scholarly journals A two-lane mechanism for selective biological ammonium transport

2020 ◽  
Vol 2 (7A) ◽  
Author(s):  
Gordon Williamson ◽  
Gaetan Dias Mirandela ◽  
Giulia Tamburrino ◽  
Melanie Boeckstaens ◽  
Adriana Bizior ◽  
...  
Keyword(s):  
Transport Process ◽  
Dual Problem ◽  
Functional Complementation ◽  
Ammonium Transport ◽  
Biological Transport ◽  
Transporter Family ◽  
The Family ◽  
Highly Hydrophobic ◽  
Dynamics Simulations ◽  
Competing Ions

The transport of charged molecules across biological membranes faces the dual problem of accommodating charges in a highly hydrophobic environment while maintaining selective substrate translocation. A particular controversy has existed around the mechanism of ammonium exchange by the ubiquitous Amt/Mep/Rh transporter family, an essential process in all kingdoms of life. Here, using a combination of SSME electrophysiology, yeast functional complementation, and extended molecular dynamics simulations, we reveal a unique two-lane pathway for electrogenic NH4+transport in two archetypal members of the family. The pathway underpins a mechanism by which charged H+and neutral NH3 are carried separately across the membrane after NH4+deprotonation. This mechanism defines a new principle of achieving transport selectivity against competing ions in a biological transport process.

scholarly journals A two-lane mechanism for selective biological ammonium transport

2019 ◽  
Author(s):  
Gordon Williamson ◽  
Giulia Tamburrino ◽  
Gaëtan Dias Mirandela ◽  
Mélanie Boeckstaens ◽  
Marcus Bage ◽  
...  
Keyword(s):  
Transport Process ◽  
Dual Problem ◽  
Functional Complementation ◽  
Ammonium Transport ◽  
Biological Transport ◽  
Transporter Family ◽  
The Family ◽  
Highly Hydrophobic ◽  
Dynamics Simulations ◽  
Competing Ions

AbstractThe transport of charged molecules across biological membranes faces the dual problem of accommodating charges in a highly hydrophobic environment while maintaining selective substrate translocation. A particular controversy has existed around the mechanism of ammonium exchange by the ubiquitous Amt/Mep/Rh transporter family, an essential process in all kingdoms of life. Here, using a combination of electrophysiology, yeast functional complementation and extended molecular dynamics simulations, we reveal a unique two-lane pathway for electrogenic NH4+ transport in two archetypal members of the family. The pathway underpins a mechanism by which charged H+ and neutral NH3 are carried separately across the membrane after NH4+ deprotonation. This mechanism defines a new principle of achieving transport selectivity against competing ions in a biological transport process.

scholarly journals A two-lane mechanism for selective biological ammonium transport

eLife ◽  
2020 ◽  
Vol 9 ◽  
Author(s):  
Gordon Williamson ◽  
Giulia Tamburrino ◽  
Adriana Bizior ◽  
Mélanie Boeckstaens ◽  
Gaëtan Dias Mirandela ◽  
...  
Keyword(s):  
Dual Problem ◽  
Functional Complementation ◽  
Ammonium Transport ◽  
Biological Transport ◽  
The Family ◽  
Domains Of Life ◽  
The Subject ◽  
Highly Hydrophobic ◽  
Dynamics Simulations ◽  
Competing Ions

The transport of charged molecules across biological membranes faces the dual problem of accommodating charges in a highly hydrophobic environment while maintaining selective substrate translocation. This has been the subject of a particular controversy for the exchange of ammonium across cellular membranes, an essential process in all domains of life. Ammonium transport is mediated by the ubiquitous Amt/Mep/Rh transporters that includes the human Rhesus factors. Here, using a combination of electrophysiology, yeast functional complementation and extended molecular dynamics simulations, we reveal a unique two-lane pathway for electrogenic NH4+ transport in two archetypal members of the family, the transporters AmtB from Escherichia coli and Rh50 from Nitrosomonas europaea. The pathway underpins a mechanism by which charged H+ and neutral NH3 are carried separately across the membrane after NH4+ deprotonation. This mechanism defines a new principle of achieving transport selectivity against competing ions in a biological transport process.

