CIPSM - Research Area A

Research Area A

2021

Cohesin-dockerin code in cellulosomal dual binding modes and its allosteric regulation by proline isomerization

2020

Recent evolution of a TET-controlled and DPPA3/STELLA-driven pathway of passive DNA demethylation in mammals

High force catch bond mechanism of bacterial adhesion in the human gut

Self-Healing Dyes—Keeping the Promise?

DNA origami-based single-molecule force spectroscopy elucidates RNA Polymerase III pre-initiation complex stability

2019

Finding Reactive Configurations: A Machine Learning Approach for Estimating Energy Barriers Applied to Sirtuin 5

DNA origami-based single-molecule force spectroscopy unravels the molecular basis of RNA Polymerase III pre-initiation complex stability

The Photoaddition of a Psoralen to DNA Proceeds via the Triplet State

Low-Scaling Self-Consistent Minimization of a Density Matrix Based Random Phase Approximation Method in the Atomic Orbital Space

Bisacylphosphane oxides as photo-latent cytotoxic agents and potential photo-latent anticancer drugs

Plasmon-assisted Förster resonance energy transfer at the single-molecule level in the moderate quenching regime

Calculating free energies from the vibrational density of states function: Validation and critical assessment

Identifying Free Energy Hot-Spots in Molecular Transformations

Interchromophoric Interactions Determine the Maximum Brightness Density in DNA Origami Structures

A folding switch regulates interleukin 27 biogenesis and secretion of its α-subunit as a cytokine

2018

Single-molecule force spectroscopy reveals folding steps associated with hormone binding and activation of the glucocorticoid receptor

A single residue switch reveals principles of antibody domain integrity

Precision and accuracy of single-molecule FRET measurements—a multi-laboratory benchmark study

Towards Structural Biology with Super-Resolution Microscopy

Decay Pathways of Thymine Revisited

Structure and mechanism of the two-component α-helical pore-forming toxin YaxAB

PAM: A Framework for Integrated Analysis of Imaging, Single-Molecule, and Ensemble Fluorescence Data

Crosstalk-free multicolor RICS using spectral weighting

Quantifying Expansion Microscopy with DNA Origami Expansion Nanorulers

Optical voltage sensing using DNA origami

Time-resolved infrared studies of the unfolding of a light triggered b-hairpin peptide

Site-specific labelling of native mammalian proteins for singlemolecule FRET measurements

A self-assembled nanoscale robotic arm controlled by electric fields

Transferring the entatic-state principle to copper photochemistry

Single Pair Förster Resonance Energy Transfer: A Versatile Tool To Investigate Protein Conformational Dynamics

Bap (Sil1) regulates the molecular chaperone BiP by coupling release of nucleotide and substrate

2017

Photophysics of diphenyl-pyrazole compounds in solutions and α-synuclein aggregates

Biotechnological mass production of DNA origami

Gigadalton-scale shape-programmable DNA assemblies

Short-range second order screened exchange correction to RPA correlation energies

Efficient and Accurate Born–Oppenheimer Molecular Dynamics for Large Molecular Systems

Distance-including rigorous upper bounds and tight estimates for two-electron integrals over long- and short-range operators

Mechanically switching single-molecule fluorescence of GFP by unfolding and refolding

Determinants of the assembly and function of antibody variable domains

Protein-mediated RNA folding governs sequence-specific interactions between rotavirus genome segments

Multiplexing molecular tension sensors reveals piconewton force gradient across talin-1

Effects of Fluorophore Attachment on Protein Conformation and Dynamics Studied by spFRET and NMR Spectroscopy

Inhibition of the V-ATPase by Archazolid A: A New Strategy to Inhibit EMT

Low-scaling first-order properties within second-order Møller-Plesset perturbation theory using Cholesky decomposed density matrices

Hybrid CPU/GPU Integral Engine for Strong-Scaling Ab Initio Methods

Communication: Almost error-free resolution-of-the-identity correlation methods by null space removal of the particle-hole interactions

Employing OpenCL to Accelerate Ab Initio Calculations on Graphics Processing Units

Nanomechanics of the substrate binding domain of Hsp70 determine its allosteric ATP-induced conformational change

3D motion of vesicles along microtubules helps them to circumvent obstacles in cells

Screening methods for linear-scaling short-range hybrid calculations on CPU and GPU architectures

Azido Pentoses: A New Tool To Efficiently Label Mycobacterium tuberculosis Clinical Isolates

Self-assembly of genetically encoded DNA-protein hybrid nanoscale shapes

Ingredients to TICT Formation in Donor Substituted Hemithioindigo

Quantum-Chemical Study of the Discrimination against dNTP in the Nucleotide Addition Reaction in the Active Site of RNA Polymerase II

