Water-mediated long-range interactions between the internal vibrations of remote proteins

2015 ◽  
Vol 17 (10) ◽  
pp. 6728-6733 ◽  
Author(s):  
Anna Kuffel ◽  
Jan Zielkiewicz
Keyword(s):  
Long Range ◽  
Protein Interactions ◽  
Interfacial Water ◽  
Protein Protein Interactions ◽  
Partial Synchronization ◽  
Long Range Interactions ◽  
Internal Vibrations

We demonstrated that interfacial water can influence and mediate long-range protein–protein interactions leading to a partial synchronization of internal movements of proteins.

scholarly journals Correction: Water-mediated long-range interactions between the internal vibrations of remote proteins

2016 ◽  
Vol 18 (18) ◽  
pp. 13130-13130
Author(s):  
Anna Kuffel ◽  
Jan Zielkiewicz
Keyword(s):  
Long Range ◽  
Chem Phys ◽  
Long Range Interactions ◽  
Phys Chem Chem Phys ◽  
Internal Vibrations

Correction for ‘Water-mediated long-range interactions between the internal vibrations of remote proteins’ by Anna Kuffel et al., Phys. Chem. Chem. Phys., 2015, 17, 6728–6733.

scholarly journals Hydrophobic Mismatch Controls the Mode of Membrane-Mediated Interactions of Transmembrane Peptides

Membranes ◽  
2022 ◽  
Vol 12 (1) ◽  
pp. 89
Author(s):  
Oleg V. Kondrashov ◽  
Peter I. Kuzmin ◽  
Sergey A. Akimov
Keyword(s):  
Long Range ◽  
Protein Interactions ◽  
Lipid Membranes ◽  
Theory Of Elasticity ◽  
Membrane Thickness ◽  
Protein Protein Interactions ◽  
Elastic Deformations ◽  
Transmembrane Peptides ◽  
Cooperative Action ◽  
Cellular Processes

Various cellular processes require the concerted cooperative action of proteins. The possibility for such synchronization implies the occurrence of specific long-range interactions between the involved protein participants. Bilayer lipid membranes can mediate protein–protein interactions via relatively long-range elastic deformations induced by the incorporated proteins. We considered the interactions between transmembrane peptides mediated by elastic deformations using the framework of the theory of elasticity of lipid membranes. An effective peptide shape was assumed to be cylindrical, hourglass-like, or barrel-like. The interaction potentials were obtained for membranes of different thicknesses and elastic rigidities. Cylindrically shaped peptides manifest almost neutral average interactions—they attract each other at short distances and repel at large ones, independently of membrane thickness or rigidity. The hourglass-like peptides repel each other in thin bilayers and strongly attract each other in thicker bilayers. On the contrary, the barrel-like peptides repel each other in thick bilayers and attract each other in thinner membranes. These results potentially provide possible mechanisms of control for the mode of protein–protein interactions in membrane domains with different bilayer thicknesses.

scholarly journals ­­Mitochondrial ATP synthase dimers spontaneously associate due to a long-range membrane-induced force­

2018 ◽  
Vol 150 (5) ◽  
pp. 763-770 ◽  
Author(s):  
Claudio Anselmi ◽  
Karen M. Davies ◽  
José D. Faraldo-Gómez
Keyword(s):  
Long Range ◽  
Atp Synthase ◽  
Protein Interactions ◽  
Simulation Analysis ◽  
Protein Complexes ◽  
Protein Protein Interactions ◽  
Inner Mitochondrial Membrane ◽  
Atp Production ◽  
Mitochondrial Atp Synthase ◽  
Atp Synthases

Adenosine triphosphate (ATP) synthases populate the inner membranes of mitochondria, where they produce the majority of the ATP required by the cell. From yeast to vertebrates, cryoelectron tomograms of these membranes have consistently revealed a very precise organization of these enzymes. Rather than being scattered throughout the membrane, the ATP synthases form dimers, and these dimers are organized into rows that extend for hundreds of nanometers. The rows are only observed in the membrane invaginations known as cristae, specifically along their sharply curved edges. Although the presence of these macromolecular structures has been irrefutably linked to the proper development of cristae morphology, it has been unclear what drives the formation of the rows and why they are specifically localized in the cristae. In this study, we present a quantitative molecular-simulation analysis that strongly suggests that the dimers of ATP synthases organize into rows spontaneously, driven by a long-range attractive force that arises from the relief of the overall elastic strain of the membrane. The strain is caused by the V-like shape of the dimers, unique among membrane protein complexes, which induces a strong deformation in the surrounding membrane. The process of row formation is therefore not a result of direct protein–protein interactions or a specific lipid composition of the membrane. We further hypothesize that, once assembled, the ATP synthase dimer rows prime the inner mitochondrial membrane to develop folds and invaginations by causing macroscopic membrane ridges that ultimately become the edges of cristae. In this way, mitochondrial ATP synthases would contribute to the generation of a morphology that maximizes the surface area of the inner membrane, and thus ATP production. Finally, we outline key experiments that would be required to verify or refute this hypothesis.