Leaf-Inspired Authentically Complex Microvascular Networks for Deciphering Biological Transport Process

2019 ◽  
Vol 11 (35) ◽  
pp. 31627-31637 ◽  
Author(s):  
Marco E. Miali ◽  
Marianna Colasuonno ◽  
Salvatore Surdo ◽  
Roberto Palomba ◽  
Rui Pereira ◽  
...  
Keyword(s):  
Transport Process ◽  
Biological Transport ◽  
Microvascular Networks

scholarly journals Molecular Dynamics Simulations of resistin and RELMβ proteins: Insight into structural dynamics

2021 ◽  
Author(s):  
L. América Chi Uluac ◽  
M. Cristina Vargas González
Keyword(s):  
Molecular Dynamics ◽  
High Temperature ◽  
Molecular Dynamics Simulations ◽  
Structural Dynamics ◽  
Protein Structures ◽  
Globular Domain ◽  
The Family ◽  
Network Of Hydrogen Bonds ◽  
Dynamics Simulations ◽  
Metabolic Dysfunctions

Diabetes mellitus and high levels of resistin are risk factors for COVID-19, suggest- ing a shared mechanism for their contribution to the increased severity of COVID-19. Resistin belongs to the family of resistin-like molecules (RELMs) whose implications for inflammatory and metabolic dysfunctions warrant its study in order to shed light on the etiology of these concerning pathologies. In this work, our objective is to char- acterize the structural dynamics of the reported crystallized resistin-like molecules. We performed molecular dynamics simulations of all-atom solvated protein at physiological and high temperatures for the three mouse structures reported so far. We found that in all the structures studied, there is a loss of helicity as a first step of protein denat- uration. There is a high stability of the globular β-sheet domain in resistin protein structures that is not conserved for RELMβ. At high temperature, we found a partial interconversion of α-helices into β-sheets in all proteins, indicating that this propensity is not only found during aggregation but also heating. We had been able to identify a largely persistent hydrogen-bond network shared by all the proteins in the interchain globular domain at room temperature. This network of hydrogen bonds is conserved considerably at high temperature in resistin structures, but not in RELMβ. These findings may guide future studies to increase our understanding of the different and shared mechanisms of action of RELMs.

Single glucose molecule transport process revealed by force tracing and molecular dynamics simulations

2018 ◽  
Vol 3 (5) ◽  
pp. 517-524 ◽  
Author(s):  
Yangang Pan ◽  
Yuebin Zhang ◽  
Pianchou Gongpan ◽  
Qingrong Zhang ◽  
Siteng Huang ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Glucose Transport ◽  
Single Molecule ◽  
Transport Process ◽  
Theoretical Methods ◽  
Molecule Transport ◽  
Glucose Molecule ◽  
Dynamics Simulations

Single-molecule glucose transport was illuminated using both experimental and theoretical methods.

Chloride-dependent conformational changes in the GlyT1 glycine transporter

2020 ◽  
Author(s):  
Yuan-Wei Zhang ◽  
Stacy Uchendu ◽  
Vanessa Leone ◽  
Richard T. Bradshaw ◽  
Ntumba Sangwa ◽  
...  
Keyword(s):  
Conformational Changes ◽  
Ion Pair ◽  
Cysteine Residues ◽  
Glycine Transporter ◽  
Open Conformation ◽  
Transporter Family ◽  
Transport Cycle ◽  
Dynamics Simulations ◽  
Insight Into

AbstractThe human GlyT1 glycine transporter requires chloride for its function. However, the mechanism by which Cl- exerts its influence is unknown. To examine the role that Cl- plays in the transport cycle, we measured the effect of Cl- on both glycine binding and conformational changes. The ability of glycine to displace the high-affinity radioligand [3H]CHIBA-3007 required Na+ and was potentiated over 1000-fold by Cl-. We generated GlyT1b mutants containing reactive cysteine residues in either the extracellular or cytoplasmic permeation pathways and measured changes in the reactivity of those cysteine residues as indicators of conformational changes in response to ions and substrate. Na+ increased accessibility in the extracellular pathway and decreased it in the cytoplasmic pathway, consistent with stabilizing an outward-open conformation as observed in other members of this transporter family. In the presence of Na+, both glycine and Cl- independently shifted the conformation of GlyT1b toward an outward-closed conformation. Together, Na+, glycine and Cl- stabilized an inward-open conformation of GlyT1b. We then examined whether Cl- acts by interacting with a conserved glutamine to allow formation of an ion pair that stabilizes the closed state of the extracellular pathway. Molecular dynamics simulations of a GlyT1 homologue indicated that this ion pair is formed more frequently as that pathway closes. Mutation of the glutamine blocked the effect of Cl-, and substituting it with glutamate or lysine resulted in outward- or inward-facing transporter conformations, respectively. These results provide novel and unexpected insight into the role of Cl- in this family of transporters.

