Klaus R. Liedl

last updated 6/2019

Peer-Reviewed Publications


The Hydrogenobyric Acid Structure Reveals the Corrin Ligand as an Entatic State Module Empowering B12 Cofactors for Catalysis CDR-H3 loop ensemble in solution - conformational selection upon antibody binding Mechanism of Olefin Metathesis with Neutral and Cationic Molybdenum Imido Alkylidene N-Heterocyclic Carbene Complexes Toward novel inhibitors against KdsB: a highly specific and selective broad-spectrum bacterial enzyme Understanding Structure-Activity Relationships for Trypanosomal Cysteine Protease Inhibitors by Simulations and Free Energy Calculations


Structural basis for the bi-functionality of human oxaloacetate decarboxylase FAHD1 Novel Types of Hypermodified Fluorescent Phyllobilins from Breakdown of Chlorophyll in Senescent Leaves of Grapevine (Vitis vinifera) An Unexpected Switch in Peptide Binding Mode: From Simulation to Substrate Specificity Low frequency vibrational anharmonicity and nuclear spin effects of Cl-(H2) and Cl-(D2) Phase Diagram of a Stratum Corneum Lipid Mixture Identification of dual Sigma1 receptor modulators/acetylcholinesterase inhibitors with antioxidant and neurotrophic properties, as neuroprotective agents Electrostatic recognition in substrate binding to serine proteases Cu[B2(SO4)4] and Cu[B(SO4)2(HSO4)] - Two Silicate Analogue Borosulfates Differing in their Dimensionality: A Comparative Study of Stability and Acidity Discovery of Retinoic Acid-Related Orphan Receptor γt Inverse Agonists via Docking and Negative Image-Based Screening The fumarylacetoacetate hydrolase (FAH) superfamily of enzymes: multifunctional enzymes from microbes to mitochondria Peptidic Macrocycles-Conformational Sampling and Thermodynamic Characterization Highly Electrophilic, Catalytically Active and Redox-Responsive Cobaltoceniumyl and Ferrocenyl Triazolylidene Coinage Metal Complexes Cobaltocenylidene, a mesoionic metalloceno carbene, stabilized in a Gold (III) complex Pyro-Phyllobilins - Elusive Chlorophyll Catabolites Lacking a Critical Carboxylate Function of the Natural Chlorophylls Characterizing the Diversity of the CDR-H3 Loop Conformational Ensembles in Relationship to Antibody Binding Properties


CaB2S4O16: A Borosulfate Exhibiting a New Structure Type with Phyllosilicate Analogue Topology High-Pressure Synthesis and Characterization of the Ammonium Yttrium Borate (NH4)YB8O14 Mechanisms Responsible for ω-Pore Currents in Cav Calcium Channel Voltage-Sensing Domains Balance between hydration enthalpy and entropy is important for ice binding surfaces in Antifreeze Proteins Ag[B(SO4)2] - Synthesis, Crystal Structure, and Characterization of the First Precious-Metal Borosulfate Molecular Connectivity Predefines Polypharmacology: Aliphatic Rings, Chirality, and sp3 Centers Enhance Target Selectivity Crystal structure of Pla l 1 reveals both structural similarity and allergenic divergence within the Ole e 1-like protein family Molecular dynamics simulation studies of novel β-lactamase inhibitor Conformational Flexibility Differentiates Naturally Occurring Bet v 1 Isoforms Structure of the Major Apple Allergen Mal d 1 Binding Pose Flip Explained via Enthalpic and Entropic Contributions Determinants of Macromolecular Specificity from Proteomics-Derived Peptide Substrate Data Carbonic acid monoethyl ester as a pure solid and its conformational isomerism in the gas-phase Discovery and Characterization of Diazenylaryl Sulfonic Acids as Inhibitors of Viral and Bacterial Neuraminidases High-pressure synthesis and crystal structure of In3B5O12 Gaining in pan-affinity towards sigma 1 and sigma 2 receptors. SAR studies on arylalkylamines


