scholarly journals Structural basis for the geometry-driven localization of a small protein

2015 ◽  
Vol 112 (15) ◽  
pp. E1908-E1915 ◽  
Author(s):  
Richard L. Gill ◽  
Jean-Philippe Castaing ◽  
Jen Hsin ◽  
Irene S. Tan ◽  
Xingsheng Wang ◽  
...  
Keyword(s):  
Lipid Bilayers ◽  
Structural Basis ◽  
Supported Lipid Bilayers ◽  
Curvature Sensing ◽  
Preferential Localization ◽  
Acyl Chains ◽  
Shape Sensing ◽  
Α Helix ◽  
Dynamics Simulations ◽  
Curved Membranes

In bacteria, certain shape-sensing proteins localize to differently curved membranes. During sporulation in Bacillus subtilis, the only convex (positively curved) surface in the cell is the forespore, an approximately spherical internal organelle. Previously, we demonstrated that SpoVM localizes to the forespore by preferentially adsorbing onto slightly convex membranes. Here, we used NMR and molecular dynamics simulations of SpoVM and a localization mutant (SpoVMP9A) to reveal that SpoVM’s atypical amphipathic α-helix inserts deeply into the membrane and interacts extensively with acyl chains to sense packing differences in differently curved membranes. Based on binding to spherical supported lipid bilayers and Monte Carlo simulations, we hypothesize that SpoVM’s membrane insertion, along with potential cooperative interactions with other SpoVM molecules in the lipid bilayer, drives its preferential localization onto slightly convex membranes. Such a mechanism, which is distinct from that used by high curvature-sensing proteins, may be widely conserved for the localization of proteins onto the surface of cellular organelles.

scholarly journals Proteomic analysis of monolayer-integrated proteins on lipid droplets identifies amphipathic interfacial α-helical membrane anchors

2018 ◽  
Vol 115 (35) ◽  
pp. E8172-E8180 ◽  
Author(s):  
Camille I. Pataki ◽  
João Rodrigues ◽  
Lichao Zhang ◽  
Junyang Qian ◽  
Bradley Efron ◽  
...  
Keyword(s):  
Lipid Droplets ◽  
Coarse Grained ◽  
Structural Basis ◽  
Endoplasmic Reticulum Membrane ◽  
Membrane Surfaces ◽  
Common Motif ◽  
Cysteine Scanning Mutagenesis ◽  
Α Helix ◽  
Dynamics Simulations ◽  
Integral Proteins

Despite not spanning phospholipid bilayers, monotopic integral proteins (MIPs) play critical roles in organizing biochemical reactions on membrane surfaces. Defining the structural basis by which these proteins are anchored to membranes has been hampered by the paucity of unambiguously identified MIPs and a lack of computational tools that accurately distinguish monolayer-integrating motifs from bilayer-spanning transmembrane domains (TMDs). We used quantitative proteomics and statistical modeling to identify 87 high-confidence candidate MIPs in lipid droplets, including 21 proteins with predicted TMDs that cannot be accommodated in these monolayer-enveloped organelles. Systematic cysteine-scanning mutagenesis showed the predicted TMD of one candidate MIP, DHRS3, to be a partially buried amphipathic α-helix in both lipid droplet monolayers and the cytoplasmic leaflet of endoplasmic reticulum membrane bilayers. Coarse-grained molecular dynamics simulations support these observations, suggesting that this helix is most stable at the solvent–membrane interface. The simulations also predicted similar interfacial amphipathic helices when applied to seven additional MIPs from our dataset. Our findings suggest that interfacial helices may be a common motif by which MIPs are integrated into membranes, and provide high-throughput methods to identify and study MIPs.

