Editorial pubs.acs.org/JPCL
Emerging Themes in Biophysical Chemistry his issue of JPC Letters includes Perspectives concerned with biophysical chemistry; therefore, it is appropriate to describe not only these articles but other related articles that have recently appeared in the journal. A common theme in this work is the growing sophistication in understanding protein structure and function that is developing as a result of the interplay of molecular dynamics, NMR, X-ray, and other techniques. The Perspective by Braselmann and Clark1 is concerned with protein folding, with emphasis on folding pathways important in vivo that are distinct from studies of in vitro pathways that have dominated the field. In particular, the authors focus on vectorial folding mechanisms, whereby the folding of a protein evolves sequentially from one end of the peptide either as the growing peptide comes out of the ribosome or as a complete peptide emerges across a membrane. Autotransporter proteins are an example of the latter, and for Gram-negative bacteria, these proteins cross both the inner and outer membranes as they are released from the cell, with the first membrane involving N- to C-terminal transport and the second C- to Nterminal transport. The Perspective describes physical measurements and models that have been used to understand the second membrane crossing, including comparisons of in vivo and in vitro measurements and a qualitative description of the vectorial folding process. The Perspective by J. W. Peng2 provides an overview of the use of NMR to determine protein structures and dynamics. NMR is well-suited to study dynamics for time scales that are important to proteins (picosecond to millisecond), and it is now able to study proteins with masses larger than 100 kDa, making it a general tool for protein folding studies. The Perspective surveys the different kinds of measurements that are being done, including both isotropic and anisotropic interactions between magnetic dipoles and quadrupole interactions. Special attention is given to the use of transverse relaxation optimized spectroscopy (TROSY) methods, which provide internal motion order parameter results for large proteins. Treptow and Klein3 present a Perspective on the use of molecular dynamics methods to describe voltage-gated cation channels (VGCCs). Although there are four classes of these channels, corresponding to Na+, Ca2+, K+, and nonselective cationic channels, there are strong structural similarities in the proteins found in these channels, including a central pore domain that is flanked by a voltage sensor domain. MD simulation methods have played an important role in characterizing ion channel functions, revealing channel gating motions and ion transport properties. A key property of ion channels is the selectivity factor, in which ions pass coherently through a narrow pore, gated by protein motion and driven by an external potential. Also described in the Perspective are issues that relate to channel selectivity and regulation. The Perspective by Nguyen and Berry4 focuses on graphene/ cell interfacial devices and the principles defining the modulation of charge carrier properties in graphene and its
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© 2012 American Chemical Society
derivatives via interaction with cellular membranes. Graphene’s high sensitivity in these applications evolves from several factors, including the carrier cloud confined within an atomthick layer on the nanodiamond surface, quantum-capacitanceinduced doping enhancement, closely spaced electronic bands, and a large surface area. The effect of cell wall electronegativity is discussed, along with the dynamic changes in the graphene chemical potential as a result of doping with specific carriers. Among papers published in JPC Lett. in the Biophysical area this year, there have been several that relate to the themes mentioned in these Perspectives. The determination of protein conformations using NMR methods has been described by Shi et al,5 while infrared methods and theory are used for this purpose in a paper by Torii.6 Also, Chu et al.7 have recently described quasielastic neutron scattering studies of protein dynamics at low temperatures, showing that there is no change in this dynamics as one tunes through water phase transitions. Another paper is by Wallace and Chen,8 who used molecular dynamics calculations to study the pH-dependent mechanism of assembly of spider silk proteins. Assembly of proteins is also featured in the recent work by Kurut et al.,9 who used molecular dynamics to show how the anisotropic charge distributions in 1:1 mixtures of lysozyme and α-lactalbumin lead to self-assembly into well-defined micrometer-sized spheres.
George C. Schatz,, Editor-in-Chief
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Northwestern University, Evanston, Illinois 60208-3113, United States
REFERENCES
(1) Braselmann, E.; Clark, P. Autotransporters: The Cellular Environment Reshapes a Folding Mechanism to Promote Protein Transport. J. Phys. Chem. Lett. 2012, 3, 1063−1071. (2) Peng, J. W. Exposing the Moving Parts of Proteins with NMR Spectroscopy. J. Phys. Chem. Lett. 2012, 3, 1039−1051. (3) Treptow, W.; Klein, M. Computer Simulation Studies of VoltageGated Cation Channels. J. Phys. Chem. Lett. 2012, 3, 1017−1023. (4) Nguyen, P.; Berry, V. Graphene Interfaced with Biological Cells: Opportunities and Challenges. J. Phys. Chem. Lett. 2012, 3, 1024− 1029. (5) Shi, P.; Li, D.; Li, J.; Chen, H.; Wu, F.; Xiong, Y.; Tian, C. Application of Site-Specific 19F Paramagnetic Relaxation Enhancement to Distinguish two Different Conformations of a Multidomain Protein. J. Phys. Chem. Lett. 2011, 3, 34−37. (6) Torii, H. Mechanism of the Secondary Structure Dependence of the Infrared Intensity of the Amide II Mode of Peptide Chains. J. Phys. Chem. Lett. 2011, 3, 112−116. (7) Chu, X.-q.; Mamontov, E.; O’Neill, H.; Zhang, Q. Apparent Decoupling of the Dynamics of a Protein from the Dynamics of its Aqueous Solvent. J. Phys. Chem. Lett. 2012, 3, 380−385. (8) Wallace, J. A.; Shen, J. K. Unraveling a Trap-and-Trigger Mechanism in the pH-Sensitive Self-Assembly of Spider Silk Proteins. J. Phys. Chem. Lett. 2012, 3, 658−662. Published: April 19, 2012 1072
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The Journal of Physical Chemistry Letters
Editorial
(9) Kurut, A.; Persson, B. A.; Åkesson, T.; Forsman, J.; Lund, M. Anisotropic Interactions in Protein Mixtures: Self Assembly and Phase Behavior in Aqueous Solution. J. Phys. Chem. Lett. 2012, 3, 731−734.
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