Chlorophyll-Derived Yellow Phyllobilins of Higher Plants as Medium-Responsive Chiral Photoswitches DPPC-cholesterol phase diagram using coarse-grained Molecular Dynamics simulations Orthorhombic HP-REOF (RE= Pr, Nd, Sm-Gd)-High-Pressure Syntheses and Single-Crystal Structures (RE= Nd, Sm, Eu) Enthalpic and Entropic Contributions to Hydrophobicity Localization of Millisecond Dynamics: Dihedral Entropy from Accelerated MD Interaction mechanisms of a melatonergic inhibitor in the melatonin synthesis pathway Kinetic barriers in the isomerization of substituted ureas: implications for computer-aided drug design Protease Inhibitors in View of Peptide Substrate Databases Uses of FAHD1 Chlorophyll Catabolites in Fall Leaves of the Wych Elm Tree Present a Novel Glycosylation Motif Sequence diversity of NanA manifests in distinct enzyme kinetics and inhibitor susceptibility Asymmetric arginine dimethylation of RelA provides a repressive mark to modulate TNFα/NF-κB response Prediction of blood:air and fat:air partition coefficients of volatile organic compounds for the interpretation of data in breath gas analysis Quantitative Correlation of Conformational Binding Enthalpy with Substrate Specificity of Serine Proteases New High-Pressure Gallium Borate Ga2B3O7(OH) with Photocatalytic Activity Fold stability during endolysosomal acidification is a key factor for allergenicity and immunogenicity of the major birch pollen allergen


A Cross-Reactive Human Single-Chain Antibody for Detection of Major Fish Allergens, Parvalbumins, and Identification of a Major IgE-Binding Epitope Characterizing Protease Specificity: How Many Substrates Do We Need? Matched Peptides: Tuning Matched Molecular Pair Analysis for Biopharmaceutical Applications Dynamics Govern Specificity of a Protein-Protein Interface: Substrate Recognition by Thrombin FAH Domain Containing Protein 1 (FAHD-1) Is Required for Mitochondrial Function and Locomotion Activity in C. elegans Antipneumococcal activity of neuraminidase inhibiting artocarpin CACNA1D De Novo Mutations in Autism Spectrum Disorders Activate Cav1.3 L-Type Calcium Channels High-Pressure Synthesis of Cd(NH3)2[B3O5(NH3)]2: Pioneering the Way to the Substance Class of Ammine Borates Unique Macrocycles in the Taiwan Traditional Chinese Medicine Database. Strong Nonadditivity as a Key Structure-Activity Relationship Feature: Distinguishing Structural Changes from Assay Artifacts Independent Metrics for Protein Backbone and Side-chain Flexibility: Time Scales and Effects of Ligand Binding Complementary assays helping to overcome challenges for identifying neuraminidase inhibitors Identification of FAH domain containing protein 1 (FAHD1) as oxaloacetate decarboxylase Structure, Thermal Behavior, and Vibrational Spectroscopy of the Silver Borate AgB3O5 Interface dynamics explain assembly dependency of influenza neuraminidase catalytic activity Ice nucleation by water-soluble macromolecules


Ligand Binding Modulates the Structural Dynamics and Compactness of the Major Birch Pollen Allergen Non-13CO2 targeted breath tests: a feasibility study A conserved acidic residue in phenylalanine hydroxylase contributes to cofactor affinity and catalysis Precursors for cytochrome P450 profiling breath tests from an in silico screening approach Charge Anisotropy: Where Atomic Multipoles Matter Most A gatekeeper helix determines the substrate specificity of Sjögren-Larsson Syndrome enzyme fatty aldehyde dehydrogenase The Impact of Nitration on the Structure and Immunogenicity of the Major Birch Pollen Allergen Bet v 1.0101 Dynamic regulation of phenylalanine hydroxylase Heteroaromatic π-stacking Energy Landscapes Matched Molecular Pair Analysis: Significance and the Impact of Experimental Uncertainty Specificity of a protein-protein interface: Local dynamics direct substrate recognition of effector caspases (How to) Profit from Molecular Dynamics-based Ensemble Docking


Deriving Static Atomic Multipoles from the Electrostatic Potential Computer-guided approach to access the anti-influenza activity of licorice constituents Substrate-Driven Mapping of the Degradome by Comparison of Sequence Logos Substrate Sequences Tell Similar Stories as Binding Cavities A novel paramagnetic relaxation enhancement tag for nucleic acids: A tool to study structure and dynamics of RNA An additional substrate binding site in a bacterial phenylalanine hydroxylase Compounds for the treatment of influenza Entropy from State Probabilities: Hydration Entropy of Cations Reciprocal regulation of PKA and Rac signaling Matrix isolation studies of carbonic acid - the vapour phase above the β-polymorph Cleavage Entropy as Quantitative Measure of Protease Specificity Characterisation of Nox4 Inhibitors from Edible Plants


