A5071376755- Protein Structure and Dynamics
- Enzyme Structure and Function
- Signaling Pathways in Disease
- Microtubule and mitosis dynamics
- Computational Drug Discovery Methods
- Photosynthetic Processes and Mechanisms
- Advanced NMR Techniques and Applications
- Biochemical and Molecular Research
- Protein Kinase Regulation and GTPase Signaling
- Toxin Mechanisms and Immunotoxins
- Mass Spectrometry Techniques and Applications
- Hemoglobin structure and function
- RNA and protein synthesis mechanisms
- Chronic Myeloid Leukemia Treatments
- Bacterial Genetics and Biotechnology
- Photoreceptor and optogenetics research
- Fungal Plant Pathogen Control
- Protein Tyrosine Phosphatases
- Machine Learning in Bioinformatics
- Medical Imaging Techniques and Applications
- Molecular spectroscopy and chirality
- Various Chemistry Research Topics
- Melanoma and MAPK Pathways
- Receptor Mechanisms and Signaling
- Spectroscopy and Quantum Chemical Studies
Howard Hughes Medical Institute
2016-2025
Brandeis University
2016-2025
Scripps Research Institute
2025
University of Groningen
2010
Biotechnology Institute
2010
Martin Luther University Halle-Wittenberg
1997-2005
University of California, Berkeley
1997-2002
Max Planck Research Unit for Enzymology of Protein Folding
1993-1997
Max Planck Society
1997
Lawrence Berkeley National Laboratory
1997
Internal protein dynamics are intimately connected to enzymatic catalysis. However, enzyme motions linked substrate turnover remain largely unknown. We have studied of an during catalysis at atomic resolution using nuclear magnetic resonance relaxation methods. During catalytic action the cyclophilin A, we detect conformational fluctuations active site that occur on a time scale hundreds microseconds. The rates strongly correlate with microscopic turnover. present results, together available...
Protein actions are usually discussed in terms of static structures, but function requires motion. We find a strong correlation between phosphorylation-driven activation the signaling protein NtrC and microsecond time-scale backbone dynamics. Using nuclear magnetic resonance relaxation, we characterized motions three functional states: unphosphorylated (inactive), phosphorylated (active), partially active mutant. These dynamics indicative exchange inactive conformations. Both states...
AlphaFold2 (ref. 1) has revolutionized structural biology by accurately predicting single structures of proteins. However, a protein's biological function often depends on multiple conformational substates2, and disease-causing point mutations cause population changes within these substates3,4. We demonstrate that clustering multiple-sequence alignment sequence similarity enables to sample alternative states known metamorphic proteins with high confidence. Using this method, named...
With early life likely to have existed in a hot environment, enzymes had cope with an inherent drop catalytic speed caused by lowered temperature. Here we characterize the molecular mechanisms underlying thermoadaptation of enzyme catalysis adenylate kinase using ancestral sequence reconstruction spanning 3 billion years evolution. We show that evolution solved enzyme's key kinetic obstacle-how maintain on cooler Earth-by exploiting transition-state heat capacity. Tracing activity and...
The advent of biocatalysts designed computationally and optimized by laboratory evolution provides an opportunity to explore molecular strategies for augmenting catalytic function. Applying a suite nuclear magnetic resonance, crystallography, stopped-flow techniques enzyme elementary proton transfer reaction, we show how directed gradually altered the conformational ensemble protein scaffold populate narrow, highly active accelerate this transformation nearly nine orders magnitude. Mutations...
Abstract AlphaFold2 (AF2) has revolutionized structural biology by accurately predicting single structures of proteins and protein-protein complexes. However, biological function is rooted in a protein’s ability to sample different conformational substates, disease-causing point mutations are often due population changes these substates. This sparked immense interest expanding AF2’s capability predict We demonstrate that clustering an input multiple sequence alignment (MSA) similarity...
The controversial question of how thiamine diphosphate, the biologically active form vitamin B 1 , is activated in different enzymes has been addressed. Activation coenzyme was studied by measuring thermodynamics and kinetics deprotonation at carbon 2-position (C2) diphosphate pyruvate decarboxylase transketolase use nuclear magnetic resonance spectroscopy, proton/deuterium exchange, analogs, site-specific mutant enzymes. Interaction a glutamate with nitrogen 1′-position pyrimidine ring...
Packaging of cyclophilin A (CypA) into HIV-1 virions is essential for efficient replication; however, the reason this unknown. Incorporation mediated through binding to Gly-89–Pro-90 peptide bond N-terminal domain capsid (CA N ). Despite fact that CypA a peptidyl-prolyl cis/trans isomerase, catalytic activity on CA has not been observed previously. We show here, using NMR exchange spectroscopy, does only bind but also catalyzes efficiently isomerization bond. In addition, conformational...
Evolution of dynamics affects function The drug Gleevac inhibits Abl kinases and is used to treat multiple cancers. closely related Src also play a role in cancer but are not inhibited effectively by Gleevac. Nevertheless, Gleevac-bound structures nearly identical. Based on this structural information protein sequence data, Wilson et al. reconstructed the common ancestor Abl. Mutations that affected conformational caused affinity be gained evolutionary trajectory toward lost Src. Science ,...
Rational design and directed evolution have proved to be successful approaches increase catalytic efficiencies of both natural artificial enzymes. Protein dynamics is recognized as important, but due the inherent flexibility biological macromolecules it often difficult distinguish which conformational changes are directly related function. Here, we use on an impaired mutant proline isomerase CypA identify two second-shell mutations that partially restore its activity. We show kinetically,...
We elucidate the molecular mechanisms of two distinct activation strategies (autophosphorylation and TPX2-mediated activation) in human Aurora A kinase. Classic allosteric is play where either loop phosphorylation or TPX2 binding to a conserved hydrophobic groove shifts equilibrium far towards active conformation. resolve controversy about mechanism autophosphorylation by demonstrating intermolecular long-lived dimer combining X-ray crystallography with functional assays. then address...
Protein tyrosine phosphatase SHP2 functions as a key regulator of cell cycle control, and activating mutations cause several cancers. Here, we dissect the energy landscape wild-type oncogenic mutation E76K. NMR spectroscopy X-ray crystallography reveal that exchanges between closed, inactive open, active conformations. E76K shifts this equilibrium toward open state. The previously unknown conformation is characterized, including active-site WPD loop in inward outward Binding allosteric...
The interconversion between inactive and active protein states, traditionally described by two static structures, is at the heart of signalling. However, how folded states interconvert largely unknown due to inability experimentally observe transition pathways. Here we explore free energy landscape bacterial response regulator NtrC combining computation nuclear magnetic resonance, discover unexpected features underlying efficient We find that functional are defined purely in kinetic not...