Vanishing-Overhead Linear-Scaling Random Phase Approximation by Cholesky Decomposition and an Attenuated Coulomb-Metric

Influence of Coupling and Embedding Schemes on QM Size Convergence in QM/MM Approaches for the Example of a Proton Transfer in DNA

The Endothelial Glycocalyx Controls Interactions of Quantum Dots with the Endothelium and Their Translocation across the Blood–Tissue Border

Rapid Design of Knowledge-Based Scoring Potentials for Enrichment of Near-Native Geometries in Protein-Protein Docking

Concerted regulation of ISWI by an autoinhibitory domain and the H4 N-terminal tail

actinin-titin-interaction-a-dynamic-and-mechanically-stable-cluster-of-bonds-in-the-muscle-z-disk

2016

Optical control of a receptor-linked guanylyl cyclase using a photoswitchable peptidic hormone

Protein-protein and peptide-protein docking and refinement using ATTRACT in CAPRI

Recognition of the 3′ splice site RNA by the U2AF heterodimer involves a dynamic population shift

The Preserved HTH-Docking Cleft of HIV-1 Integrase Is Functionally Critical

Computation of indirect nuclear spin–spin couplings with reduced complexity in pure and hybrid density functional approximations

A Dynamic Equilibrium of Three Hydrogen-Bond Conformers Explains the NMR Spectrum of the Active Site of Photoactive Yellow Protein

Single-molecule dissection of stacking forces in DNA

Twisted Hemithioindigo Photoswitches: Solvent Polarity Determines the Type of Light-Induced Rotations

SAXS Data Alone can Generate High-Quality Models of Protein-Protein Complexes

Knotting and unknotting of a protein in single molecule experiments

En route from artificial to natural: Evaluation of inhibitors of mannose-specific adhesion of Escherichia coli under flow

Cell membrane penetration and mitochondrial targeting by platinum-decorated ceria nanoparticles

Secretory cargo sorting by Ca²⁺-dependent Cab45 oligomerization at the trans-Golgi network

Artificial Formation and Tuning of Glycoprotein Networks on Live Cell Membranes: A Single-Molecule Tracking Study

Sequence-Independent Cloning and Post-Translational Modification of Repetitive Protein Polymers through Sortase and Sfp-Mediated Enzymatic Ligation

Genetically designed biomolecular capping system for mesoporous silica nanoparticles enables receptor-mediated cell uptake and controlled drug release

Single-molecule force spectroscopy on polyproteins and receptor–ligand complexes: The current toolbox

Folding and assembly of the large molecular machine Hsp90 studied in single-molecule experiments

Cryo-EM Data Are Superior to Contact and Interface Information in Integrative Modeling

A Stable Mutant Predisposes Antibody Domains to Amyloid Formation through Specific Non-Native Interactions

Communication: An effective linear-scaling atomic-orbital reformulation of the random-phase approximation using a contracted double-Laplace transformation

2015

Quantum Yield of Cyclobutane Pyrimidine Dimer Formation Via the Triplet Channel Determined by Photosensitization

UV-Induced Charge Transfer States in DNA Promote Sequence Selective Self-Repair

Switching first contact: photocontrol of E. coli adhesion to human cells

The Antibody Light-Chain Linker Is Important for Domain Stability and Amyloid Formation

Monovalent Strep-Tactin for strong and site-specific tethering in nanospectroscopy

A tunable azine covalent organic framework platform for visible light-induced hydrogen generation

2’-Methoxyacetophenone: An Efficient Photosensitizer for Cyclobutane Pyrimidine Dimer Formation

Structural, Biochemical, and Computational Studies Reveal the Mechanism of Selective Aldehyde Dehydrogenase 1A1 Inhibition by Cytotoxic Duocarmycin Analogues

Microdomain Formation Controls Spatiotemporal Dynamics of Cell-Surface Glycoproteins

Nucleotides regulate the mechanical hierarchy between subdomains of the nucleotide binding domain of the Hsp70 chaperone DnaK

Live-cell observation of cytosolic HIV-1 assembly onset reveals RNA-interacting Gag oligomers

Importance of dipole moments and ambient polarity for the conformation of Xaa–Pro moieties – a combined experimental and theoretical study

Mapping Mechanical Force Propagation through Biomolecular Complexes

Unraveling the Base Excision Repair Mechanism of Human DNA Glycosylase

Kinetic and Theoretical Studies of Beta-Lactone Reactivity—A Quantitative Scale for Biological Application

Fully Blind Peptide-Protein Docking with pepATTRACT

Dewar Lesion Formation in Single- and Double-Stranded DNA is Quenched by Neighboring Bases

