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ProteinFoldingAndDynamics
PROTEIN FOLDING & DYNAMICS
WEBINAR
Ben Schuler
Gilad Haran
Hagen Hofmann
Jane Clarke
Department of Chemistry, University of Cambridge
Making Sense of Disorder
Monday 04.05.
7:00 PDT - 10:00 EDT - 14:00 UTC
15:00 UK - 16:00 CET - 17:00 IL
Zoom: Inactive
YouTube: https://www.youtube.com/watch?v=uQ4bq0ASNE8
Monday 18.05.
8:00 PDT - 11:00 EDT - 15:00 UTC
16:00 UK - 17:00 CET - 18:00 IL
Astbury Centre for Structural and Molecular Biology, University of Leeds
Early Steps in Amyloid Assembly:
The Achilles Heel of a Disease Mechanism
Many amyloid precursors are intrinsically disordered, while others are folded, yet both can assemble into the highly organised cross-bstructures characteristic of amyloid. Understanding how this conformational transition occurs is not clear, with the initiating steps in aggregation being particularly difficult to study because of the dynamics and heterogeneity of the species involved. Focussing on the IDP α-synuclein (αSyn), linked to pathology in Parkinson’s disease, and b2-microglobulin involved in Dialysis Amyloidosis, I will discuss our understanding of the early steps in amyloid formation and describe how we are beginning to target these steps specifically to prevent amyloid formation.
Zoom: Inactive
YouTube: https://www.youtube.com/watch?v=I1ehplDAmXs
Sheena Radford
Monday 01.06.
8:00 PDT - 11:00 EDT - 15:00 UTC
16:00 UK - 17:00 CET - 18:00 IL
Ken A. Dill
Laufer Center for Physical and Quantitative Biology, Stony Brooks University
How the forces on proteomes manifest as cell behaviors
Cells adapt to their environments. Adaptive forces in homeostasis or evolution are expressed in terms of growth laws and fitness landscapes. Some aspects of fitness arise from specific actions of individual proteins. But other aspects arise from more physical, less specific, more universal actions of all proteins in the proteome. We are modeling how protein folding, aggregation, diffusion, and chaperoning contribute to cellular adaptations.
Zoom: Inactive
YouTube: https://www.youtube.com/watch?v=sOkdlszfsaY
Monday 15.06.
8:00 PDT - 11:00 EDT - 15:00 UTC
16:00 UK - 17:00 CET - 18:00 IL
Lewis E. Kay
Department of Molecular Genetics, Biochemistry and Chemistry, University of Toronto
The important role of dynamics in the function and misfunction of molecular machines
Protein molecules play critical roles in cellular function and they catalyze many of the biochemical reactions that are necessary for life. The three-dimensional shapes of these molecules are crucial for guiding proper function and they can change with time due to interactions with other molecules, various stresses on the cell or simply the result of random fluctuations. Although very detailed static pictures of protein molecules have been produced using traditional biophysical tools, macromolecular function and misfunction is, in many cases, intimately coupled to flexibility and knowledge of molecular motions therefore becomes critical. For the past 3 decades my laboratory has developed biophysical techniques, focusing on solution based Nuclear Magnetic Resonance spectroscopy for the study of biomolecular dynamics. A brief description of some of the methods we have derived will be given along with examples to illustrate the critical importance of dynamics to protein function and misfunction.
Zoom: Inactive
YouTube: https://www.youtube.com/watch?v=zbx8exkZOgQ
Martin Gruebele
Department of Chemistry, University of Illinois at Urbana-Champaign
Protein folding and association dynamics: from in silico to in vitro to in vivo
Protein folding and binding reactions are generally quite fast and involve small free energy differences. As a result, they can be sensitive to the environment that biases protein energy landscapes. I will discuss molecular dynamics simulations, test-tube experiments, in-cell measurements, and measurements in living animals that highlight the sensitivity of protein dynamics to its solvation environment.
Monday 29.06.
8:00 PDT - 11:00 EDT - 15:00 UTC
16:00 UK - 17:00 CET - 18:00 IL
Zoom: Inactive
YouTube: https://www.youtube.com/watch?v=SAQo2wq2Irk
Monday 13.07.
8:00 PDT - 11:00 EDT - 15:00 UTC
16:00 UK - 17:00 CET - 18:00 IL
Jane Dyson
Department of Integrative Structural and Computational Biology, The Scripps Research Institute
NMR Dynamics Studies of Protein Folding Intermediates
Jane Dyson and Peter Wright
The transient intermediate states that are populated as a protein folds are difficult to access and study. Both kinetic and equilibrium biophysical methods have been used to probe these states, using chemically or physically unfolded and partly folded states as models. NMR gives unique information on the local motions of a protein chain. The ps-ns time scale motions of the polypeptide backbone in unfolded and partly folded states, measured using relaxation rates, can give important insights into the factors that contribute to progress along the folding pathway. In addition, we can study states at low populations within a conformational ensemble using relaxation dispersion measurements that probe ms-ms motions, which are of particular interest in the folding processes of proteins.
