Highlighting Biophysics Research During Sickle Cell Awareness Month

September is National Sickle Cell Awareness Month in the United States. Sickle cell disease is an inherited blood disorder that affects approximately 100,000 Americans and millions worldwide. It is particularly common among people whose ancestors come from Sub-Saharan Africa, South America, Cuba, Central America, Saudi Arabia, India, and Mediterranean countries such as Turkey, Greece, and Italy.

To recognize the awareness month, we spoke with BPS member George Em Karniadakis, Brown University, and his collaborators Xuejin Li, Brown University, and Ming Dao, MIT, about their research related to sickle cell disease. Their research was also featured on the cover of the July 11, 2017, issue of Biophysical Journal.


What is the connection between your research and sickle cell disease?

Sickle cell disease (SCD) is the first identified molecular disease affecting more than 270,000 new patients each year. Our interests are in modeling multiscale biological systems using new mathematical and computational tools that we develop in our teams at Brown University and MIT in conjunction with carefully selected microfluidic experiments at MIT. We have an ongoing NIH-funded joint project that focuses on developing such validated predictive models for the sickle cell disease (SCD). In this project, with close collaboration between clinicians, experimentalists, applied mathematicians and physical chemists, we have been  developing new predictive patient-specific models of SCD, linking sub-cellular, cellular, and vessel-level phenomena spanning across four orders of magnitude in spatio-temporal scales. So far we have developed a validated patient-specific and data-driven multiscale modeling approach to probe the biophysical mechanisms involved in SCD from hemoglobin polymerization to vaso-occlusion.

Why is your research important to those concerned about sickle cell disease?

SCD is one of the most common genetic blood disorders that can cause several types of chronic and acute complications such as vaso-occlusive crises (VOC), hemolytic anemia, and sequestration crisis. It is also the first identified molecular disease (as early as 1947 by Linus Pauling), and the underlying molecular cause of the disease has been understood for more than half a century. However, progress in developing treatments to prevent painful VOC and associated symptoms has been slow. Consequently, we have been developing a “first-principles” multiscale approach that can handle the disparity of molecular, mesoscopic and macroscopic phenomena involved in SCD simultaneously. Such simulations could potentially answer questions concerning the links among sickle hemoglobin (HbS) polymerization, cell sickling, blood flow alteration, and eventually VOC. We hope, in turn, that these models will help in assessing effective drug strategies to combat the clinical symptoms of this genetic blood disorder.


Figure 1. Dynamic behavior of individual sickle RBCs flowing in microfluidic channel. Inside the yellow circles are trapped sickle RBCs at the microgates, and inside the white circles are deformable RBCs, which are capable of circumnavigating trapped cells ahead of them by choosing a serpentine path (indicated by the white arrows).

How did you get into this area of research?

We have been working on multiscale modeling of blood disorders for more than 10 years.  In the very beginning, we were interested in developing new computational paradigms in multiscale simulations, which would enable us to perform multiscale realistic simulation of blood flow in the brain of a patient with an aneurysm. We then realized that the mesoscopic modeling of red blood cells (RBCs) and hemorheology in general seems to be the most effective approach for modeling malaria and other hematologic disorders. Then, we shifted our attention to the particle-based modeling of blood flow by employing the dissipative particle dynamics (DPD) method, which can seamlessly represent the RBC membrane, cytoskeleton, cytosol, surrounding plasma, and even the parasite in the malaria-infected RBCs. We developed multiscale RBC models and employed them to predict mechanical and rheological properties of RBCs and quantify molecular-level mechanical forces involved in bilayer–cytoskeletal dissociation in blood disorder. In 2012, we started to work on SCD, after realizing that no multiscale simulation studies of SCD had been conducted before – our work is the first of its kind!

How long have you been working on it?

As we mentioned above, we have been working in this field for more than 10 years.

Do you receive public funding for this work? If so, from what agency?