Application of Enhanced Sampling Monte Carlo Methods for High-Resolution Protein-Protein Docking in Rosetta

Role of the cytosolic loop C2 and the C-terminus of YidC in ribosome binding and insertion activity

A Base-Independent Repair Mechanism for DNA Glycosylase—No Discrimination Within the Active Site

C-5 Propynyl Modifications Enhance the Mechanical Stability of DNA

Walther-Nernst-Denkmünze to CIPSM researcher Christoph Bräuchle

Multifunctional polymer-capped mesoporous silica nanoparticles for pH-responsive targeted drug delivery

Hsp90 regulates the dynamics of its cochaperone Sti1 and the transfer of Hsp70 between modules

Dynamic DNA devices and assemblies formed by shape-complementary, non–base pairing 3D components

Tip localization of an atomic force microscope in transmission microscopy with nanoscale precision

CIPSM researcher Hendrik Dietz is awarded with the 2015 Leibniz-Preis

A magnetic stirring setup for applications in ultrafast spectroscopy of photo-sensitive solutions

A reduced-scaling density matrix-based method for the computation of the vibrational Hessian matrix at the self-consistent field level

Preselective Screening for Linear-Scaling Exact Exchange-Gradient Calculations for Graphics Processing Units and General Strong-Scaling Massively Parallel Calculations

Calculated Nuclear Magnetic Resonance Spectra of Polytwistane and Related Hydrocarbon Nanorods

Super-Resolution Imaging of ESCRT-Proteins at HIV-1 Assembly Sites

Side-binding proteins modulate actin filament dynamics

Early Events of DNA Photodamage

A Compact Native 24-Residue Supersecondary Structure Derived from the Villin Headpiece Subdomain

A Web Interface for Easy Flexible Protein-Protein Docking with ATTRACT

Photocontrolled chignolin-derived β-hairpin peptidomimetics

2014

Parallel Force Assay for Protein-Protein Interactions

Spin Component-Scaled Second-Order Møller−Plesset Perturbation Theory for Calculating NMR Shieldings

iATTRACT: Simultaneous global and local interface optimization for protein–protein docking refinement

Cell-Penetrating and Neurotargeting Dendritic siRNA Nanostructures

The charged linker of the molecular chaperone Hsp90 modulates domain contacts and biological function

Identification of charge separated states in thymine single strands

Making Fast Photoswitches Faster—Using Hammett Analysis to Understand the Limit of Donor–Acceptor Approaches for Faster Hemithioindigo Photoswitches

Watson–Crick Base Pairing Controls Excited-State Decay in Natural DNA

Chaperone Action at the Single-Molecule Level

Total Synthesis of the Proposed Structure of Trichodermatide A

Pulsed Interleaved Excitation Fluctuation Imaging Jelle

Communication: A reduced scaling J-engine based reformulation of SOS-MP2 using graphics processing units

A Residue-specific Shift in Stability and Amyloidogenicity of Antibody Variable Domains

Ribose-Protonated DNA Base Excision Repair: A Combined Theoretical and Experimental Study

The Lateral Membrane Organization and Dynamics of Myelin Proteins PLP and MBP Are Dictated by Distinct Galactolipids and the Extracellular Matrix

Cholesky-decomposed density MP2 with density fitting: Accurate MP2 and double-hybrid DFT energies for large systems

Primary reactions in photosynthetic reaction centers of Rhodobacter sphaeroides – Time constants of the initial electron transfer

Native chemical ligation for conversion of sequence-defined oligomers into targeted pDNA and siRNA carriers

Eukaryotic and archaeal TBP and TFB/TF(II)B follow different promoter DNA bending pathways

Force-dependent isomerization kinetics of a highly conserved proline switch modulates the mechanosensing region of filamin

Mechanism of the Decay of Thymine Triplets in DNA Single Strands

Novel Derivatives of 1‑Cyclohexyl-4-[3-(5-methoxy-1,2,3,4- tetrahydronaphthalen-1-yl)propyl]piperazine (PB28) with Improved Fluorescent and σ Receptors Binding Properties

Charge separation and charge delocalization identified in long-living states of photoexcited DNA

Fingerprinting DNA Oxidation Processes: IR Characterization of the 5-Methyl-2′-Deoxycytidine Radical Cation

Benchmarking Hydrogen and Carbon NMR Chemical Shifts at HF, DFT, and MP2 Levels

Photostabilit von 4,4’-Dihydroxythioindigo: ein Mimetikum des Indigo

2013

Transition state and ground state properties of the helix–coil transition in peptides deduced from high-pressure studies