Zoom: Inactive
YouTube: https://www.youtube.com/watch?v=ZpgmZQl82hc
Dave Thirumalai
Department of Chemistry, The University of Texas at Austin
Iterative Annealing Mechanism for GroEL
Most cytosolic proteins fold spontaneously as envisioned by Anfinsen. However, there are number of proteins that require the chaperone machinery to reach their functionally competent states. Using theory, simple arguments, and simulations using coarse-grained models I will describe the workings of the E. Coli. chaperonin GroEL. A framework based on the Iterative Annealing Mechanism that unifies inefficient folding under non-permissive conditions, GroEL allostery, and function will be presented. If time permits some open problems will be discussed.
Monday 27.07.
8:00 PDT - 11:00 EDT - 15:00 UTC
16:00 UK - 17:00 CET - 18:00 IL
Zoom: Inactive
YouTube: https://www.youtube.com/watch?v=pQS437khveA
Peter G. Wolynes
Department of Chemistry, Rice University
Protein Dynamics and the Brain
The brain is a molecular computer. How the brain computes, and feels and learns and remembers remain great mysteries. Neurobiologists have, however, identified some key protein actors in the mechanisms of learning and memory. I will describe some theoretical and computational efforts in understanding some of the molecular aspects of 1) Hebbian learning through the regulatable assembly of the actin cytoskeleton in dendritic spines, 2) the hypothesis that long-term memory involves a functional prion protein and 3) some aspects of the physical chemistry of aggregation processes that are involved in the pathogenesis of Huntington’s disease and Alzheimer’s disease.
Monday 10.08.
8:00 PDT - 11:00 EDT - 15:00 UTC
16:00 UK - 17:00 CET - 18:00 IL
Zoom: Inactive
YouTube: https://www.youtube.com/watch?v=-rA86LgToxI
Robert T. Sauer
Department of Biology, Massachusetts Institute of Technology
Protein recognition, unfolding, and translocation by the AAA+ ClpXP protease
ClpX is a AAA+ unfoldase and translocase that works with the ClpP peptidase to perform ATP-dependent degradation of target proteins in organisms from bacteria to mammals. I will discuss cryo-EM structures of ClpXP with bound substrates, biochemical experiments, and single-molecule optical-trapping studies that provide insight into ClpXP mechanism.
Monday 24.08.
8:00 PDT - 11:00 EDT - 15:00 UTC
16:00 UK - 17:00 CET - 18:00 IL
Zoom: Inactive
YouTube: https://www.youtube.com/watch?v=kcqFq23LEQk
Taekjip Ha
Department of Biophysics, Johns Hopkins University
Conformational Control: From Single Molecules to Biotechnologies
Cellular functions of biological molecules are often controlled through conformational switching mediated by protein phosphorylation and protein-protein interactions. Single molecule biophysical studies of bacterial enzymes that unwind DNA in an ATP-dependent and ATP-independent manner taught us how their functions are controlled by conformational switching. We exploited these conformal control mechanisms to create new enzyme behaviors suitable for biotechnological applications (rapid pathogen detection, accurate genome-editing and genome imaging,…) and for new research avenues (co-transcriptional RNA folding, very fast DNA repair studies,…).
Monday 07.09.
8:00 PDT - 11:00 EDT - 15:00 UTC
16:00 UK - 17:00 CET - 18:00 IL
Zoom: Inactive
YouTube: https://www.youtube.com/watch?v=Yx4KuBynfvs
Matthias Rief
Department of Physics, Technical University Munich
Forces in Chaperone-Mediated Protein Unfolding and Cell Adhesion
Many process in our cells are mechanical. Single molecule methods allow studying the forces involved in those processes. In my talk I will discuss 2 examples. In the first part, I will show how the concerted action of the hsp70 chaperone and its co-chaperones completely unfold the glucocorticoid receptor. In the second part of my talk, I will discuss how the cytoskeletal proteins talin and kindlin co-operate to strengthen their mechanical bond to the cell adhesion protein integrin.
Monday 21.09.
8:00 PDT - 11:00 EDT - 15:00 UTC
16:00 UK - 17:00 CET - 18:00 IL
Zoom: Inactive
YouTube: https://www.youtube.com/watch?v=hayRBV2dnS8
Monday 05.10.
8:00 PDT - 11:00 EDT - 15:00 UTC
16:00 UK - 17:00 CET - 18:00 IL
Susan Marqusee
Department of Molecular and Cell Biology, University of California Berkeley
Modulation of the Energy Landscape by Cellular Factors
The amino acid sequence of a protein encodes more than the native three-dimensional structure; it encodes the entire energy landscape – an ensemble of conformations whose energetics and dynamics are finely tuned for folding, binding, turnover, and function. Small variations in the sequence and environment modulate this landscape and can have effects that range from undetectable to pathological. I will present our recent results probing how cellular factors such as the ribosome, translation and ubiquitination affect the energetics and dynamics of a protein.
Zoom: Inactive
YouTube: https://www.youtube.com/watch?v=3cOtBnDjFpQ
Monday 19.10.