scholarly journals Quantitative Estimation of Long-Range Interactions at the Nanoscale

2018 ◽  
Author(s):  
Vishesh Sood ◽  
Sunandan Dhar ◽  
Dhirendra S. Katti
Keyword(s):  
Surface Tension ◽  
Long Range ◽  
Protein Interactions ◽  
Quantitative Estimation ◽  
Surface Characteristics ◽  
Acid Base ◽  
Biologically Relevant ◽  
Nanoparticle Agglomeration ◽  
Biological Responses ◽  
Long Range Interactions

AbstractNano-bio interfaces attune nanoparticle-mediated biological responses. The nano-bio interface, like all interfacial interactions, is governed by non-covalent long-range interactions (LRIs). These LRIs include electrostatic, electrodynamic and acid-base interactions. There is a lack of understanding about the contribution of LRIs at the nano-bio interface for want of suitable methods for the estimation of dispersive, acidic, and basic components of the surface tension of nanoparticles. To address this, we developed an experimental and theoretical framework for the estimation of surface tension components of nanoparticles and biomacromolecules by partitioning them in a biphasic system. The work presented here is the first instance in the literature for estimating the surface tension components of nanoparticles and biomacromolecules suspended in aqueous suspensions. We also observed that LRIs have a deterministic role in biologically relevant phenomena such as salt-induced nanoparticle agglomeration and protein-nanoparticle interaction. Collectively, the results presented in this work provide a rapid and inexpensive framework for predicting the energetics of nanoparticle-nanoparticle and nanoparticle-protein interactions by estimating average ensemble surface characteristics like surface tension and surface charge density.

scholarly journals Identifying Optimal Lipid Raft Characteristics Required To Promote Nanoscale Protein-Protein Interactions on the Plasma Membrane

2006 ◽  
Vol 26 (1) ◽  
pp. 313-323 ◽  
Author(s):  
Dan V. Nicolau ◽  
Kevin Burrage ◽  
Robert G. Parton ◽  
John F. Hancock
Keyword(s):  
Plasma Membrane ◽  
Long Range ◽  
Protein Interactions ◽  
Small Diameter ◽  
Equilibrium Concentration ◽  
Membrane Microdomains ◽  
Small Scale ◽  
Protein Protein Interactions ◽  
Protein Mobility ◽  
Dynamic Partitioning

ABSTRACT The dynamic lateral segregation of signaling proteins into microdomains is proposed to facilitate signal transduction, but the constraints on microdomain size, mobility, and diffusion that might realize this function are undefined. Here we interrogate a stochastic spatial model of the plasma membrane to determine how microdomains affect protein dynamics. Taking lipid rafts as representative microdomains, we show that reduced protein mobility in rafts segregates dynamically partitioning proteins, but the equilibrium concentration is largely independent of raft size and mobility. Rafts weakly impede small-scale protein diffusion but more strongly impede long-range protein mobility. The long-range mobility of raft-partitioning and raft-excluded proteins, however, is reduced to a similar extent. Dynamic partitioning into rafts increases specific interprotein collision rates, but to maximize this critical, biologically relevant function, rafts must be small (diameter, 6 to 14 nm) and mobile. Intermolecular collisions can also be favored by the selective capture and exclusion of proteins by rafts, although this mechanism is generally less efficient than simple dynamic partitioning. Generalizing these results, we conclude that microdomains can readily operate as protein concentrators or isolators but there appear to be significant constraints on size and mobility if microdomains are also required to function as reaction chambers that facilitate nanoscale protein-protein interactions. These results may have significant implications for the many signaling cascades that are scaffolded or assembled in plasma membrane microdomains.

Protein-protein interactions of the p53 family with the Bcl-2 family in hepatocellular carcinoma

2011 ◽  
Vol 49 (08) ◽  
Author(s):  
LC König ◽  
M Meinhard ◽  
C Sandig ◽  
MH Bender ◽  
A Lovas ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
Protein Interactions ◽  
Protein Protein Interactions ◽  
P53 Family
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