scholarly journals flhDC, the Flagellar Master Operon ofXenorhabdus nematophilus: Requirement for Motility, Lipolysis, Extracellular Hemolysis, and Full Virulence in Insects

2000 ◽  
Vol 182 (1) ◽  
pp. 107-115 ◽  
Author(s):  
Alain Givaudan ◽  
Anne Lanois
Keyword(s):  
Wild Type Strain ◽  
Phase Variation ◽  
Functional Complementation ◽  
Null Mutant ◽  
Wild Type ◽  
Virulence Phenotype ◽  
The Family ◽  
Flagellar Regulon ◽  
Swarming Behavior

ABSTRACT Xenorhabdus is a major insect pathogen symbiotically associated with nematodes of the family Steinernematidae. This motile bacterium displays swarming behavior on suitable media, but a spontaneous loss of motility is observed as part of a phenomenon designated phase variation which involves the loss of stationary-phase products active as antibiotics and potential virulence factors. To investigate the role of one of the transcriptional activators of flagellar genes, FlhDC, in motility and virulence, theXenorhabdus nematophilus flhDC locus was identified by functional complementation of an Escherichia coli flhD null mutant and DNA sequencing. Construction of X. nematophilus flhD null mutants confirmed that the flhDC operon controls flagellin expression but also revealed that lipolytic and extracellular hemolysin activity is flhDC dependent. We also showed that the flhD null mutant displayed a slightly attenuated virulence phenotype in Spodoptera littoraliscompared to that of the wild-type strain. Thus, these data indicated that motility, lipase, hemolysin, or unknown functions controlled by the flhDC operon are involved in the infectious process in insects. Our investigation expands the view of the flagellar regulon as a checkpoint coupled to a major network involving bacterial physiological aspects as well as motility.

scholarly journals Structure and Formation Mechanism of Antimicrobial Peptides Temporin B- and L-Induced Tubular Membrane Protrusion

2021 ◽  
Vol 22 (20) ◽  
pp. 11015
Author(s):  
Shan Zhang ◽  
Ming Ma ◽  
Zhuang Shao ◽  
Jincheng Zhang ◽  
Lei Fu ◽  
...  
Keyword(s):  
Antimicrobial Peptides ◽  
Morphological Changes ◽  
Membrane Surface ◽  
Coarse Grained ◽  
Tubular Structures ◽  
Membrane Pore ◽  
Anionic Phospholipids ◽  
Bactericidal Activities ◽  
Highly Hydrophobic ◽  
Dynamics Simulations

Temporins are a family of antimicrobial peptides (AMPs) isolated from frog skin, which are very short, weakly charged, and highly hydrophobic. They execute bactericidal activities in different ways from many other AMPs. This work investigated morphological changes of planar bilayer membranes composed of mixed zwitterionic and anionic phospholipids induced by temporin B and L (TB and TL) using all-atom and coarse-grained molecular dynamics simulations. We found that TB and TL fold to α-helices at the membrane surface and penetrate shallowly into the bilayer. These short AMPs have low propensity to induce membrane pore formation but possess high ability to extract lipids out. At relatively high peptide concentrations, the strong hydrophobicity of TB and TL promotes them to aggregate into clusters on the membrane surface. These aggregates attract a large amount of lipids out of the membrane to release compression induced by other dispersed peptides binding to the membrane. The extruded lipids mix evenly with the peptides in the cluster and form tubule-like protrusions. Certain water molecules follow the movement of lipids, which not only fill the cavities of the protrusion but also assist in maintaining the tubular structures. In contrast, the peptide-free leaflet remains intact. The present results unravel distinctive antimicrobial mechanisms of temporins disturbing membranes.