8:00 PDT - 11:00 EDT - 15:00 UTC
16:00 UK - 17:00 CET - 18:00 IL
Henry Chapman
Deutsches Elektronen-Synchrotron DESY
A Research Center of the Helmholtz Association
Serial crystallography and diffraction with X-ray FELs
Using X-ray free-electron laser pulses it is possible to outrun the effects of radiation damage, allowing room temperature measurements of macromolecular crystals at high resolution with a dose thousands of times higher than usually tolerable. Since an X-ray FEL pulse ultimately destroys the sample, measurements are carried out in a serial fashion, one sample at a time. This has led to the paradigm of serial crystallography, requiring rapid sample delivery, high frame-rate detectors and software to aggregate data into what is essentially a three-dimensional powder diffraction pattern. High-resolution room-temperature protein structures have been determined from crystals less than 0.01 micron^3 in volume, and high-resolution diffraction can be recorded from 2D macromolecular crystals or single fibrils. The method is especially useful for time-resolved crystallography, radiation-sensitive samples, small crystals, and studies of the dependence of structure on physical conditions and environments. The opportunities for this method have not been fully explored, and all aspects of the method are still under active development. I will outline some of these opportunities and developments.
Zoom: Inactive
YouTube: https://www.youtube.com/watch?v=21GuC-RJqP4
Monday 02.11.
8:00 PST - 11:00 EST - 16:00 UTC
16:00 UK - 17:00 CET - 18:00 IL
Ivet Bahar
Department of Computational and Systems Biology, University of Pittsburgh, School of Medicine
It is widely established that understanding protein dynamics is essential to bridging structure and function. One major challenge in computational modeling of protein dynamics is the computational cost and time required for viewing events of biological significance, the time scale and cooperative nature of which is often beyond the reach of conventional molecular dynamics simulations. Among coarse-grained models that have been developed for addressing this issue, elastic network models (ENMs) found wide usage in molecular biophysics and structural biology. The global motions predicted by ENMs have proven in numerous applications in the last two decades to provide a good description of molecular machinery and allosteric behavior complementing experimental data, despite the simplicity of the model and the lack of specificity. Application to supramolecular structures, including cryo-EM structures, has been a major utility of these models. More recently, ENMs proved useful to exploring chromosomal dynamics, using data from Hi-C experiments to reconstruct in silico the connectivity of the chromatin and provide a physical basis for gene regulation transcription and cell type differentiation. Finally, we will show how machine learning algorithms that incorporate ENM predictions provide an improved assessment of the effect of mutations on function, compared to those based on sequence and structure exclusively, and we discuss future directions.
Zoom: Inactive
YouTube: https://www.youtube.com/watch?v=8DBAlYsvlbI
William A. Eaton
NIH, NIDDK, Laboratory of Chemical Physics
Modern Kinetics of Protein Folding; a Retrospective
Modern kinetics of protein folding began in the early 1990’s with the introduction of nanosecond laser pulses to trigger the folding reaction, providing an almost 10^6-fold improvement in time resolution over the stopped-flow kinetic method being employed at the time. These experiments marked the beginning of the so-called “fast-folding” subfield that investigated the nanosecond-microsecond kinetics of protein structural elements for the first time, as well as the previously inaccessible kinetics of sub-millisecond folding proteins. Using single molecule spectroscopy, the microsecond time for crossing the free energy barrier separating folded and unfolded states (the transition path time) can now also be measured. I will trace the history of the fast-folding subfield using primarily results from my lab and provide a perspective on what I regard as the remaining outstanding problems in the kinetics and mechanism of protein folding.
Monday 16.11.
8:00 PST - 11:00 EST - 16:00 UTC
16:00 UK - 17:00 CET - 18:00 IL
Zoom: Inactive
YouTube: https://www.youtube.com/watch?v=mBw82Fq7tJ8&t=1s
Amnon Horovitz
Department of Structural Biology, Weizmann Institute of Science
Monday 30.11.
8:00 PST - 11:00 EST - 16:00 UTC
16:00 UK - 17:00 CET - 18:00 IL
Zoom: Inactive
YouTube: https://www.youtube.com/watch?v=Bt48OqVSEGw
Dissecting allosteric mechanisms and protein interactions using native mass-spectrometry
Native mass spectrometry (MS) is an ideal method for studying allosteric systems because it provides a way for measuring the relative concentrations of many co-existing species. Two applications of this approach will be described. In the first one, I will show that native MS can be used to distinguish between the classical sequential and concerted allosteric models. Distinguishing between these models has been difficult because ligand binding curves are insensitive to ligation intermediates. Using native MS, it was possible to show that the chaperonin GroEL undergoes concerted intra-ring conformational changes. In the second application, I will show that native MS can be used in conjunction with double-mutant cycles to determine the energetic coupling between residues involved in inter-protein interactions. Coupling constants for the interaction between wild-type and ALS disease-causing mutant superoxide dismutase 1 subunits were measured using this approach and found to correlate with disease severity.
Monday 14.12.