Yes, we receive support from NHLBI, the institute within NIH focusing on blood disorders based on the interagency funding initiative pioneered by Dr. Grace Peng. For those who are interested in this multiscale consortium they can visit: https://www.imagwiki.nibib.nih.gov/

Have you had any surprise findings thus far?

Plenty! For example, at the vessel scale, using computer models, we have discovered that it is the soft and sticky type of RBCs that initiate the blockage process and lead to sickle cell crises and not the rigid sickle cells! This is the first study to identify a specific biophysical mechanism through which vaso-occlusion takes place. At the cellular scale, we have developed a tiny microfluidic device that can analyze the behavior of blood from SCD patients. Informed from the microfluidic experiments conducted by Dr. Ming Dao’s group at MIT, we have developed a unique patient-specific predictive model of sickle RBCs to characterize the complex behavior of sickle RBCs in narrow capillary-like microenvironment. At the sub-cellular (molecular) scale, we have developed a particle HbS model for studying the growth dynamics of polymer fibers (recent cover of Biophysical Journal). The simulations provide new details of how SCD manifests inside RBCs, which could help other medical researchers in developing new treatments.

What is particularly interesting about the work from the perspective of other researchers?

It is known that the primary cause of the clinical phenotype of SCD is the intracellular polymerization of sickle hemoglobin (HbS) resulting in sickling of RBCs in deoxygenated conditions. However, the clinical expression of SCD is heterogeneous, making it hard to predict the risk of VOC, and resulting in a serious challenge for disease management. Our data-driven stochastic multiscale models, based on particle methods, can be used to explore and understand the dynamics of collective processes associated with vaso-occlusion that links together sub-cellular, cellular, and vessel phenomena. A similar computational framework can be applied to study blood flow in other hematologic disorders, including malaria, hereditary spherocytosis and elliptocytosis, as well as other blood pathological conditions in patients with diabetes mellitus or AIDS.  For example, in ongoing work we have quantified the biophysical characteristics of RBCs in type-2 diabetes mellitus (T2DM), from which the simulation results and their comparison with currently available experimental data are helpful in identifying a specific parametric model that best describes the main hallmarks of T2DM RBCs.  Perhaps, the most important extension is to connect such multiscale models to all the “omics” technologies (genomics, proteomics, metabolomics, etc.) to implement the vision of precision medicine advocated both in the U.S. and around the world.

What is particularly interesting about the work from the perspective of the public?

Our studies provide new insight into what causes painful episodes in people with SCD. Using the computational models we could probe different mechanisms and validate diverse hypotheses regarding vaso-occlusion.  For example, we have shown that the rigid crescent-shaped RBCs —the hallmark of SCD — do not cause these blockages on their own. Instead, softer, deformable RBCs are known as cells that start the process by sticking to arteriolar and capillary walls. The rigid crescent-shaped cells then stack up behind these softer cells, creating a sort of a traffic jam.

Currently, hydroxyurea (HU) is the only approved medication in widespread use for the treatment of SCA, and it is thought to work by promoting the production of fetal hemoglobin, which can reduce sickling rate. Using the computational models, we can now run simulations that include fetal hemoglobin, which could help in establishing better dosage guidelines or in identifying a subgroup of patients who would benefit from this treatment or proposing a different type of treatment for others.

In addition, based on our own experience and knowledge, we also presented a short review in SIAM NEWs,   which provides the broader public with a general idea of computational modeling of blood disorders, including SCD. Here is the link to the review: https://sinews.siam.org/Details-Page/in-silico-medicine-multiscale-modeling-of-hematological-disorders.

Do you have a cool image you want to share with the blog post related to this research?