Isomerization- and Temperature-Jump-Induced Dynamics of a Photoswitchable β-Hairpin

Sensitivity of ab Initio vs Empirical Methods in Computing Structural Effects on NMR Chemical Shifts for the Example of Peptides

Multifunctional Mesoporous Silica Nanoparticles as a Universal Platform for Drug Delivery

Mechanical Stability of the Antibody Domain CH3 Homodimer in Different Oxidation States

Deamination, Oxidation, and C−C Bond Cleavage Reactivity of 5‑Hydroxymethylcytosine, 5‑Formylcytosine, and 5‑Carboxycytosine

Testing the diffusing boundary model for the helix–coil transition in peptides

Fluorescence Microscopy Studies of Porous Silica Materials

Pulsed Interleaved Excitation: Principles and Applications

Rigid DNA Beams for High-Resolution Single-Molecule Mechanics†

Molecular Tweezers with Varying Anions: A Comparative Study

Tracking Image Correlation: Combining Single-Particle Tracking and Image Correlation

Uptake Kinetics and Nanotoxicity of Silica Nanoparticles Are Cell Type Dependent

Targeted Drug Delivery in Cancer Cells with Red-Light Photoactivated Mesoporous Silica Nanoparticles

An extrapolation method for the efficient calculation of molecular response properties within Born–Oppenheimer molecular dynamics

A linear- and sublinear-scaling method for calculating NMR shieldings in atomic orbital-based second-order Møller-Plesset perturbation theory

Real-time observation of the conformational dynamics of mitochondrial Hsp70 by spFRET

Anle138b: a novel oligomer modulator for disease-modifying therapy of neurodegenerative diseases such as prion and Parkinson’s disease

Pre-selective screening for matrix elements in linear-scaling exact exchange calculations

Electrostatics Control Actin Filament Nucleation and Elongation Kinetics

A family of macrodomain proteins reverses cellular mono-ADP-ribosylation

A fast analysis method to quantify nanoparticle uptake on a single cell level

Force as a single molecule probe of multidimensional protein energy landscapes

Following the energy transfer in and out of a polyproline–peptide

2012

Controlling The Mobility Of Oligonucleotides In The Nanochannels Of Mesoporous Silica

Rapid Folding of DNA into Nanoscale Shapes at Constant Temperature

Dynamic force sensing of filamin revealed in single-molecule experiments

Cryo-EM structure of a 3D DNA-origami object

Synthetic Lipid Membrane Channels Formed by Designed DNA Nanostructures

Enhanced Bioactivity of Internally Functionalized Cationic Dendrimers with PEG Cores

Calcium-dependent folding of single calmodulin molecules

Magnesium-free self-assembly of multi-layer DNA objects

Release pathways of interferon α2a molecules from lipid twin screw extrudates revealed by single molecule fluorescence microscopy

Differential pH-dependent cellular uptake pathways among foamy viruses elucidated using dual-colored fluorescent particles

Amyloid-Like Structures Formed by Azobenzene Peptides: Light-Triggered Disassembly

Dynamics of ultraviolet-induced DNA lesions: Dewar formation guided by pre-tension induced by the backbone

Tuning Nanoparticle Uptake: Live-Cell Imaging Reveals Two Distinct Endocytosis Mechanisms Mediated by Natural and Artificial EGFR Targeting Ligand

ONIOM approach for non-adiabatic on-the-fly molecular dynamics demonstrated for the backbone controlled Dewar valence isomerization

Three-Dimensional Tracking of Carbon Nanotubes within Living Cells

Quantitative Live-Cell Imaging of Human Immunodeficiency Virus (HIV-1) Assembly

Cascaded Photoinduced Drug Delivery to Cells from Multifunctional Core–Shell Mesoporous Silica

DNA Origami Gatekeepers for Solid-State Nanopores

Light-Switchable Hemithioindigo–Hemistilbene-Containing Peptides: Ultrafast Spectroscopy of the Z → E Isomerization of the Chromophore and the Structural Dynamics of the Peptide Moiety

Direct Visualization of Dye and Oligonucleotide Diffusion in Silica Filaments with Collinear Mesopores

Factors Affecting the Quantification of Biomolecular Interactions by Fluorescence Cross-Correlation Spectroscopy

Combining MFD and PIE for Accurate Single-Pair Förster Resonance Energy Transfer Measurements

Effects of Hofmeister Ions on the α-Helical Structure of Proteins

Superhelical Architecture of the Myosin Filament-Linking Protein Myomesin with Unusual Elastic Properties

Mechanism of UV-Induced Formation of Dewar Lesions in DNA

Heat shock protein 90’s mechanochemical cycle is dominated by thermal fluctuations