8:00 PST - 11:00 EST - 16:00 UTC
16:00 UK - 17:00 CET - 18:00 IL
Steven G. Boxer
Department of Chemistry, Stanford University
Electric Fields and Enzyme Catalysis
We have developed the vibrational Stark effect to probe electrostatics and dynamics in organized systems, in particular in proteins where vibrational probes can report on functionally important electric fields. The strategy involves deploying site-specific vibrational probes whose sensitivity to an electric field is measured in a calibrated external electric field. Once calibrated, these probes, typically nitriles or carbonyls, can be used to probe changes in electric field due to mutations, ligand binding, pH effects, light-induced structural changes, etc. We can also obtain information on absolute fields by combining vibrational solvatochromism and MD simulations, checked by the vibrational Stark effect calibration. This frequency-field calibration can be applied to quantify functionally relevantelectric fields at the active site of enzymes. Using ketosteroid isomerase as a model system, we correlate the field sensed at the bond involved in enzymatic catalysis with the rate of the reaction it catalyzes, including variations in this rate in a series of mutants and variants using non-canonical amino acids. This provides the first direct connection between electric fields and function: for this system electrostatic interactions are a dominant contribution to catalytic proficiency. Using the vibrational Stark effect, we can now consistently re-interpret results already in the literature and provide a framework for parsing the electrostatic contribution to catalysis in both biological and non-biological systems. Extensions of this approach to other classes of enzymes, to effects of electrostatics on pathways of photoisomerization in proteins, and to the evolutionary trajectories of enzymes responsible for antibiotic resistance will be described if time permits.
Zoom: Inactive
YouTube: https://www.youtube.com/watch?v=UlziL7jHWwc
Monday 11.01.
8:00 PST - 11:00 EST - 16:00 UTC
16:00 UK - 17:00 CET - 18:00 IL
Michael Woodside
Department of Physics, University of Alberta
Observing misfolding and prion-like conversion in single protein molecules
Protein misfolding is linked to a wide range of neurodegenerative diseases. In several of these diseases, misfolded isoforms of the disease-linked proteins are infectious, capable of converting natively folded molecules to make new copies of the misfolded isoform and thereby propagate the misfolding, as first seen in prion diseases. However, the mechanisms of prion-like misfolding remain unclear. I will present work using force spectroscopy to observe misfolding in single molecules of PrP and SOD1, related respectively to prion disease and ALS, exploring the mechanisms of misfolding and observing the templated conversion of single molecules into misfolded isoforms.
Zoom: Inactive
YouTube: https://www.youtube.com/watch?v=gqHUiULsc3E
Monday 25.01.
8:00 PST - 11:00 EST - 16:00 UTC
16:00 UK - 17:00 CET - 18:00 IL
Marina Rodnina
Max Planck Institute for Biophysical Chemistry, Goettingen
The pathways of co-translational folding
Protein domains start to fold co-translationally, while they are being synthesized on the ribosome. Co-translational folding is vectorial; it starts in the confined space of the polypeptide exit tunnel of the ribosome and is modulated by the speed of translation. Defects in protein folding cause many human diseases; thus, understanding the co-translational folding is of eminent importance. We mapped the pathways of co-translational folding for two proteins of different topology, a small five-helix domain HemK and a five-stranded beta-barrel protein CspA. In solution, both proteins fold by a concerted two-state mechanism. On the ribosome, HemK and CspA start to fold inside the exit tunnel and undergo several structural rearrangements that are not sampled in solution. HemK folds vectorially as soon as the N-terminal α-helical segments are synthesized. As nascent chain grows, consecutive helical segments dock onto each other and continue to rearrange at the vicinity of the ribosome. CspA forms compact non-native structures inside and at the vestibule of the exit tunnel and adopts the native fold only after the release from the ribosome. These results show how the ribosome defines the folding landscape of protein domains.
Zoom: Inactive
YouTube: https://www.youtube.com/watch?v=EHWcOoNwzQQ
Monday 08.02.
8:00 PST - 11:00 EST - 16:00 UTC
16:00 UK - 17:00 CET - 18:00 IL
Angela Gronenborn
Department of Structural Biology, University of Pittsburgh
Not so crystal clear - crystallins and cataract
Cataracts are the leading cause of blindness in the world, with approximately 17 million cases per year. The disease is caused by protein aggregation in the eye lens, involving its major constituents, the crystallins. While the congenital form of the disease results from crystallin gene mutations, the age-related degenerative disease involves 'aged' crystallin proteins. Currently, the only available treatment is surgery, widely used in the developed world. However, access to surgery is not available to a significant fraction of the world population. Therefore, it is important to provide a structural understanding of cataract formation, if novel therapeutic approaches are to be developed to delay or slow the progression of cataracts. We are investigating the dynamics, structure and folding of human γD and bB crystallins, both WT and mutants that are associated with congenital or age-related cataract. We solved NMR and X-ray crystal structures of several variants and analyzed their dynamic behavior by solution NMR spectroscopy and SAXS. In this lecture I will report on our studies.
Zoom: Inactive
YouTube: https://www.youtube.com/watch?v=h70K1ea09iw&t=1s
Monday 01.03.