scholarly journals Structural Features of the Glutamate Transporter Family

1999 ◽  
Vol 63 (2) ◽  
pp. 293-307 ◽  
Author(s):  
Dirk Jan Slotboom ◽  
Wil N. Konings ◽  
Juke S. Lolkema
Keyword(s):  
Amino Acid ◽  
Glutamate Transporter ◽  
Glutamate Transporters ◽  
Amino Acid Sequences ◽  
Neutral Amino Acid ◽  
Amino Acid Transporters ◽  
Conserved Sequence ◽  
Transporter Family ◽  
The Family ◽  
Membrane Spanning

SUMMARY Neuronal and glial glutamate transporters remove the excitatory neurotransmitter glutamate from the synaptic cleft and thus prevent neurotoxicity. The proteins belong to a large and widespread family of secondary transporters, including bacterial glutamate, serine, and C4-dicarboxylate transporters; mammalian neutral-amino-acid transporters; and an increasing number of bacterial, archaeal, and eukaryotic proteins that have not yet been functionally characterized. Sixty members of the glutamate transporter family were found in the databases on the basis of sequence homology. The amino acid sequences of the carriers have diverged enormously. Homology between the members of the family is most apparent in a stretch of approximately 150 residues in the C-terminal part of the proteins. This region contains four reasonably well-conserved sequence motifs, all of which have been suggested to be part of the translocation pore or substrate binding site. Phylogenetic analysis of the C-terminal stretch revealed the presence of five subfamilies with characterized members: (i) the eukaryotic glutamate transporters, (ii) the bacterial glutamate transporters, (iii) the eukaryotic neutral-amino-acid transporters, (iv) the bacterial C4-dicarboxylate transporters, and (v) the bacterial serine transporters. A number of other subfamilies that do not contain characterized members have been defined. In contrast to their amino acid sequences, the hydropathy profiles of the members of the family are extremely well conserved. Analysis of the hydropathy profiles has suggested that the glutamate transporters have a global structure that is unique among secondary transporters. Experimentally, the unique structure of the transporters was recently confirmed by membrane topology studies. Although there is still controversy about part of the topology, the most likely model predicts the presence of eight membrane-spanning α-helices and a loop-pore structure which is unique among secondary transporters but may resemble loop-pores found in ion channels. A second distinctive structural feature is the presence of a highly amphipathic membrane-spanning helix that provides a hydrophilic path through the membrane. Recent data from analysis of site-directed mutants and studies on the mechanism and pharmacology of the transporters are discussed in relation to the structural model.

scholarly journals Insights into the Role of Membrane Lipids in the Structure, Function and Regulation of Integral Membrane Proteins

2021 ◽  
Vol 22 (16) ◽  
pp. 9026
Author(s):  
Kenta Renard ◽  
Bernadette Byrne
Keyword(s):  
Membrane Proteins ◽  
Membrane Protein ◽  
Conformational Changes ◽  
Protein Interactions ◽  
Membrane Lipids ◽  
Protein Protein Interactions ◽  
Technological Advances ◽  
Highly Hydrophobic ◽  
Dynamics Simulations ◽  
And Function

Membrane proteins exist within the highly hydrophobic membranes surrounding cells and organelles, playing key roles in cellular function. It is becoming increasingly clear that the membrane does not just act as an appropriate environment for these proteins, but that the lipids that make up these membranes are essential for membrane protein structure and function. Recent technological advances in cryogenic electron microscopy and in advanced mass spectrometry methods, as well as the development of alternative membrane mimetic systems, have allowed experimental study of membrane protein–lipid complexes. These have been complemented by computational approaches, exploiting the ability of Molecular Dynamics simulations to allow exploration of membrane protein conformational changes in membranes with a defined lipid content. These studies have revealed the importance of lipids in stabilising the oligomeric forms of membrane proteins, mediating protein–protein interactions, maintaining a specific conformational state of a membrane protein and activity. Here we review some of the key recent advances in the field of membrane protein–lipid studies, with major emphasis on respiratory complexes, transporters, channels and G-protein coupled receptors.

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