Research projects in Marklund Group

Macromolecules such as proteins carry out the functions of all life at the microscopic level. As such, they are of particular interest for life science in academia and industry. Macromolecules are not static however and typically do not function in isolation. Their interactions and dynamics are therefore of critical importance for our understanding of how they work, but also for how their function or dysfunction can be manipulated, for example, for therapeutic purposes.

Numerous experimental techniques can be used to probe various aspects of these dynamics, each with their own specific requirements, limitations, and advantages. Complementing experiments are advanced computational methods that can provide insights where current experiments fall short. Our research harness and develop such computational methods to reveal the dynamics and interactions of macromolecules, and to ultimately understand their function and role in cellular life.

Collision cross-section calculations

Ion-mobility spectrometry is a century-old technique that recently has experienced a renaissance in the wake of the boom for native mass spectrometry. This technique offers a somewhat unique option to separately probe the structure of heterogeneous samples, including macromolecules that occupy a range of different states, in a single experiment. Molecular modelling is vital for making structural interpretations of the collision cross-sections derived from the experimental data however. We develop collision cross-section calculators (IMPACT) to bridge the gap between structure models and experimental observations. To enable the study of very large data sets and very large structures, high performance is critical.

In order to facilitate integration with other modelling tools, IMPACT can also be used as a software library, alleviating much of the overhead associated with creating intermediate files and invoking the software. Using such tools we interpret the data from specific experiments, but we also explore the fundamental properties and limits of the structural information that can be obtained from the data. The latter aims to support the optimal design of experiments and to explore the physical principles governing the architecture of macromolecules.

Protonation states of proteins in gas-phase

While the native environment of biological macromolecules are most often in solution, mass spectrometry and related techniques require that the sample is transferred to the gas phase. The more we know about the processes that the sample molecules undergo during this transfer, the better we can make use of these very powerful techniques. There are currently many unanswered yet fundamental questions that need answering, which we approach by combinations of modelling and experiments in collaboration with leading mass spectrometrists. One of the major questions is the location of protons on a gas-phase protein and its impact on the structure of the latter. The pursuit of a comprehensive understanding of the proton dynamics require novel computational tools and carefully selected model systems.

Manipulation of proteins in gas-phase using electric fields

Electrospray ionisation and many other techniques for delivery of molecules into the gas phase creates a non-zero net charge on the molecules, which can be used to manipulate the molecules in flight, and is routinely exploited for separation in mass-spectrometric techniques. Macromolecules often additionally carry a dipole moment, which in principle offers another handle for manipulation in the gas phase, namely the orientation of molecules along the direction of a strong electric field. This principle has been proposed as a means to augment ion-mobility spectrometry and a partial solution to the orientation problem in coherent diffractive imaging with free-electron lasers. Despite these anticipated benefits, this phenomenon has remained virtually unexplored in the context of macromolecules. We use molecular dynamics simulations in combination with collision cross-section calculations and state-of-the art alignment algorithms from the imaging community to explore the prospects of achieving orientation of macromolecules in the gas phase, the permissive experimental parameter ranges, and a quantitative assessment of the benefits for ion-mobility spectrometry and diffractive imaging.

Steered molecular dynamics simulations based on ion-mobility data

Ion-mobility spectrometry reports, when coupled to native mass spectrometry, on the overall structure of gas-phase macromolecules. While the technique in principle is capable of picking up small changes to the structure, the structural information obtained from the experiment alone is not sufficient for a complete reconstruction of the structure. Modelling thus plays an important role, and we are working on integrating our collision cross-section calculator IMPACT with the state-of-the-art molecular dynamics suite GROMACS. This is a novel application representing a step change in the use of of ion-mobility data. We aim to use this method to interrogate the structural dynamics of proteins for which important conformations remain out of reach for traditional techniques such as X-ray crystallography.

Structural dynamics of soluble and membrane proteins

Structural dynamics are inherent to proteins and other macromolecules, and essential for their function. Aided by the technical advances made within the group, experimental collaborations, and molecular dynamics, we interrogate these dynamics, aiming to unravel the workings of biomolecular systems.