Structure of a double-domain phosphagen kinase reveals an asymmetric arrangement of the tandem domains

2015 ◽  
Vol 71 (4) ◽  
pp. 779-789 ◽  
Author(s):  
Zhiming Wang ◽  
Zhu Qiao ◽  
Sheng Ye ◽  
Rongguang Zhang
Keyword(s):  
Bound States ◽  
Hydrophobic Interactions ◽  
Crystal Packing ◽  
Protein Structures ◽  
Structural Basis ◽  
Phosphagen Kinase ◽  
Domain Arrangement ◽  
Α Helix ◽  
Dynamics Simulations ◽  
Shaped Domain

Tandem duplications and fusions of single genes have led to magnificent expansions in the divergence of protein structures and functions over evolutionary timescales. One of the possible results is polydomain enzymes with interdomain cooperativities, few examples of which have been structurally characterized at the full-length level to explore their innate synergistic mechanisms. This work reports the crystal structures of a double-domain phosphagen kinase in both apo and ligand-bound states, revealing a novel asymmetric L-shaped arrangement of the two domains. Unexpectedly, the interdomain connections are not based on a flexible hinge linker but on a rigid secondary-structure element: a long α-helix that tethers the tandem domains in relatively fixed positions. Besides the connective helix, the two domains also contact each other directly and form an interdomain interface in which hydrogen bonds and hydrophobic interactions further stabilize the L-shaped domain arrangement. Molecular-dynamics simulations show that the interface is generally stable, suggesting that the asymmetric domain arrangement crystallographically observed in the present study is not a conformational state simply restrained by crystal-packing forces. It is possible that the asymmetrically arranged tandem domains could provide a structural basis for further studies of the interdomain synergy.

Effect of Alkyl Chain Length on Molecular Heat Transfer Characteristics in Lipid Bilayers

2011 ◽  
Author(s):  
Takeo Nakano ◽  
Gota Kikugawa ◽  
Taku Ohara
Keyword(s):  
Thermal Conductivity ◽  
Thermal Resistance ◽  
Lipid Bilayers ◽  
Chain Length ◽  
Phosphatidyl Choline ◽  
Acyl Chain ◽  
Nonequilibrium Molecular Dynamics ◽  
Acyl Chain Length ◽  
Acyl Chains ◽  
Dynamics Simulations

Nonequilibrium molecular dynamics simulations are carried out on single component lipid bilayers with ambient water in order to investigate the effect of acyl chain length on heat transport characteristics along and across the membranes. In this study, dipalmitoyl-phosphatidyl-choline (DPPC), dilauroyl-phosphatidyl-choline (DLPC), and stearoyl-myristoyl-phosphatidyl-choline (SMPC) which has two acyl chains of both sixteen C atoms, both twelve C atoms, and eighteen and fourteen C atoms, respectively, were used as lipid molecules. In the direction along the membranes, thermal conductivity corresponds with that of each membrane. On the other hand, in the direction across membrane, the highest thermal resistance exists at the center of lipid bilayer where lipid acyl chains face each other. However, asymmetric chain length reduces thermal resistance at the interface between lipid monolayers. Therefore, thermal conductivity across the membrane which consists of asymmetric chain length is higher than those which consist of symmetric chain length.

scholarly journals Raf promotes dimerization of the Ras G-domain with increased allosteric connections

2021 ◽  
Vol 118 (10) ◽  
pp. e2015648118
Author(s):  
Morgan R. Packer ◽  
Jillian A. Parker ◽  
Jean K. Chung ◽  
Zhenlu Li ◽  
Young Kwang Lee ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Lipid Bilayers ◽  
Size Exclusion ◽  
Supported Lipid Bilayers ◽  
Erk Pathway ◽  
Signaling Complex ◽  
Macromolecular Assembly ◽  
High Affinity ◽  
Exclusion Chromatography ◽  
Dynamics Simulations

Ras dimerization is critical for Raf activation. Here we show that the Ras binding domain of Raf (Raf-RBD) induces robust Ras dimerization at low surface densities on supported lipid bilayers and, to a lesser extent, in solution as observed by size exclusion chromatography and confirmed by SAXS. Community network analysis based on molecular dynamics simulations shows robust allosteric connections linking the two Raf-RBD D113 residues located in the Galectin scaffold protein binding site of each Raf-RBD molecule and 85 Å apart on opposite ends of the dimer complex. Our results suggest that Raf-RBD binding and Ras dimerization are concerted events that lead to a high-affinity signaling complex at the membrane that we propose is an essential unit in the macromolecular assembly of higher order Ras/Raf/Galectin complexes important for signaling through the Ras/Raf/MEK/ERK pathway.

