75 research outputs found
From Bacteriorhodopsin to Spike Protein S
Membrane-bound proteins that change protonation during function use specific protein groups to bind and transfer protons. Knowledge of the identity of the proton-binding groups is of paramount importance to decipher the reaction mechanism of the protein, and protonation states of prominent are studied extensively using experimental and computational approaches. Analyses of model transporters and receptors from different organisms, and with widely different biological functions, indicate common structure-sequence motifs at internal proton-binding sites. Proton-binding dynamic hydrogen-bond networks that are exposed to the bulk might provide alternative proton-binding sites and proton-binding pathways. In this perspective article I discuss protonation coupling and proton binding at internal and external carboxylate sites of proteins that use proton transfer for function. An inter-helical carboxylate-hydroxyl hydrogen-bond motif is present at functionally important sites of membrane proteins from archaea to the brain. External carboxylate-containing H-bond clusters are observed at putative proton-binding sites of protonation-coupled model proteins, raising the question of similar functionality in spike protein S
Computational Molecular Biophysics of Membrane Reactions
Proteins are nanoscale molecules that perform functions essential for biological life. Membranes surrounding cells, for example, contain receptor proteins that mediate communication between the cell and the external milieu, membrane transporters that transport ions and larger compounds across the membranes, and enzymes that catalyze chemical reactions. Likewise, soluble proteins found in interior of the cell include motor proteins that move other proteins around, enzymes that bind to and repair breaks in the DNA, and proteins that help control the cellular clock. Mutations in genes that encode proteins can cause disease, as is the case of cystic fibrosis, a disease that associates with mutation of a chloride channel called the cystic fibrosis transmembrane conductance regulator.1 The essential functions they perform in the cell makes proteins essential drug
targets for modern bio-medical applications. An important example here is the programmed death ligand-1 (PD-L1), which is a valuable target for modern immunotherapy.2-4 Predicting how a protein responds to a drug molecule, or using the protein as inspiration for biotechnological applications, require knowledge of how that protein works. As proteins are dynamic entities and protein dynamics are essential for function,5-8 describing the mechanism of action of a protein requires knowledge about the protein motions in fluid environments. Theoretical biophysics provides valuable tools to characterize protein
reaction mechanisms and protein motions at the atomic level of detail.
This Habilitation Thesis presents research on using theoretical biophysics approaches to decipher how proteins work. The focus of the research is on membrane proteins and reactions that occur at lipid membrane interfaces. The central question I address is the role of dynamic hydrogen (H) bonds in protein function and membrane interactions. The methods used include quantum mechanical (QM) computations of small molecules, combined quantum mechanics/molecular mechanics (QM/MM) of chemical reactions in
protein environments, classical mechanical computations of large protein and membrane systems, and bridging numerical simulations to bioinformatics. In my research group we developed algorithms to identify H-bond networks in proteins and membrane environments, and to characterize the dynamics of these networks. To extend the applicability of numerical computations to bio-systems that bind drug-like compounds, we derive parameters for a potential energy function widely used in the field. The main research topics and specific
questions addressed are summarized below together with a discussion of the computational approaches used
Extended protein/water H-bond networks in photosynthetic water oxidation
Oxidation of water molecules in the photosystem II (PSII) protein complex
proceeds at the manganeseâcalcium complex, which is buried deeply in the
lumenal part of PSII. Understanding the PSII function requires knowledge of
the intricate coupling between the water-oxidation chemistry and the dynamic
proton management by the PSII protein matrix. Here we assess the structural
basis for long-distance proton transfer in the interior of PSII and for proton
management at its surface. Using the recent high-resolution crystal structure
of PSII, we investigate prominent hydrogen-bonded networks of the lumenal side
of PSII. This analysis leads to the identification of clusters of polar groups
and hydrogen-bonded networks consisting of amino acid residues and water
molecules. We suggest that long-distance proton transfer and conformational
coupling is facilitated by hydrogen-bonded networks that often involve more
than one protein subunit. Proton-storing Asp/Glu dyads, such as the
D1-E65/D2-E312 dyad connected to a complex water-wire network, may be
particularly important for coupling protonation states to the protein
conformation. Clusters of carboxylic amino acids could participate in proton
management at the lumenal surface of PSII. We propose that rather than having
a classical hydrophobic protein interior, the lumenal side of PSII resembles a
complex polyelectrolyte with evolutionary optimized hydrogen-bonding networks.
