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    ProteinFoldingAndDynamics

    PROTEIN FOLDING & DYNAMICS

    WEBINAR

    Ben Schuler

    Gilad Haran

    Hagen Hofmann

     
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    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. 

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    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.

    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.

    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

    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.

    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

    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

    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

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    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

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    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. 

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    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.

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    YouTube: https://www.youtube.com/watch?v=21GuC-RJqP4

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    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

    Network models in biology: from molecular machinery and evaluation of missense variants, to chromosomal dynamics

    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.

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    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

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    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

    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.

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    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.

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    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.  
     

    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.

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    YouTube: https://www.youtube.com/watch?v=EHWcOoNwzQQ

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    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.

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    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.

    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

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    YouTube: TBA

    Monday 22.03.

    8:00 PST -  11:00 EST - 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).

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    Eugene I. Shakhnovich

    Department of Chemistry and Chemical Biology, Havard University

    TBA

    Monday 05.04.

    8:00 PST -  11:00 EST - 16:00 UTC

    16:00 UK - 17:00 CET - 18:00 IL

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    YouTube: TBA

    Monday 19.04.

    8:00 PST -  11:00 EST - 16:00 UTC

    16:00 UK - 17:00 CET - 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.

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