scholarly journals Structural basis of pH-dependent client binding by ERp44, a key regulator of protein secretion at the ER–Golgi interface

2017 ◽  
Vol 114 (16) ◽  
pp. E3224-E3232 ◽  
Author(s):  
Satoshi Watanabe ◽  
Manami Harayama ◽  
Shingo Kanemura ◽  
Roberto Sitia ◽  
Kenji Inaba
Keyword(s):  
Conformational Changes ◽  
Low Ph ◽  
Structural Basis ◽  
Secretory Proteins ◽  
Hydrogen Bonding Pattern ◽  
Mixed Disulfides ◽  
Loop Regions ◽  
Ph Dependent ◽  
Α Helix ◽  
Dynamics Simulations

ERp44 retrieves some endoplasmic reticulum (ER)-resident enzymes and immature oligomers of secretory proteins from the Golgi. Association of ERp44 with its clients is regulated by pH-dependent mechanisms, but the molecular details are not fully understood. Here we report high-resolution crystal structures of human ERp44 at neutral and weakly acidic pH. These structures reveal key regions in the C-terminal tail (C tail) missing in the original crystal structure, including a regulatory histidine-rich region and a subsequent extended loop. The former region forms a short α-helix (α16), generating a histidine-clustered site (His cluster). At low pH, the three Trx-like domains of ERp44 (“a,” “b,” and “b′”) undergo significant rearrangements, likely induced by protonation of His157 located at the interface between the a and b domains. The α16-helix is partially unwound and the extended loop is disordered in weakly acidic conditions, probably due to electrostatic repulsion between the protonated histidines in the His cluster. Molecular dynamics simulations indicated that helix unwinding enhances the flexibility of the C tail, disrupting its normal hydrogen-bonding pattern. The observed pH-dependent conformational changes significantly enlarge the positively charged regions around the client-binding site of ERp44 at low pH. Mutational analyses showed that ERp44 forms mixed disulfides with specific cysteines residing on negatively charged loop regions of Ero1α. We propose that the protonation states of the essential histidines regulate the ERp44–client interaction by altering the C-tail dynamics and surface electrostatic potential of ERp44.

Influence of Brain Gangliosides on the Formation and Properties of Supported Lipid Bilayers for Binding Kinetics Studies

2018 ◽  
Author(s):  
Luke Jordan ◽  
Nathan Wittenberg
Keyword(s):  
Lipid Bilayers ◽  
Binding Kinetics ◽  
Supported Lipid Bilayers ◽  
Dependent Manner ◽  
Concentration Dependent Manner ◽  
Supported Lipid Bilayer ◽  
Head Groups ◽  
Lipid Diffusion ◽  
Kinetics Of ◽  
Brain Gangliosides

This is a comprehensive study of the effects of the four major brain gangliosides (GM1, GD1b, GD1a, and GT1b) on the adsorption and rupture of phospholipid vesicles on SiO2 surfaces for the formation of supported lipid bilayer (SLB) membranes. Using quartz crystal microbalance with dissipation monitoring (QCM-D) we show that gangliosides GD1a and GT1b significantly slow the SLB formation process, whereas GM1 and GD1b have smaller effects. This is likely due to the net ganglioside charge as well as the positions of acidic sugar groups on ganglioside glycan head groups. Data is included that shows calcium can accelerate the formation of ganglioside-rich SLBs. Using fluorescence recovery after photobleaching (FRAP) we also show that the presence of gangliosides significantly reduces lipid diffusion coefficients in SLBs in a concentration-dependent manner. Finally, using QCM-D and GD1a-rich SLB membranes we measure the binding kinetics of an anti-GD1a antibody that has similarities to a monoclonal antibody that is a hallmark of a variant of Guillain-Barre syndrome.

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