8:00 PST - 11:00 EST - 16:00 UTC
16:00 UK - 17:00 CET - 18:00 IL
Hagen Hofmann
Department of Chemical and Structural Biology, Weizmann Institute of Science
Allostery in DNA drives phenotype switching
Allostery is a pervasive principle to regulate protein function. Here, we show that DNA also transmits allosteric signals over long distances to boost the binding cooperativity of transcription factors. Phenotype switching in Bacillus subtilis requires an all-or-none promoter binding of multiple ComK proteins. Using single-molecule FRET, we find that ComK-binding at one promoter site increases affinity at a distant site. Cryo-EM structures of the complex between ComK and its promoter demonstrate that this coupling is due to mechanical forces that alter DNA curvature. Modifications of the spacer between sites tune cooperativity and show how to control allostery, which paves new ways to design the dynamic properties of genetic circuits.
Zoom: Inactive
YouTube: https://www.youtube.com/watch?v=fXZCoa9KlaE
Nozomi Ando
Department of Chemistry and Chemical Biology, Cornell University
Thinking outside of the lattice
Correlated motions are essential for protein allostery and function, yet few experimental probes exist. In this talk, I’ll discuss how information on correlated atomic motions exists in the continuous background signal that is discarded in conventional X-ray crystallography. Despite its promise, however, this signal (known as diffuse scattering) has been very difficult to measure and interpret. I’ll discuss these historical challenges and the “making of” story behind our recent work as well as future outlook.
Monday 08.03.
8:00 PST - 11:00 EST - 16:00 UTC
16:00 UK - 17:00 CET - 18:00 IL
Zoom: Inactive
YouTube: https://www.youtube.com/watch?v=jrW5qq5413E&t=2273s
Monday 22.03.
9:00 PDT - 12:00 EDT - 16:00 UTC
16:00 UK - 17:00 CET - 18:00 IL
Joerg Enderlein
III. Institute of Physics - Biophysics, Georg-August-University Goettingen
Advanced Fluorescence Correlation Spectroscopy for
measuring molecular conformation and dynamics
The development of single molecule spectroscopy (SMS) had an enormous impact on many biophysical studies by allowing to measure full distributions of molecular parameters, instead of only average values as usually determined by ensemble measurements. One specific technique of SMS is fluorescence correlation spectroscopy (FCS) which evaluates the fluorescence intensity fluctuations observed out of a femotliter-sized confocal detection volume. Thus allows to measure molecular size and concentration of fluorescently tagged molecule at pico- to nanomolar concentrations, but also to resolve conformational dynamics and conformational transitions with a temporal resolution down to a few nanoseconds. I will present a general introduction into FCS and will then focus on several of its advanced variants. In particular, I will introduce dual-focus or 2fFCS, which allows for precise calibration-free molecular sizing. Next, fluorescence lifetime correlation spectroscopy (FLCS) will be presented which is a powerful tool for resolving intramolecular conformational fluctuations. Then, I will discuss photoelectron transfer or PET-FCS, which is a simple but powerful complement to single-molecule Förster resonance energy transfer (smFRET) when studying conformational fluctuations in intrinsically disordered proteins. Finally, I will discuss FCS on a pico- to nanosecond timescale, where it provide valuable information about molecular rotational diffusion and molecular stoichiometry (fluorescence antibunching).
Zoom: Inactive
YouTube: https://www.youtube.com/watch?v=ULzmXSo4e80
Eugene I. Shakhnovich
Department of Chemistry and Chemical Biology, Havard University
Monday 05.04.
8:00 PDT - 11:00 EDT - 16:00 UTC
16:00 UK - 17:00 CEST - 18:00 IL
Zoom: Inactive
YouTube: https://www.youtube.com/watch?v=vgvBkre4xEM
Protein biophysics in the cellular context: physics meets evolution.
I will present recent theoretical and experimental developments aimed at understanding the two-way link between protein stability and protein evolution. At the heart of these developments are models of evolutionary dynamics that merge molecular mechanisms of protein stability and folding with population genetics. Traditional population genetics models are agnostic to the physical-chemical nature of mutational effects. Rather they operate with an a’priori assumed distributions of fitness effects (DFE) of mutations from which evolutionary dynamics are derived. Alternatively some population genetics models aim to derive DFE from evolutionary observations. In departure with this tradition the novel multiscale models integrate the molecular effects of mutations on physical properties of proteins, most notably their stability, into physically intuitive yet detailed genotype-phenotype relationship (GPR) assumptions. I will present a range of models from simple analytical diffusion-based model on biophysical fitness landscapes to more sophisticated computational models of populations of model cells where genetic changes are mapped into molecular effects using biophysical modeling of proteins and ensuing fitness changes determine the fate of mutations in realistic population dynamics. Examples of insights derived from biophysics-based multiscale models include parameter-free prediction of distribution of protein stabilities in natural proteomes that explains the observation of “marginal stability” of proteins without resorting to unproven stability-activity tradeoffs, the fundamental limit on mutation rates in living organisms, physics of thermal adaptation, co-evolution of protein interactions and abundances in cytoplasm and related results, some of which I will present and discuss.