Yes, we have a cool image to share (figure 1). This image shows the different dynamic behavior between individual normal RBCs and sickle ones in microfluidic flow. Normal RBCs are round and flexible, and easily change shape to move through even the smallest blood vessels. Under deoxygenation, RBCs undergo sickling can be hard, sticky, and abnormally shaped, so they tend to get stuck at the microgates and block the blood flow. Once the adjacent microgates in the flow direction (from right to left) are blocked, the deformable RBCs (one is highlighted in white circle) appear to take a preferred path, i.e., they twist and turn along a serpentine path (as indicated by the white arrows) once they spot trapped sickle cells (one is highlighted in yellow circle) ahead of them.


On the State of Professional Opportunities for Women in Biophysics

GKP 2014At last year’s BPS meeting, while talking with several of you about how the Committee for Professional Opportunities for Women (CPOW) can better serve the BPS membership, I learned — much to my surprise — that the perception of gender equality and fairness in biophysics varies widely among our colleagues. At one extreme, some expressed disappointment that “not much has changed” since CPOW was formed in 1972; at the other, some declared “mission accomplished.” I suspect that like me, many of you will disagree with both statements, but I cannot guess where on the spectrum a consensus, if there is one, may lie.

To investigate these perceptions, CPOW will host a blog series where members can express their views on the subject by briefly answering these four questions: In your opinion,

  1. What is the current state of gender equality in science and biophysics?
  2. What is the value of having equality and true inclusiveness?
  3. What is one area that needs attention; and
  4. What is the one thing that can be done right away?

We kick off this initiative by publishing below answers from our fearless BPS Past President Suzanne Scarlata. You are encouraged to read and comment on these blog posts, and to volunteer your own answers by emailing them to Laura Phelan at lphelan@biophysics.org.

Thank you for your engagement. I look forward to hearing from you,

—Gabriela K. Popescu, CPOW Chair


Suzanne Scarlata, Worcester Polytechnic Institute

What is the current state of gender equality in science and biophysics?

Compared to where we were 20 years ago, we’ve made a great deal of progress. Women now populate key positions in companies, universities, and scientific organizations. While we are still underrepresented especially in top positions, our numbers are growing and the trend is going up. However, we are far from shattering the glass ceiling.

Women have a better support system than in years past. In previous years when only a few senior women were around, women had to rely on father figures for advice in making their way through the system, which, of course, could limit the content of conversations. Now there are more women mentors both locally and through groups like the BPS that can bring together women to share their thoughts.

For the most part, I feel that time is on our side. Most colleagues my age and younger are fairly unbiased and this percentage is increasing every decade. Just a few years ago, I attended a meeting where I was the only female speaker. One of organizers was openly misogynistic which seemed to bother my male colleagues even more than me.

What is the value of having equality and true inclusiveness?

It goes without saying that having true inclusiveness and equality is invaluable. Everyone should be able to have the opportunity to work at their full potential and be appreciated and respected for what they do.

What is one area that needs attention?

Scientifically, we need to continue to promote ourselves (unfortunately, most of us are really bad at self-promotion) and our female colleagues by suggesting them for talks, for positions on editorial boards, and other leadership positions. We need to cite their articles when appropriate and give women the credit they deserve.

Importantly, we need to continually question whether we are treating our students, post-docs, and peers with encouragement and respect. The other day, a female undergraduate biochemistry major with a high GPA told me that her male advisor thought that she should focus on a career in writing and not science once she graduates. I had different advice!

What is the one thing that can be done right away?

While some countries have experienced recent setbacks regarding gender bias, we need to be persistent in encouraging equality both in and out of the lab. Nonscientists may not be aware of the many opportunities there are for their daughters in science, or aware of the problems they might encounter. We need to encourage women at all levels so that our numbers will grow.

When Ruth Bader Ginsburg (one of the nine members of the United States Supreme Court) was asked when she thinks there will be enough women on the court, she replied, “And my answer is when there are nine.”