Dynamic Regulation of Phenylalanine Hydroxylase by Simulated Redox Manipulation Identification of PPARgamma Partial Agonists of Natural Origin (I): Development of a Virtual Screening Procedure and In Vitro Validation Porphyrin-LEGO®: synthesis of a hexafullereno-diporphyrin using porphyrins programmed for [4+2]-cycloaddition Effects of Pooling Samples on the Performance of Classification Algorithms: A Comparative Study Identification of Novel Liver X Receptor Activators by Structure-Based Modeling Local structural order in carbonic acid polymorphs: Raman and FT-IR spectroscopy Influenza neuraminidase: a drugable target for natural products


Qualitative prediction of blood-brain barrier permeability on a large and refined dataset A GRID-derived Water Network Stabilizes Molecular Dynamics Computer Simulations of a Protease Minor Groove Binders and Drugs Targeting Proteins Cover Complementary Regions in Chemical Shape Space Identification of Novel Functional Inhibitors of Acid Sphingomyelinase A Challenging System: Free Energy Prediction for Factor Xa Consideration of Water and Solvation Effects in Virtual Screening
Spectroscopic Observation of Matrix-Isolated Carbonic Acid Development of Anti-Viral Agents Using Molecular Modeling and Virtual Screening Techniques Novel neuraminidase inhibitors: identification, biological evaluation and investigations of the binding mode


Dispersion Dominated Halogen-π Interactions: Energies and Locations of Minima
Backbone Flexibility Controls Activity and Specificity of a Protein-Protein Interface: Specificity in Snake Venom Metalloproteases
One Concept, Three Implementations of 3D Pharmacophore-Based Virtual Screening: Distinct Coverage of Chemical Search Space Stabilizing of a Globular Protein by a Highly Complex Water Network: A Molecular Dynamics Simulation Study on Factor Xa Antiviral Potential and Molecular Insight into Neuraminidase Inhibiting Diarylheptanoids from Alpinia katsumadai Challenges for Computer Simulations in Drug Design


Theoretical Prediction of Hydrogen Bond Strength for Use in Molecular Modeling
Hydrogen-Bonding Patterns of Minor Groove-Binder-DNA Complexes Reveal Criteria for Discovery of New Scaffolds Raman Spectroscopic Study of the Phase Transition of Amorphous to Crystalline beta-Carbonic Acid How to Optimize Shape-Based Virtual Screening: Choosing the Right Query and Including Chemical Information


Sequence-Specific Positions of Water Molecules at the Interface between DNA and Minor Groove Binders The Protein Data Bank (PDB), Its Related Services and Software Tools as Key Components for In Silico Guided Drug Discovery


DNA minor groove pharmacophores describing sequence specific properties


Modeling the heterogeneous reaction probability for chlorine nitrate hydrolysis on ice


M.TaqI facilitates the base flipping via an unusual DNA backbone conformation Towards an understanding of DNA recognition by the methyl-CpG binding domain 1 Z-DNA's conformer substates revealed by FT-IR difference spectroscopy of non oriented left-handed double helical poly(dG-dC) The N6-methyl group of adenine further increases the BI stability of DNA compared to C5-methyl groups


Double hydrogen tunneling revisited: The breakdown of experimental tunneling criteria Sulfurous acid (H2SO3) on Io? On the formation of the sulfonate ion from hydrated sulfur dioxide Water-mediated contacts in the trp-repressor operator complex recognition process Daunomycin intercalation stabilizes distinct backbone conformations of DNA Dynamics of DNA: BI and BII phosphate backbone transitions Mechanism of cis-trans isomerization of bis(glycinator)copper(II) The ground-state tunneling splitting of various carboxylic acid dimers Cooperative effects on the formation of intercalation sites


C5-methylation of cytosine in B-DNA thermodynamically and kinetically stabilizes BI Molecular docking studies of natural cholinesterase-inhibiting steroidal alkaloids from Sarcococca saligna About the kinetic feasibility of the Lipscomb mechanism in human carbonic anhydrase II A QM-MM interface between CHARMM and TURBOMOLE: Implementation and application to systems in bulk phase and biologically active systems Influence of backbone conformations of human carbonic anhydrase II on carbon dioxide hydration: Hydration pathways and binding of bicarbonate The ground state tunneling splitting of the 2-pyridone.2-hydroxypyridine dimer Reactions of HOBr + HCl + nH2O and HOBr + HBr + nH2O Modeling anhydrous and aqua copper(II) amino acid complexes: A new molecular mechanics force field parametrization based on quantum chemical studies and experimental data Stepwise induced fit in the pico- and nanosecond time scale governs the complexation of the even-skipped transcriptional repressor homeodomain to DNA Extended method for adiabatic mode reordering The conformer substates of nonoriented B-type DNA in double helical Poly(dG-dC) Hydration of hydroxypyrrole influences binding of ImHpPyPy-β-Dp polyamide to DNA Energetic and stereochemical effects of the protein environment on substrate: A theoretical study of methylmalonyl-CoA mutase Toward elimination of discrepancies between theory and experiment The gas-phase reaction of N2O5 and H2O Exploring HBr ionization at the molecular level