Next I will describe “bottom-up experimental efforts to establish the relationship between biophysical properties of proteins (stability, activity, interactions with other proteins) and fitness. The approach is based on introducing rational introducing genetic variation on the chromosome of E.coli using genome editing approaches with subsequent concurrent evaluation of biophysical effects of mutations in vitro and fitness effect of strains that have these genetic variants in their chromosome. Carrying out this program for two genes encoding essential metabolic enzymes in E. coli – folA and adk – we obtained deep insights into the relationship between protein stability and fitness. In particular we quantitatively determined how the changes in stability affect the protein turnover in cellular environment resulting in changes in the abundance of functional protein and through that affecting the phenotype (growth rates and lag times). We established fundamental role of protein quality control – chaperone GroEL and certain proteases that modulate the fitness effects of stability-changing mutations in a predictable way. We developed a dynamic steady state theory that describes stability-dependent protein turnover and established the relationship between protein abundance and stability that is different from simple equilibrium Boltzmann distribution. These advances allowed us to get a comprehensive biophysical fitness landscapes for metabolic enzymes. Further we applied these advances to the analysis of antibiotic resistance in DHFR encoded by folA. The theory allowed predicting fitness effect of escape mutations in DHFR and IC50 against antibiotic trimethoprim with very high accuracy based only on biophysical molecular properties of numerous DHFR mutants. Altogether these results provide a clear picture of interplay between biophysical traits and evolutionary dynamics on various time scales – from evolution of modern proteomes to evolution of antibiotic resistance and provides practical tools to address the problem of pathogen escape from stressors from a fundamental physical-chemical perspective.
Monday 19.04.
8:00 PDT - 11:00 EDT - 16:00 UTC
16:00 UK - 17:00 CEST - 18:00 IL
José Nelson Onuchic
Center for Theoretical Biological Physics and Departments of Physics
and Astronomy, Chemistry, and Biosciences
Rice University
Protein sequence coevolution, energy landscapes and their connections to structural maintenance of chromosomes (SMC) proteins
Energy landscape theory has been a powerful approach to study protein folding dynamics and function. The discovery that an accurate estimate of the joint probability distribution of amino acid occupancies in protein families provides insights about residue-residue coevolution and concrete details about protein folding landscapes has also advanced structural biophysics. Our realization that the collection of couplings and local fields as parameters of such distribution is inherently connected with the thermodynamics of sequence selection towards folding and function demonstrates the importance of coevolutionary methods to understand stability and function of biomolecules. The synergy between structure based models and coevolutionary information has spearheaded the field of structure prediction, including protein and RNA, as well as accelerating the discovery of functional structural states and the prediction of protein complexes. Coevolution signals can also be used to create protein recognition metrics, which led to successful experimental efforts, and the uncovering of novel molecular interactions. This idea has opened the door to encode recognition in protein pairs. Recently this approach has been used to predict extremely large protein assemblies consisting of structural maintenance of chromosomes (SMC) and kleisin subunits which are essential for the process of chromosome segregation across all domains of life. While limited structural data exist for the proteins that comprise the (SMC)–kleisin complex, using an integrative approach combining both crystallographic data and coevolutionary information, we predicted an atomic-scale structure of the whole condensing complex in prokaryotes. Also, leveraging coevolutionary sequence information and molecular simulations with an energy landscape optimized force field, we not only developed complete structural models of several kleisin complexes in different organisms but also their motions. The coiled-coil regions of these complexes braid together. Braiding is controlled by the head domains, which are ATPase motors.
Zoom: Inactive
YouTube: https://www.youtube.com/watch?v=opjgbmVN_2Y&t=1s
Robert B. Best
NIH, NIDDK, Laboratory of Chemical Physics
From disordered proteins to complexes and assemblies
Intrinsically disordered proteins are challenging to characterize by experiment owing to the diverse ensemble of structures they populate. This gives molecular simulations a powerful role as a natural complement to experiment. I will discuss how molecular simulations can be integrated with experiments to yield new insights into the properties of individual IDP chains and their complexes with other intrinsically disordered proteins and nucleic acids. Lastly, I will talk about our work developing coarse-grained models to describe phase separation to form biomolecular coacervates.
Monday 03.05.
8:00 PDT - 11:00 EDT - 15:00 UTC
16:00 BST - 17:00 CEST - 18:00 IDT
Zoom: Inactive
YouTube: https://www.youtube.com/watch?v=NxSeqlYiIU8&t=1s
Monday 17.05.
8:00 PDT - 11:00 EDT - 15:00 UTC
16:00 BST - 17:00 CEST - 18:00 IDT
Brian Dyer
Department of Chemistry, Emory University
Protein mediated membrane fusion studied by time resolved spectroscopy
The molecular basis of transmission and pathogenesis of the influenza virus is incompletely understood. Key early steps in the viral infection process involve acidification of the viral lumen by the M2 proton channel and membrane fusion mediated by hemagglutinin. These coordinated events are triggered by the low pH of the endosome and together facilitate release of the viral contents into the cytosol of the host cell. M2 is a highly selective and unidirectional proton channel that is activated at low pH, switching on proton conductance and acidifying the viral lumen to enable release of the viral ribonucleoproteins. While the structure of M2 has been determined at neutral and low pH, the dynamics that activate proton conductance are not known. The second essential step of infection is the formation of a fusion pore, mediated by the viral coat protein hemagglutinin (HA). Hemagglutinin has served as an archetype for understanding the general mechanism of membrane fusion and it is also an important target for antiviral drug development. HA is postulated to undergo an astounding series of refolding reactions triggered by lowered pH. The proposed spring-loaded mechanism of HA mediated membrane fusion has been inferred from equilibrium structures of pre- and post-fusion states, despite the highly dynamic nature of its pH dependent structure. As a consequence, the molecular details of HA mediated membrane fusion are not known, particularly with respect to the protein-membrane interactions. We have explored the molecular mechanism of HA mediated membrane fusion and M2 mediated proton transport that enable influenza virus infection, using time-resolved infrared and fluorescence spectroscopies of these proteins reconstituted in lipid vesicles. We have characterized the functional dynamics of HA and M2 induced by low pH using the laser pH-jump as a trigger and time resolved spectroscopy to map the structural dynamics.