For Microtubule Sliding, One Arm Is Better Than Two

BPJ_113_5.c1.inddThe versatile and dynamic network of the cytoskeleton scaffold would be stagnant and lifeless if not for the tiny nanoscopic machines called molecular motors. Kinesin motors, in particular, have captured the imagination of biologists and physicists because of their ability to transform ATP into anthropomorphic walking patterns on polar microtubule filaments, which make up a significant portion of the cytoskeleton. Recent experiments have shown that kinesin motors can crosslink adjacent microtubules and facilitate sliding between them resulting in cytoplasmic streaming in Drosophila cells. This facilitates faster distribution of molecules and organelles, and determines cell-shape.

But how do motors bring about microtubule sliding? How does the collective motion of microtubules depend on the movement of motor arms? In our work, we answer these questions by studying the effect of dimeric (one active arm, one anchored arm) and tetrameric (two active arms) kinesin motors on the dynamics of confined microtubules. Through our computer simulations we find that single-armed kinesins bring about much faster dynamics in specific regions of the confinement, compared to their two-armed counterpart. This goes against the intuitive idea that more arms pull more.

The cover image for the September 5th issue of the Biophysical Journal is our rendering of filament organization for two different motor types and the effects of these differences in the large-scale structure and dynamics of confined microtubules. The green shapes on the left represent the active motor heads that walk on polar microtubules. These are depicted as a linear array of dark-blue and yellow circles. The red blob depicts the anchor belonging to the single-armed, dimeric motor. Motor arms walk in specific directions on microtubules, and stretch, producing a sliding stress between microtubules.

The structures shown in the circular confinement on top consist of sluggish filament packages formed by tetrameric motors. The arrows at the bottom represent the highly dynamic microtubule arrangement formed by dimeric motors. Here, we also depicted the trajectories that three selected microtubules have taken. The cover image was crafted to highlight the large-scale biophysical implications of seemingly trivial and counterintuitive details in biology. Through this work we emphasize the vastly different cytoskeletal dynamics due to dimeric and tetrameric motors. By way of the trajectories, we capture the active layer of microtubules close to the circular confinement we observed for the single-armed motor systems.

– Arvind Ravichandran, Gerard Vliegenthart, Guglielmo Saggiorato, Gerhard Gompper, Thorsten Auth

Thematic Meeting, Berlin 2017: Session III

Welcome back to my post-conference note. Let’s jump right into the third session on “Interpreting Experiments Through Molecular Simulations“ including talks by Ceclilia Clementi, Michael Feig and Arianna Fornili on Saturday afternoon and with Shang-Te Danny Hsu, Jana Selent and Massimiliano Bonomi on Sunday morning.

The challenges of computational biophysics aiming to bridge molecular and cellular studies is among others due to the characterization of macromolecular systems by sets of different timescales, separated by large gaps. Celilia Clementi tackles this challenge by combining coherent state analysis and Markov State Modeling. Furthermore, she introduced a theoretical framework for the optimal combination of simulation and experiments in the definition of simplified coarse-grained Hamiltonian protein models. As those simplified models loose information, the combination with experimental data makes them more realistic and provides larger time-scales. She further illustrated the method and mentioned as application the coarse-graine model of FIP35.

Next, Michael Feig investigated protein dynamics and stability with crowders in simulations and experiments. He states protein destabilization in Villin due to crowding, in order to explain the differing results from NMR vs. MD. With Villin under dilute conditions, he observed oligomer formation in MD, whereas transient oligomers form on timescales longer than rotational translation diffusion. Rotational diffusion is slowed down by additional factors. In addition to his study on Villin, he could identify transitions between conformations connecting all states of Bacterial genomic DNA, based on targeted MD.

The last talk of this Saturday was given by Arianna Fornili about identification of rescue sites for protein function. As rescue mutations can be mimicked by drugs, their locations is of interest for drug design wherefore she developed a method. Double Force Scanning (DFS) mimics mutations by external forces, using an elastic network model to represent protein dynamics. In oder to model structural perturbations, linear response theory is used. In detail, she used the Fibonacci lattice for uniform distribution for force vectors. The performance of DFS was tested on p53, predicting 80% non-rescue sides correctly, and on an evolutionary dataset, where 79% of evolutionary rescue sites where predicted correctly.

