal. of biomols. Modeling is discussed of proteins. [on SciFinder (R)]

Bei Makromolekülen spielt die Visualisierung eine wichtige Rolle, vor allem dann, wenn es um Biomoleküle wie Proteine oder DNS geht. Hier setzt das Molecular-Modeling-Paket Chimera an.

Piritrexim (PTX) (1), a lipophilic inhibitor of the human dihydrofolate reductase, has been evaluated as an anticancer agent. The synthesis of four structural variations (2-5) of PTX is reported. The PTX analogues 2-5 were obtained by reaction of suitable C3-building blocks with pyrimidine-2,4,6-triamine (14) or with cyanacetamide (7) and guanidine...

Pymol empfiehlt sich bei der Darstellung von Proteinen und Peptiden als Ergänzung zu anderen etablierten freien Programmen wie Rasmol oder Deepview.

Focusing on the similarity and divergence of GPCR subtypes and their ligand interactions, we generated dopamine D2, D3, and D4 receptor models based on the rhodopsin crystal structure and refined these with an extensive MM/MD protocol. After validation by diagnostic experimental data, subtype-specific relative positions of TM1, 2, 6, and 7 and bend...

Inhibitory glycine receptors mediate rapid synaptic inhibition in mammalian spinal cord and brainstem. The previously identified hyperekplexia mutation GLRA1(P250T), located within the intracellular TM1-2 loop of the GlyR alpha1 subunit, results in altered receptor activation and desensitization. Here, elementary steps of ion channel function of al...

Wer Proteinstrukturen am Computer modellieren oder manipulieren möchte, ist oft auf teure Software angewiesen. Eine Alternative ist der kostenfreie SwissModel-Server.

Proteinstrukturen grafisch darstellen, analysieren und manipulieren - alles kein Problem für das kostenlose Programm DeepView.

The aminopeptidase of Aeromonas proteolytica (AAP) belongs to the group of metallo-hydrolases that require two divalent cations for full activity. Such binuclear metal centers are found in several aminopeptidases, raising the question whether a common mechanism, at least partly, is likely. We have used a quantum mechanical/molecular mechanical (QM/...

Signals delivered by the immunoglobulin (Ig)-like pre-B-cell receptor (pre-BCR) are critical for efficient maturation of early precursor B (pre-B) cells. A pre-BCR contains two immunoglobulin mu-heavy chains (muHC), two surrogate light chains (SLC) consisting of the non-covalently associated polypeptides, VpreB and lambda5, and the heterodimeric si...

The binding of anhydrotetracycline (atc) in wild-type TetR(D), TetR(B), and four single tryptophan mutants of TetR(B) was investigated by UV/vis absorption, steady state, and time-resolved fluorescence spectroscopy. From absorption titration experiments with Mg2+, we conclude that binding of one [atc-Mg]+ complex in the homodimer causes changes in...

AM1 semiempirical molecular orbital calculations have been used to probe the complexation sites for naked and hydrated magnesium ions to the different conformations and protonation states of tetracycline. The calculations reveal a wealth of possible magnesium complexation sites within a small energy range, but also indicate that magnesium complexat...

Density functional theory (DFT) has been used to investigate the conformations and tautomeric forms of neutral tetracycline in aqueous solution. The results suggest that the extended conformation is 3−3.5 kcal mol-1 more stable than the twisted one for equivalent tautomers and that as many as six different tautomeric forms lie within 10 kcal mol-1...

Two dendritic fullerene (DF) monoadducts, 2 and 3, which can carry up to 9 and 18 negative charges, respectively, were examined with respect to electrostatic complexation with Cytochrome c (Cytc). To facilitate comprehensive photophysical investigations, the zinc analogue of Cytc (ZnCytc) was prepared according to a novel, modified procedure. The a...

Two dendritic fullerene (DF) monoadducts, 2 and 3, which can carry up to 9 and 18 negative charges, respectively, were examined with respect to electrostatic complexation with Cytochrome c (Cytc). To facilitate comprehensive photophysical investigations, the zinc analogue of Cytc (ZnCytc) was prepared according to a novel, modified procedure. The a...

A combined quantum mechanical/molecular mechanical (QM/MM) docking approach for the investigation of protein-inhibitor complexes is presented. Starting points for QM/MM optimizations are generated with AutoDock. The subsequent semiempirical AM1 QM/MM optimization of the complex obtained by the docking procedure gives a more detailed description of...

Rationales Wirkstoffdesign, so scheint es, baut heute hauptsächlich auf den Daten aus Genom- und Proteomanalysen auf, die mit den Werkzeugen der Chem-und Bioinformatik nur noch entschlüsselt werden müssen. Doch es kommt auch auf die Interaktionen zwischen Proteinen und wenigen Liganden oder die Änderung der Enzymaktivität nach einer Mutation an. Da...

A fruitful combination of molecular dynamics based design and modern synthetic reactions led to a conformatively rigidized cis-peptidyl proline surrogate (see picture). NMR spectroscopic experiments clearly show the existance of type VIa β-turn properties that are of interest in drug discovery.

Eine fruchtbare Kombination von Moleküldynamik-basiertem Design mit modernen Synthesereaktionen führte zu einem konformativ fixierten cis-Peptidyl-Prolin-Derivat (siehe Bild). NMR-spektroskopische Untersuchungen sprechen eindeutig für β-Schleifen-VIa-artige Eigenschaften, die bei der Entwicklung neuartiger Arzneistoffe von großem Interesse sind.

A CoMFA study was undertaken to elucidate the correlation of biological activity and structural parameters of 25 dopamine D4 antagonists. A special point of interest is that we have included the atypical D4 antagonist clozapine as a structural template for all other compounds. After comparing potential protonation sites at semiempirical (AM1) and a...

A hexaprotonated “supermacrocycle” of Schiff base macrocycles forms as the only product (>90 % yield) in a nine-component condensation of the tetrapodal pentaamine 1 with the dialdehyde 2 in the presence of protons (see scheme). The molecule is chiral, and enantiomers in the racemic mixture interconvert by inversion of the large macrocyclic ring, a...

Schiff base condensation of the pentadentate tetrapodal amine 1 with 2,6-diformyl-4-methylphenol 2 leads in a [3 + 6] condensation to a previously not described macrocycle 3 which shows C 3-symmetry. X-ray analysis shows a truncated cone shape for 3. At T ≥ 100°C, the 1H-ROESY/EXSY spectrum reveals pairwise exchange of corresponding sites, indicati...