Evolutionary Physics

ARE NETWORKS OF COEVOLVING RESIDUES INFORMATIVE OF PROTEINS’ STRUCTURAL DYNAMICS?


The intimate relation between proteins' function and structural dynamics suggests that specific networks of residue-residue interactions might be more conserved than the primary structure. The functional mechanics of proteins is exquisitely sensitive to the topology of this network, thus a change in one position of the chain ought to be associated by a compensatory one in a different position. These constraints have arguably left a distinct imprint on the distribution of sequences encoding for each specific family of proteins. It is then of crucial relevance to characterize patterns and regularities in large multiple sequence alignments reflecting these specific evolutionary 'design principles'. In particular, to identify networks of co-evolving residues, an extremely fruitful approach is based on a probabilistic model based on a set of pairwise interactions. The least constrained functional form that reproduces single- and two-site joint frequencies is that of a 21-states Potts model. We have used these approaches to identify the sequence determinants of voltage sensitivity in the family of Voltage Gated Ion Channels and to glean insight into the activation mechanism of TRP channels. We are actively developing novel methodological approaches to further explore the link between coevolution and structural dynamics.


E. Palovcak, L. Delemotte, M. Klein, and V. Carnevale. Comparative sequence analysis suggests a conserved gating mechanism for TRP channels. JOURNAL OF GENERAL PHYSIOLOGY, 2015, DOI:10.1085/jgp.201411329.

E. Palovcak, L. Delemotte, M.L. Klein, V. Carnevale Evolutionary imprint of activation: The design principles of VSDs THE JOURNAL OF GENERAL PHYSIOLOGY 143 (2), 145-156.

E. Palovcak, L. Delemotte, M. L. Klein, and V. Carnevale, Genomics-aided structural modeling of an antiparallel homodimeric fluoride channelin BIOPHYSICAL JOURNAL, vol. 106, p. 148a, 2014.

V. Carnevale, E. Palovcak, L. Delemotte, and M. Klein, Networks of coevolving residues in voltage sensor domains.in BIOPHYSICAL JOURNAL, vol. 106, p. 743a, 2014.

E. Palovcak and V. Carnevale, Correlating residue coevolution and function in a conserved voltage-sensing domain. in BIOPHYSICAL JOURNAL, vol. 104, p. 277, 2013.

FUNCTIONAL MECHANICS OF ION CHANNELS FROM THE 6-TM FAMILY


One of the most interesting case studies to investigate the connections between sequence, structural dynamics and function is the six-transmembrane-helix (6-TM) family of ion channels. Ion channels are ubiquitous proteins--one of Nature's exquisite nano-scale molecular machines--that reside in membranes of excitable cells. Their role is to convert chemical and electrical stimuli into ionic currents. Conformational changes in the part of the protein responsible for sensing a stimulus (transducer domain) trigger the gate (effector domain), which can open and close, thereby controlling the flux of ions across the cell membrane. Details of this so-called allosteric communication are of broad relevance to physiology: several drug molecules target ion channels, including neurotoxins and anesthetics, and work by interfering with the coupling between the transducer and effector domains. The 6-TM family, in particular, is characterized by a common structural template inherited from a single ancestor gene that gave rise, through differentiation, to a myriad of functions, from reporting noxious environmental conditions, to shaping the neuronal action potential, to syncing the beating of the heart.
Voltage gated ion channels (VGICs), the proteins responsible for the propagation of electrical signal in neuronal axons, belong to the 6-TM family. Despite the fact that these channels have been investigated for several decades, their function relies on molecular mechanisms that are partially unknown. In this context, our interests are focused on the energetics of the activation process of these channels and on the nature of the mechanical coupling between the voltage sensor domain and the pore domain. Besides the voltage gated ion channels, the 6-TM family comprises other physiologically relevant channels, like, for instance, the transient receptor potential (TRP) channels. TRPs play a central role in transducing diverse sensory stimuli in eukaryotes. All known TRP channels act as polymodal cellular sensors and form tetrameric assemblies similar to voltage-gated ion channels.
The fact that TRPs and VGICs are structurally similar, yet functionally distinct raises immediately a question: Is the molecular mechanism underlying polymodal gating in TRP channels different from that underpinning voltage sensitivity in voltage gated ion channels? Intriguingly, comparative sequence analysis on large, comprehensive ensembles of TRP and VGIC channel sequences highlights sequence features that are specific to TRP channels and suggests a model of TRP channel gating that differs substantially from the one mediating voltage sensitivity in VGICs. Most of our recent research efforts are directed toward understanding, via molecular dynamics simulations, the molecular details of this activation mechanism, characterizing the equilibrium and kinetic properties of this transition and, most importantly, shedding light on the role on activation of factors like lipid composition, temperature and pH.


E. Palovcak, L. Delemotte, M. Klein, and V. Carnevale. Comparative sequence analysis suggests a conserved gating mechanism for TRP channels. JOURNAL OF GENERAL PHYSIOLOGY, 2015, DOI:10.1085/jgp.201411329.

L. Delemotte, M. A. Kasimova, M. L. Klein, M. Tarek, V. Carnevale Free Energy Landscape of Ion-Channel Voltage-Sensor-Domain Activation PROC. NATL. ACAD. SCI. USA, doi: 10.1073/pnas.1416959112.

C. Amaral, V. Carnevale, M. L. Klein, W. Treptow Exploring conformational states of the bacterial voltage-gated sodium channel NavAb via molecular dynamics simulations PROC. NATL. ACAD SCI. USA 109(52), 21336-21341 (2012).

A. Barber, V. Carnevale, S.G. Raju, C. Amaral, Werner Treptow, M. L. Klein Hinge-bending motions in the pore domain of a bacterial voltage-gated sodium channel.BIOCHIMICA ET BIOPHYSICA ACTA (BBA) - BIOMEMBRANES, 1818(9), 2120-2125 (2012).