Subsequently after Ariannas talk and a short coffee break, the first poster session was started. Although it was very crowed (which might have been a live experiments from the organizers, fitting to the last session), posters of high interests have been presented, leaving the presenters no break for a small sip of water. Afterwards, the program was open for all those aiming to explore the city of Berlin. On Sunday morning, the third session was continued with talks from Shang-Te Danny Hsu, Jana Selent and Massimiliano Bonomi.

The first session of this Sunday started with a rather biological topic on the structural basis of substrate recognition and chaperone activity of ribosome-associated trigger factor (TF) regulated by monomer-dimer-equilibrium from Shang-Te Danny Hsu. As the structure contains highly dynamic regions, those parts could not be easily resolved. This was also confirmed by solid state NMR studies, showing ribosome binding-induced conformational change in the ribosome binding domain of TF (TF-RBD). Shang-Te revealed TF substrate specificity by peptide array analysis, originating from recognition of averaged property rather than an exact sequence. Produced SAXS data showed a misfit between those and the crystal structure of TF. Further studies using pulse dipolar ESR spectroscopy revealed multiple dimer configurations of TF, which could be identified by chemical cross-linking. Furthermore, he modeled a dynamical system using several different techniques such as crystallography, NMR, SAXS. Comment: good luck for your PhD student 😉

Next, Jana Selent presented her work on the functional dynamics of the distal C-tail of arrestin. As introduced by her, phosphorylation of the GPCR C-tail triggers the arrestin pre-complex, including a partial C-tail displacement of arrestin. To investigate the role of the distal C-tail, she performed all-atom MD simulations and site-directed mutagenesis studies. She described its conformational space with preference to bind to positively charged residues. Tryptophan-induced dynamic quenching was increased for some residues. Furthermore, she investigated the mechanism of IP6-induced displacement, where IP6 displaces residue 393 to 400 but not further down upon binding to GPCR. As second topic, she investigated the C-edge loop of arrestin. By MD simulations, she showed that C-edge loop of pre-activated arrestin was able to penetrate the membrane, in contrast to activated arrestin. This was confirmed by quenching mutagenesis experiments. Finally, she postulates a step-wise binding process from unbound GPCR over an arrestin-GPCR pre-complex including the displacement of the distal C-tail and the penetration of the C-edge into the membrane, followed by the high affinity complex.

The last talk for this session was hold by Massimiliano Bonomi on integrative structural and dynamical biology with PLUMED-ISDB. As computational and experimental technique have their challenges or errors, a hybrid or integrative method could provide a more realistic view. By providing the module PLUMED-ISDB, he presents a way to investigate heterogeneous systems by including experimental data with a priori information. It uses a Bayesian inference method which accounts for data noise and averaged ensembles. He applied this metainference approach to cryo-EM data, able to explain the data better with a lower resolution as a mixture of dynamics and noise.

At last, he addresses challenges to the community, to those I could not agree more and therefore will end my post with his wishes: More distribution of ensembles of the community like structural models, model populations and protocols; the establishment of robust methods for ensemble comparison and validation; and a way to facilitate comparison of different ensemble modeling approaches by sharing methodologies.



Thematic Meeting, Berlin 2017: Session I & Session II

Just a blink and this fantastic conference was over. Equally my time for writing some posts passed by, which preparation I fairly underestimated. So, now I would like to share my notes with you. Hope you enjoy reading my post-conference posts, to remember the great talks or get an impression, what you missed! Let’s start with session I & II!

After planning this meeting thoroughly together with Helen Berman, Andrea Cavalli and Gerhard Hummer for several years, Kresten Lindorff-Larsen addressed the opening remarks emphasizing what they aimed for this program and how much they looked forward to tackle it. And they were not alone! Finally, the first session on “Disordered Protein Ensembles” started, including talks by Adriaan Bax, Tanja Mittag, Teresa Head-Gordon and Paul Robustelli on Friday and Martin Blackledge and Birthe Kragelund on Saturday morning.
For me it was the first time I heard such comprehensive collection of talks about (intrinsically) disordered proteins (IDP) and this session had a great mixture of experimental methods to computational strategies and the benefit of their conjunction.