Zoom: Inactive
YouTube: https://www.youtube.com/watch?v=8_WT7KMWo8k&t=2s
Monday 31.05.
8:00 PDT - 11:00 EDT - 15:00 UTC
16:00 BST - 17:00 CEST - 18:00 IDT
Peter Hamm
Department of Chemistry, University of Zurich
A Nonequilibrium Approach to Allosteric Communication
With the term "allostery" one describes the coupling of two separated sites of a protein, where binding of a ligand at the so-called allosteric site changes the function of the protein at a remote active site. Allostery is one of the fundamental mechanisms of regulatory processes in life. The very question of how these two sites communicate with each other remains an intriguing and controversial problem, with the ultimate question of how an allosteric signal ``propagates'' through a protein. Transient IR spectroscopy provides the time resolution combined with the chemical selectivity necessary to study these nonequilibrium processes. In these experiments, an allosteric protein is light-trigger with the help of a photo-isomerizing azobenzene moiety, which is incorporated into the protein in a way that it mimics an allosteric process, and the response of the protein is recorded by transient IR spectroscopy. I will discuss a variety of protein systems that we have designed for that purpose, as well as ongoing experiments.
Zoom: Inactive
YouTube: https://www.youtube.com/watch?v=j1TfBDvHCco
Elizabeth Rhoades
Department of Chemistry, Penn Arts & Sciences
It takes tau to tangle: functional studies of a dysfunctional protein
Tau is an intrinsically disordered neuronal protein which is thought to have a role in stabilizing axonal microtubules. We are interested in understanding the tau’s functional mechanisms as relevant to the unique properties of axonal microtubules. Here, we use single molecule fluorescence and fluorescence correlation spectroscopy to characterize the interactions of tau with soluble tubulin. We identify a novel tubulin-binding domain of tau and demonstrate that it that it is independently capable of polymerizing tubulin into microtubules. We propose a model for tau function which highlights the role of this novel domain.
Monday 14.06.
8:00 PDT - 11:00 EDT - 15:00 UTC
16:00 BST - 17:00 CEST - 18:00 IDT
Zoom: Inactive
YouTube: https://www.youtube.com/watch?v=sR1A9SCj52Q
Joan-Emma Shea
Department of Chemistry and Biochemistry, Department of Physics, UCSB
Fibrillization and Liquid-Liquid Phase Separation of the Tau Peptide
Intrinsically disordered peptides (IDP) are a special class of proteins that do not fold to a unique three-dimensional shape. These proteins play important roles in the cell, from signaling to serving as structural scaffolds. Under pathological conditions, they can self-assemble into structures that are toxic to the cell, and a number of neurodegenerative diseases are associated with this self-assembly process. My talk will focus on the Tau protein, an IDP that binds to microtubules and can form fibrillar aggregates, a process that has been linked with Alzheimer’s disease. In addition to forming fibrils, the Tau protein can also phase separate into a protein rich and a protein depleted phase, a process known as liquid-liquid phase separation (LLPS). This process may play a protective role in the cell against pathological fibrillization. I will present molecular dynamics and field theoretic simulations that map out the phase diagram for Tau LLPS, and use this phase diagram to predict the conditions under which Tau can be driven towards LLPS under cellular conditions.
Monday 28.06.
8:00 PDT - 11:00 EDT - 15:00 UTC
16:00 BST - 17:00 CEST - 18:00 IDT
Zoom: Inactive
YouTube: https://www.youtube.com/watch?v=sxHkkgAZ828
Rohit Pappu
Department of Biomedical Engineering, Center for Science & Engineering of Living Systems, Washington University in St. Louis
Emergent structures, functions, and phase behavior driven by charge-rich disordered proteins
This talk will focus on new findings that have emerged from our studies of disordered proteins that are enriched in ionizable residues. Features such as differences in Lys vs. Arg contents, charge regulation of Glu-rich regions, the interplay between acidic groups and polar moieties, and the blocky patterning of Lys / Glu rich regions give rise to rich complexities across multiple length scales. The talk will highlight physical principles underlying the evolutionarily conserved sequence features of charge-rich regions, their roles in dictating the functions of polymerizing enzymes, the regulation of thermoresponsive phase transitions, and in determining the compositional specificity of biomolecular condensates.
Monday 12.07.
8:00 PDT - 11:00 EDT - 15:00 UTC
16:00 BST - 17:00 CEST - 18:00 IDT
Zoom: Inactive
YouTube: https://www.youtube.com/watch?v=C0z_89ClQrM&t=1s
Monday 26.07.