This article is part of a Special Issue entitled: Photosynthesis Research for
Sustainability: from Natural to Artificial
Hydrogen bond dynamics in membrane protein function
Changes in inter-helical hydrogen bonding are associated with the
conformational dynamics of membrane proteins. The function of the protein
depends on the surrounding lipid membrane. Here we review through specific
examples how dynamical hydrogen bonds can ensure an elegant and efficient
mechanism of long-distance intra-protein and proteinâlipid coupling,
contributing to the stability of discrete protein conformational substates and
to rapid propagation of structural perturbations. This article is part of a
Special Issue entitled: Protein Folding in Membranes
Dynamic water bridging and proton transfer at a surface carboxylate cluster of photosystem II
Proton-transfer proteins are often exposed to the bulk clusters of carboxylate groups that might bind protons transiently. This raises important questions as to how the carboxylate groups of a protonated cluster interact with each other and with water, and how charged protein groups and hydrogen-bonded waters could have an impact on proton transfers at the cluster. We address these questions by combining classical mechanical and quantum mechanical computations with the analysis of cyanobacterial photosystem II crystal structures from Thermosynechococcus elongatus. The model system we use consists of an interface between PsbO and PsbU, which are two extrinsic proteins of photosystem II. We find that a protonated carboxylate pair of PsbO is part of a dynamic network of proteinâwater hydrogen bonds which extends across the protein interface. Hydrogen-bonded waters and a conserved lysine sidechain largely shape the energetics of proton transfer at the carboxylate cluster
Graph-Based Analyses of Dynamic Water-Mediated Hydrogen-Bond Networks in Phosphatidylserine: Cholesterol Membranes
Phosphatidylserine lipids are anionic molecules present in eukaryotic plasma membranes, where they have essential physiological roles. The altered distribution of phosphatidylserine in cells such as apoptotic cancer cells, which, unlike healthy cells, expose phosphatidylserine, is of direct interest for the development of biomarkers. We present here applications of a recently implemented Depth-First-Search graph algorithm to dissect the dynamics of transient water-mediated lipid clusters at the interface of a model bilayer composed of 1-palmytoyl-2-oleoyl-sn-glycero-2-phosphatidylserine (POPS) and cholesterol. Relative to a reference POPS bilayer without cholesterol, in the POPS:cholesterol bilayer there is a somewhat less frequent sampling of relatively complex and extended water-mediated hydrogen-bond networks of POPS headgroups. The analysis protocol used here is more generally applicable to other lipid:cholesterol bilayers
Voltage Sensing in Bacterial Protein Translocation
The bacterial channel SecYEG efficiently translocates both hydrophobic and hydrophilic proteins across the plasma membrane. Translocating polypeptide chains may dislodge the plug, a half helix that blocks the permeation of small molecules, from its position in the middle of the aqueous translocation channel. Instead of the plug, six isoleucines in the middle of the membrane supposedly seal the channel, by forming a gasket around the translocating polypeptide. However, this hypothesis does not explain how the tightness of the gasket may depend on membrane potential. Here, we demonstrate voltage-dependent closings of the purified and reconstituted channel in the presence of ligands, suggesting that voltage sensitivity may be conferred by motor protein SecA, ribosomes, signal peptides, and/or translocating peptides. Yet, the presence of a voltage sensor intrinsic to SecYEG was indicated by voltage driven closure of pores that were forced-open either by crosslinking the plug to SecE or by plug deletion. We tested the involvement of SecYâs half-helix 2b (TM2b) in voltage sensing, since clearly identifiable gating charges are missing. The mutation L80D accelerated voltage driven closings by reversing TM2bâs dipolar orientation. In contrast, the L80K mutation decelerated voltage induced closings by increasing TM2bâs dipole moment. The observations suggest that TM2b is part of a larger voltage sensor. By partly aligning the combined dipole of this sensor with the orientation of the membrane-spanning electric field, voltage may drive channel closure
Potential energy function for a photoâswitchable lipid molecule
Photoâswitchable lipids are synthetic lipid molecules used in photoâpharmacology to alter membrane lateral pressure and thus control opening and closing of mechanosensitive ion channels. The molecular picture of how photoâswitchable lipids interact with membranes or ion channels is poorly understood. To facilitate allâatom simulations that could provide a molecular picture of membranes with photoâswitchable lipids, we derived force field parameters for atomistic computations of the azobenzeneâbased fatty acid FAAzoâ4. We implemented a Phytonâbased algorithm to make the optimization of atomic partial charges more efficient. Overall, the parameters we derived give good description of the equilibrium structure, torsional properties, and nonâbonded interactions for the photoâswitchable lipid in its trans and cis intermediate states, and crystal lattice parameters for transâFAAzoâ4. These parameters can be extended to allâatom descriptions of various photoâswitchable lipids that have an azobenzene moiety
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