Starting with Adriaan Bax, he observed protein folding and misfolding by pressure jump NMR with special focus on HIV-1 Protease. The challenge in there is indeed the pressure but by managing this, he observed pressure-induced fully reversible unfolding including slow exchange time scale. Additionally, monomer exchange faster than stable dimer. He further looked into single residue cis-trans isomerisation. By investigating hydrogen bonding network stability, he sees a significant shift towards low pressure. For Abeta(1-40) fibril formation, real time NMR signals disappear after dropping pressure from 2.4 kbar to 1 bar, which is then heterogeneous, but rapidly reappears after jumping to high pressure. For his third system (Ubiquitin), the showed the influence of pressure by revealing an intermediate state, leaving open that this might also be due to mutations.

Next Tanja Mittag studied the effect of multi-site phosphorylation on conformations of intrinsically disordered proteins, exemplary S. cerevisiae transcription factor Ash1. Ash1 is expected to be collapsed and to expand upon multi-site phosphorylation but SAXS shows only little differences. By following an ensemble optimization method, she identified preferences for expanded conformations to be insensitive to screening of long-range electrostatic interactions, but reacting to the presence of weak local structural preferences. She identifies sequence features, mainly a relationship between proline and charged amino acids, deriving intrinsic sequence code expansion. She argues against chain compaction upon multi-site phosphorylation due to proline isomerization or presence of pSer/Arg or pThr/Arg salt bridges. Additionally, all-atom simulations could reproduce the experimental observations. Finally, she states that a large enough concentration of Prolines distributed along a sequence can buffer changes in net charge per residue while changes in local conformation occur.

After a refreshing coffee break, Teresa Head-Gordon presented new methods for generating and evaluating conformational ensembles. She looked at secondary structure propensities for Abeta42 and Abeta43 and observed differences in N-terminus and central hydrophobic core with REMD simulation, indicating either bad force-fields, poor sampling or both. There she introduced Temperature Cool-Waking (TCW) using annealed importance sampling and could indicate poor sampling. She states that TCW and polarizable forcefields work for folded proteins and are robust for IDPs, whereas Boltzmann priors may be questionable for IDPs. Monte-Carlo side chain ensemble (MC-SCE) has implemented a sophisticated energy function to distinguish different side chain packings based on Boltzmann factor. She concluded that MC-SCE and entropy expansions are informative about improved catalysis.

For the last talk of the first day, Raul Robustelli from D.E. Shaw Research gave insights in ongoing force field development, focusing on ordered and disordered protein states. The problem of current force fields for IDPs is that they tend to being structurally too compact relative to experiments. In this context, he stated the importance of an improved water model, as water dispersion energies have been systematically underestimated. Therefore, he introduced the TIP4P-D water model. Enhanced hydrogen bond potential and ‘fractional’ charges showed improved fits of non-bonded parameters to quantum data. As those analysis fit nicely, still further improvements have to be conducted, e.g. to challenge the over-representation of beta sheets.

With Paul Robustelli, an interesting first day at the “Conformational Ensembles from Experimental Data and Computer Simulations” conference ended and everybody went over to the welcome reception to enjoy a beautiful evening on the terrace outside. Perfect time for some networking. You can find some impression on twitter (@BiophysicalSoc).