About the stability of sulfurous acid (H2SO3) and its dimer Characterization of the vitamin E-binding properties of human plasma afamin PvuII-endonuclease induces structural alterations at the scissile phosphate group of its cognate DNA Reactions of HOCl + HCl + nH2O and HOCl + HBr + nH2O An accurate semiclassical method to predict ground-state tunneling splittings The optimal tunneling path for the proton transfer in malonaldehyde Restructuring of hydration shells rules the low-temperature dynamics of B-DNA via its two conformer substates Indirect readout of the trp-repressor-operator complex by B-DNA's backbone conformation transitions Towards the experimental decomposition rate of carbonic acid (H2CO3) in aqueous solution The structure, modeling and dynamics of 2,7-diisopropoxy-1,8-diarylnaphthalenes Influence of netropsin's charges on the minor groove width of d(CGCGAATTCGCG)2


Exocyclic groups in the minor groove influence the backbone conformation of DNA BI ↔ BII substate transitions induce changes in the hydration of B-DNA, potentially mediating signal transduction from the minor to the major groove Significance of ligand tails for interaction with the minor groove of B-DNA Calculation of sequence-dependent free energies of hydration of dipeptides formed by alanine and glycine Water-mediated proton transfer: A mechanistic investigation on the example of the hydration of sulfur oxides Complex of B-DNA with polyamides freezes DNA backbone flexibility Structural flexibility of the d(CGAGTACTCG)2 B-DNA decamer and its complex with two polyamides The reaction rate constant of chlorine nitrate hydrolysis The structure, modeling and dynamics of hindered 5,6-diarylacenaphthenes Prediction of the structure of human Janus kinase 2 (JAK2) comprising the two carboxy-terminal domains reveals a mechanism for autoregulation Estimation of the BII conformer substate population in nonoriented hydrated B-DNA via curve resolution of infrared spectra


B-DNA's BII conformer substate population increases with decreasing water activity. 2. A Fourier transform infrared spectroscopic study of nonoriented d(CGCGAATTCGCG)2 B-DNA's BII conformer substate population increases with decreasing water activity. 1. A molecular dynamics study of d(CGCGAATTCGCG)2 The role of water in B-DNA's BI to BII conformer substate interconversion: a combined study by calorimetry, FT-IR spectroscopy and computer simulation Toward elimination of discrepancies between theory and experiment: The rate constant of the atmospheric conversion of SO3 to H2SO4 Elbow flexibility and ligand-induced domain rearrangements in antibody Fab NC6.8: Large effects of a small hapten B-DNA's dynamics and conformational substates revealed by calorimetric enthalpy relaxation and Fourier transform infrared spectroscopy Simulation of EcoRI dodecamer netropsin complex confirms class I complexation mode Automated docking of ligands to antibodies: Methods and applications Nonoriented d(CGCGAATTCGCG)2 dodecamer persists in B-form even at low water activity On the surprising kinetic stability of carbonic acid (H2CO3) On the competing hydrations of sulfur dioxide and sulfur trioxide in our atmosphere


Investigation of Cu2+ hydration and the Jahn-Teller effect in solution by QM/MM Monte Carlo simulations Temperature-dependent ways of proton transfer - A benchmark study on cyclic HF oligomers Application of multi variant data analysis methods to Comparative Molecular Field Analysis (CoMFA) data: Proton affinities and pKa prediction for nucleic acids components Helix morphology changes in B-DNA induced by spontanous BI ↔ BII substate interconversion Unexpected BII conformer substate population in unoriented hydrated film of the d(CGCGAATTCGCG)2 dodecamer and of native B-DNA from salmon testes Why are copper(II) amino acid complexes not planar in their crystal structures? An ab initio and molecular dynamics study Ligand binding to antibody IgE Lb4: Assessment of binding site preferences using microcalorimetry, docking and free energy simulations