8:00 PDT - 11:00 EDT - 15:00 UTC
16:00 BST - 17:00 CEST - 18:00 IDT
Mei Hong
Department of Chemistry, Massachusetts Institute of Technology (MIT)
Structure and Dynamics of Membrane Proteins in Infectious Diseases
Viroporins are small ion channels that are important for the lifecycle and pathogenicity of many enveloped viruses. Elucidating their structure, dynamics and mechanism of action is important for our fundamental understanding of ion channels and for designing channel inhibitors as antiviral drugs. Using solid-state NMR spectroscopy, we have obtained rich insights into the proton conduction mechanism of influenza virus M2 proteins. These insights come from measurement of the proton transfer equilibria and rates of a crucial histidine residue in M2 when bound to cholesterol-containing lipid bilayers. We also measured water dynamics and water orientations in closed and open M2 channels, giving complementary information about the mixed hydrogen-bonded chain between water and histidine for proton transport in these channels. Applying solid-state NMR, we recently determined the structure of the SARS-CoV-2 envelope (E) protein, the equivalent viroporin in coronaviruses. The five-helix bundle structure shows the binding site of the inhibitor hexamethylene amiloride, and provides a framework for understanding the cation conduction mechanism of E.
Zoom: Inactive
YouTube: https://www.youtube.com/watch?v=8TiyZkn9VXo
Monday 09.08.
8:00 PDT - 11:00 EDT - 15:00 UTC
16:00 BST - 17:00 CEST - 18:00 IDT
Marius Clore
NIH, NIDDK, Laboratory of Chemical Physics
Probing transient pre-nucleation oligomerization of huntingtin at atomic resolution by NMR
Huntington’s disease is a fatal, autosomal, neurodegenerative condition that arises from CAG expansion within exon-1 of the huntingtin gene that encodes a polyglutamine (polyQ) repeat. Although the huntingtin protein is very large (~350 kDa), proteolysis and/or incomplete mRNA splicing generates mutated N-terminal fragments encoded by exon-1 that aggregate to form neuronal inclusion bodies in pathological states. The N-terminal region of huntingtin encoded by exon 1, httex1, comprises three distinct regions or domains: a 16-residue N-terminal amphiphilic sequence (httNT), a polyQ tract of variable length, and a proline rich domain (PRD) with two polyproline repeats of 11 (P11) and 10 (P10) residues. In this talk we will summarize out work on the earliest pre-nucleation transient oligomerization events involving httex1 using NMR experiments designed to probe rapidly exchanging systems (sub-millisecond time range) involving sparsely-populated excited states. We show that a branched assembly mechanism is involved comprising on- and off-pathways. In the on-pathway branch, the major monomeric species self-associates to form a productive helical coiled-coil dimer of the NT region that goes on to form a four-helix bundle tetramer comprising a dimer-of-dimers. In the off-pathway branch, a “non-productive” dimer ensemble with partially helical character is formed that does not undergo further oligomerization. The importance of pre-nucleation tetramerization is evidenced by the fact that inhibition of tetramer formation blocks fibrillization. Thus on-pathway tetramerization constitutes the prenucleation trigger or molecular switch that hugely increases the probability of occurrence of intermolecular polyQ contacts (by effectively increasing the local concentration of the polyQ tracts) and hence polyQ fibril formation. It is therefore clear that blocking productive dimer and/or tetramer formation may provide a fruitful avenue for preventing or delaying the onset of Huntington’s disease. Inhibition of pre-nucleation oligomerization can be achieved in a number of ways: (a) perturbing the productive dimer and/or tetramer interface; (b) sequestration of httex1 through binding of the httNT sequence to chaperones; and (c) allosteric, long-range inhibition by interaction of intracellular proline-binding proteins with the proline rich domain (PRD).
Zoom: https://weizmann.zoom.us/j/91996717818?pwd=eDY0c0NlZlNSbnRlR3lhTzJQTzlnZz09
YouTube: TBA
How I plan to study protein folding and dynamics by proving theorems
Biophysicists visualize biomolecular folding as motion along one-dimensional “folding coordinates” (aka “reaction coordinates” or “order parameters”) over free energy barriers. Various rate theories, such as transition state theory and Kramers’ theory of diffusive barrier crossing, differ in their assumptions regarding the mathematical specifics of this motion. Direct experimental observation of the motion along reaction coordinates requires single-molecule experiments performed with unprecedented time resolution. Toward this goal, recent single-molecule studies achieved time resolution sufficient to catch biomolecules in the act of crossing free energy barriers as they fold, bind to their targets, or undergo other large structural changes, offering a window into the elusive folding/binding/reaction “mechanisms”. In this talk, I will discuss how one can use these emerging data to answer several questions of principle. For example, is motion along the folding reaction coordinate diffusive, how heterogeneous is the ensemble of paths leading from the unfolded to the folded state, is there conformational memory, and is reduction to just one degree of freedom to represent the folding mechanism justified? I will show how these questions can be formulated as strict, experimentally testable mathematical inequalities and illustrate their utility in application to experimental and atomistic simulation data. No math beyond freshmen calculus is needed to understand this talk.