Day two started with Martin Blackledges talk about “Large-scale Protein Conformational Dynamics from NMR and Molecular Simulation. From Fundamental Biophysics to Biological Function”. He aims to understand large-scale domain motion in influenza, where temperature is a key factor. Problematically is that its crystal conformation cannot bind to importin alpha. For NMR, its 2 domains do not interact with each other, rather having an open and a closed form. He finds that highly conserved salt bridges are involved in stabilizing the closed formation. He uses chemical exchange saturation transfer (CEST) to measure interconversion rate and population of substates. Using integrated structurally dynamics (NMR, smFRET, SAXS) CEST analyses are supported and dynamic interconversion between open and closed form of H5Na influenza 627 are revealed .
To explain how IDPs interact with their physiological partners, Martin introduced Asteroids, a selection tool of ensemble descriptions of intrinsically disordered systems, which was tested using target ensembles. In order to understand the mechanism of highly dynamic IDPs interactions, first their intrinsic dynamics have to be understood and therefore he developed a physical framework by comparing conformational sampling between 274 -298 K.
Using the ABSURD (average block selection using relaxation data) procedure, he could reproduce the experimental data, overcoming current limitations of MD simulations of IDPs. It identifies ensembles of trajectories of IDPs and can thereby map extent of inter-residue dynamic correlation.

The last talk for this session was held by Birthe Kragelund on dynamics and disorder in class 1 Cytokine receptors. She states that disorder is an important and integral part of membrane proteins as intrinsically disordered regions (IDRs) co-structure them as regulatory platforms with the need of structural information on bound state. Still, they are often not recognized. For membrane proteins, other players come into account. Disordered lipid binding motifs still need to be identified and understood, especially short linear motifs. In general, she combined experimental and computational techniques, including NMR, X-ray scattering, mass spectrometry, simulation and molecular modeling, solving the prolactin receptor monomeric structure. As the transmembrane domain is a weak dimer with highly specific interactions, its study is more challenging. She could identify two conformations, providing more insights into its dynamical function, e.g. that specificity can be modified by one single methyl group. Finally, she describes the multiple transmembrane domain states which are influenced by lipid composition, kinase binding and dimerization.

After the coffee break, the second session started on “Integrative and Hybrid Methods” with Andrej Sali, Alexandre Bonvin and Ji-Joon Song started.

Andrej Sali introduced us his research on integrative structure determination, where he uses experiments, physical theory and statistical inference to maximize accuracy, resolutions, completeness and efficiency. He presented 4 general steps of his integrative modeling platform (IMP), first naming gathering of information by experimental data, statistical inference and physical principles, second designing system representation and scoring, third followed by sampling and finally analysis and validation. Following this workflow for the Spindle Pole Body, he obtained a validated structure including insights into functional implications of the model.

Next, Alexandre Bonvin presented his integrative modeling platform HADDock (high ambiguity driven docking). It incorporates ambiguous and low-resolution data to aid the docking of up to 6 molecules and has a powerful algorithm to handle flexibility at the interface including refinement in explicit solvent. Using RNA-polymerase II, he introduced DisVis for explorative modeling and consistency quantification of information content of distance restraints solely based on geometric considerations. It can provide information about possible interfaces and calculable information to guide modeling but does not account for conformational changes and energetics.

Ji-Joon Song focused with his talk on the human importin4_histone H3/H4 Asfla complex, which is a perfect example for a successful integrative structural approach, as he was able to solve the whole complex by combining several techniques, such as x-ray crystallography, SAXS, EM, Mass spectrometry, biological application and modeling. He also stated that C-importin4 directly interacts with histon H3 peptide via a highly acid patch. The validation of the complex via single particle electron microscopy, small angle x-ray scattering and cross-linking mass spectrometry confirmed conformational flexibility.

Closing his talk, many discussions were extended during a manifold but time-wise rather tight lunch outside at the venue. Enjoying the sun we were waiting for the next session, curious what surprises there might be… You want to know what happened? Check out my next post on the third session about “Interpreting Experiments through Molecular Simulations”!



Berlin calling – let’s get thrilled!

Hey folks! I am Johanna Tiemann and as you can read I got the honor to post some comments and personal perspectives of this Biophysical Society thematic meeting, ‘Conformational Ensembles from Experimental Data and Computer Simulations’ that will be held in Berlin, Germany from the 25th to the 29th of August 2017.