Born-Oppenheimer ab initio QM/MM dynamics simulation of Na+ and K+ in water: From structure making to structure breaking effects Toward elimination of discrepancies between theory and experiment: Double proton transfer in dimers of carboxylic acids Conformationally induced changes in the electronic structures of some flexible benzenes. A molecular orbital model B-DNA's BI → BII conformer substate dynamics is coupled with water migration Predictions of rate constants and estimates for tunneling splittings of concerted proton transfer in small cyclic water clusters Comparative molecular field analysis of artemisinin derivatives: Ab initio versus semiempirical optimized structures Ligand-induced domain movement in an antibody Fab: Molecular dynamics studies confirm the unique domain movement observed experimentally for Fab NC6.8 upon complexation and reveal its segmental flexibility The hydration shell structure of Li+ investigated by Born-Oppenheimer ab initio QM/MM dynamics Highly accurate estimates of hydrogen-bond energies relying on basis set convergence patterns Carbonic acid in the gas phase and its astrophysical relevance Reactivity and regioselectivity of hydroxyl radical addition to halogenated ethenes Dangers of counterpoise corrected hypersurfaces. Advantages of basis set superposition improvement Quantitative analysis of the structural requirements for blockade of the N-methyl-D-aspartate receptor at the phencyclidine binding site Structure, reaction enthalpies, entropies, and free energies of cation-molecule complexes. A theoretical study by means of the ab initio complete bases set CBS-Q method Large curvature tunneling effects reveal concerted hydrogen exchange rates in cyclic hydrogen fluoride clusters comparable to carboxylic acid dimers Improving the predictive quality of CoMFA models


How acidic are thiocarboxylic S-acids and thiosilanoic S-acids (X-YOSH, X = H, F, Cl, CH3, NH2; Y = C, Si)? A critical analysis of electronic density functionals for structural, energetic, dynamic, and magnetic properties of fluoride clusters Solvation of Ca2+ in water studied by Born-Oppenheimer ab initio QM/MM dynamics New insights into the dynamics of concerted proton tunneling in cyclic water and hydrogen fluoride clusters Reaction-path dynamics of hydroxyl radical reactions with ethane and haloethanes Has the dimer of carbonic acid a lower energy than its constituents water and carbon dioxide? Theoretical study on the local anesthetic-receptor interaction


Gas-phase acidities of HM(=X)XH (M=C, Si; X=O, S) acids calculated by ab initio molecular orbital methods at the G2 level of theory A QM/MM simulation method applied to the solution of Li+ in liquid ammonia Bidirectional molecular dynamics: Interpretation in terms of a modern formulation of classical mechanics Comparative molecular field analysis of haptens docked to the multispecific antibody IgE(Lb4) Different electrostatic descriptors in comparative molecular field analysis: A comparison of molecular electrostatic and Coulomb potentials Comparative docking studies on ligand binding to the multi specific antibodies IgE-La2 and IgE-Lb4 Structure and gas-phase acidity of oxalic acid and its disila derivative. A theoretical study by means of the DFT quantum theoretical method Prediction of IgE(Lb4)-ligand complex structures by automated docking Heteroligation of a mouse monoclonal IgE antibody (La2) with small molecules, analyzed by computer-aided automated docking


Hydrogen transitions between (HF)n Cnh structures (n=2-5) via Dnh transition states as models for hydrogen tunneling in hydrogen fluoride clusters Interaction of local anesthetics with an anionic receptor site. An ab initio SCF study on procaine, lidocaine, tocainide and mexiletine and their HCO2- complexes Cation binding effect on hydrogen bonding and the energetics of proton transfer in the system (CH3)3NH+-OCOH Salt induced peptide formation: on the selectivity of the copper induced peptide formation under possible prebiotic conditions


Migratory aptitude of hydrogen and stabilization of the transition-state by the non-migrating substituent in 1,2-migrations to electron deficient nitrogen 1,2-Carbon to nitrogen migrations. Part 2. Ab initio study on the rearrangement of (α-methylazo)alkyl isocyanates 1,2-Shift of Carbon to Electron-Deficient Nitrogen Is Not a Nucleophilic Rearrangement. Ab Initio Study on a 1,2-Rearrangement in 1,2,4 Triazolium Salts


Structure and acidity of carbamic acid and its thio, dithio, and sila derivatives Evaporation cycle experiments - A simulation of salt-induced peptide synthesis under possible prebiotic conditions


Ab initio calculations concerning the reaction mechanism of copper(II) catalyzed glycine condensation in aqueous sodium chloride solution
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