Originally from Munich, Germany, I studied Bioinformatics in Berlin and joined Peter Hildebrand’s lab at Charité Medical University already during my Bachelor and Master thesis. The cluster of knowledge within the lab and institute (e.g. Klaus Peter Hofmann and others) stimulated my fascination about G-protein coupled receptors (GPCR), modeling, simulating and coding. So here I am in my second year PhD that I started in Berlin and now continue in Leipzig. First time I saw the announcement for this meeting I got excited as the Harnack house is located at the green and cozy campus of my Alma Mater, the Free University of Berlin. Although it is rather off the beaten track, it is great to get out of the hectic city center of Berlin and focus on science. As a venue for a conference it is pleasant as you will not be that much distracted by the busy city life but rather can get in touch intensively with each other. If you still have energy to spare after a day of very interesting talks and posters, the night life of Berlin is definitely worth to visit, especially during the weekend (plus there is public transport during the whole night). If you need some advice what to see in Berlin – I am happy to share my experience ;-).

During my time as student assistant and PhD student, I already attended several interesting conferences and workshops but this will be my first BPS meeting and the first time as a blogger at such an event. Of course, I got excited when I noticed the organizing committee, as I already had the pleasure of meeting Andrea Cavalli and Kresten Lindorff-Larsen at a CECAM meeting in Lausanne 2016, leaving no doubt that this conference will be full of highlights with a great mixture of computational and experimental topics.

So what else is there to say about me? I am an enthusiastic, always smiling structural biologist. Within the lab of Peter Hildebrand and with great collaborations, I develop tools for protein modeling (especially loop prediction) and the placement of internal water molecules. Oh, and I like moving pictures, so I put GPCRs and their binding partners in a box and simulate them. To enhance understanding of complex dynamic processes and promote scientific transparency, I want to make analysis and especially visualization of those dynamics with our tools more accessible to others. When I am not driving water molecules in my simulations crazy, I try to see the world while hopping from one conference to another or I can be found abroad with friends, cycling, climbing or trying some new sports. I also like taking pictures, so be warned – you might end up in one with me 😉

Coming to the end, I am looking forward to attending this very interesting BPS meeting and see you all later!

Cheers, Johanna Tiemann

Exploring the Interstitial Space

BPJ_113_4.c1.inddThe cover art for the August 22nd issue of Biophysical Journal was composed with the intention of incorporating elements from both the theoretical and experimental sides of modern biology. It depicts the interstitial space present between cells that adhere to one another with varying degrees of adhesiveness. The top right shows an electron micrograph of a tissue from a frog embryo, in which the interstitial space appears as pale, approximately triangular gaps. One such triangular gap is inset by a 3D representation of a gap derived from our theoretical model, acting as a visual link between theory and experiment. The size and interconnectedness of the modelled interstitial space increases as the eye moves towards the lower left, reflecting the different gap shapes and sizes predicted for different conditions of cell adhesion. The interstitial space is filled with fluid (in fact just over a quarter of the water in the human body is contained in the interstitial space!), and this is reflected in the watery, liquid-like appearance of the model. The electron micrograph and 3D model are reminiscent of the moon and stars – this is meant to invoke a feeling of a new frontier being explored, as biologists move more and more towards mathematical and computational modeling as a means to describe the living world around us. The cover art was produced using Blender, an open-source 3D modeling program, which has helped us to visualize and internalize the geometry of the interstitial space as the model became more complex with more interacting elements.

While our study made use of frog early embryos, interstitial spaces are present in all animals, from invertebrates to vertebrates, and in both diseased and healthy tissues. The interstitial space is involved in fluid balance in the body, transport of metabolites and signaling molecules, and determination of the mechanical properties of a tissue, and it is curious that even in tissues where the cells are very tightly packed, this space is maintained.

—Serge E. Parent, Debanjan Barua, and Rudolf Winklbauer.