scholarly journals Structural, functional and computational studies of membrane recognition by Plasmodium Perforin-Like Proteins 1 and 2.

2021 ◽  
Author(s):  
Sophie Williams ◽  
Xiulian Yu ◽  
Tao Ni ◽  
Robert Gilbert ◽  
Phillip Stansfeld
Keyword(s):  
Life Cycle ◽  
Lipid Bilayers ◽  
Membrane Binding ◽  
Binding Activity ◽  
Life Cycles ◽  
Site Directed Mutagenesis ◽  
Parasite Life Cycle ◽  
Dynamics Simulations ◽  
Membrane Recognition

Perforin-like proteins (PLPs) play key roles in the mechanisms associated with parasitic disease caused by apicomplexans such as Plasmodium (malaria) and Toxoplasma. The T. gondii PLP1 (TgPLP1) mediates tachyzoite egress from cells, while the five Plasmodium PLPs carry out various roles in the life cycle of the parasite and with respect to the molecular basis of disease. Here we focus on Plasmodium vivax PLP1 and PLP2 (PvPLP1 and PvPLP2) compared to TgPLP1; PvPLP1 is important for invasion of mammalian hosts by the parasite and establishment of a chronic infection, PvPLP2 is important during the symptomatic blood stage of the parasite life cycle. Determination of the crystal structure of the membrane-binding APCβ domain of PvPLP1 reveals notable differences with that of TgPLP1, which are reflected in its inability to bind lipid bilayers in the way that TgPLP1 and PvPLP2 can be shown to. Molecular dynamics simulations combined with site-directed mutagenesis and functional assays allow a dissection of the binding interactions of TgPLP1 and PvPLP2 on lipid bilayers, and reveal a similar tropism for lipids found enriched in the inner leaflet of the mammalian plasma membrane. In addition to this shared mode of membrane binding PvPLP2 displays a secondary synergistic interaction side-on from its principal bilayer interface. This study underlines the substantial differences between the biophysical properties of the APCβ domains of Apicomplexan PLPs, which reflect their significant sequence diversity. Such differences will be important factors in determining the cell targeting and membrane-binding activity of the different proteins, in their different developmental roles within parasite life cycles.

Parasite life-cycle studies: a plea to resurrect an old parasitological tradition

2017 ◽  
Vol 91 (6) ◽  
pp. 647-656 ◽  
Author(s):  
I. Blasco-Costa ◽  
R. Poulin
Keyword(s):  
Life Cycle ◽  
Large Scale ◽  
Integrative Taxonomy ◽  
Life Cycles ◽  
Intermediate Hosts ◽  
Parasite Life Cycle ◽  
Quantitative Evidence ◽  
Research Areas ◽  
Food Web Ecology ◽  
And Control

AbstractMany helminth taxa have complex life cycles, involving different life stages infecting different host species in a particular order to complete a single generation. Although the broad outlines of these cycles are known for any higher taxon, the details (morphology and biology of juvenile stages, specific identity of intermediate hosts) are generally unknown for particular species. In this review, we first provide quantitative evidence that although new helminth species are described annually at an increasing rate, the parallel effort to elucidate life cycles has become disproportionately smaller over time. We then review the use of morphological matching, experimental infections and genetic matching as approaches to elucidate helminth life cycles. Next we discuss the various research areas or disciplines that could benefit from a solid knowledge of particular life cycles, including integrative taxonomy, the study of parasite evolution, food-web ecology, and the management and control of parasitic diseases. Finally, we end by proposing changes to the requirements for new species descriptions and further large-scale attempts to genetically match adult and juvenile helminth stages in regional faunas, as part of a plea to parasitologists to bring parasite life-cycle studies back into mainstream research.

scholarly journals Energy-harnessing problem solving of primordial life: modeling the emergence of catalytic host-parasite life cycles

2021 ◽  
Author(s):  
Bernard Conrad ◽  
Magnus Pirovino
Keyword(s):  
Life Cycle ◽  
Problem Solving ◽  
Life Forms ◽  
Life Cycles ◽  
Darwinian Evolution ◽  
Volterra Equations ◽  
Genome Replication ◽  
Parasite Life Cycle ◽  
Functional Features ◽  
Host Parasite

AbstractAll life forms on earth ultimately descended from a primordial population dubbed the last universal common ancestor or LUCA via Darwinian evolution. Extant living systems share two salient functional features, a metabolism extracting and transforming energy required for survival, and an evolvable, informational polymer – the genome – conferring heredity. Genome replication invariably generates essential and ubiquitous genetic parasites. Here we model the energetic, replicative conditions of LUCA-like organisms and their parasites, as well as adaptive problem solving of host-parasite pairs. We show using the Lotka-Volterra equations that three host-parasite pairs – individually a unit of a host and a parasite that is itself parasitized – are sufficient for robust and stable homeostasis, forming a life cycle. This catalytic life cycle efficiently captures, channels and transforms energy, enabling dynamic host survival and adaptation. We propose a Malthusian fitness model for an original quasispecies evolving through a host-parasite life cycle.

scholarly journals Determination of bending rigidity and tilt modulus of lipid membranes from real-space fluctuation analysis of molecular dynamics simulations

2017 ◽  
Vol 19 (25) ◽  
pp. 16806-16818 ◽  
Author(s):  
M. Doktorova ◽  
D. Harries ◽  
G. Khelashvili
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Lipid Bilayers ◽  
Lipid Membranes ◽  
Real Space ◽  
Fluctuation Analysis ◽  
Bending Rigidity ◽  
Wide Range ◽  
Dynamics Simulations

Computational methodology that allows to extract bending rigidity and tilt modulus for a wide range of single and multi-component lipid bilayers from real-space analysis of fluctuations in molecular dynamics simulations.

scholarly journals A Theoretical Assessment of the Structure Determination of Multi-Span Membrane Proteins by Oriented Sample Solid-State NMR Spectroscopy

2020 ◽  
Vol 73 (3) ◽  
pp. 246 ◽  
Author(s):  
Daniel K. Weber ◽  
Gianluigi Veglia
Keyword(s):  
Solid State ◽  
Membrane Proteins ◽  
Lipid Bilayers ◽  
Solid State Nmr ◽  
Direct Determination ◽  
Oriented Sample ◽  
Dynamics Simulations ◽  
G Protein Coupled ◽  
Theoretical Assessment

Oriented sample solid-state NMR (OS-ssNMR) spectroscopy allows the direct determination of the structure and topology of membrane proteins reconstituted into aligned lipid bilayers. Although OS-ssNMR theoretically has no upper size limit, its application to multi-span membrane proteins has not been established because most studies have been restricted to single- or dual-span proteins and peptides. Here, we present a critical assessment of the application of this method to multi-span membrane proteins. We used molecular dynamics simulations to back-calculate [15N-1H] separated local field (SLF) spectra from a G protein-coupled receptor (GPCR) and show that fully resolved spectra can be obtained theoretically for a multi-span membrane protein with currently achievable resonance linewidths.

Anisotropy of Nanoindentation – a tool for the determination of nanocrystal orientation ?

2003 ◽  
Vol 779 ◽  
Author(s):  
David Christopher ◽  
Steven Kenny ◽  
Roger Smith ◽  
Asta Richter ◽  
Bodo Wolf ◽  
...  
Keyword(s):  
Crystal Surface ◽  
Scanning Force Microscopy ◽  
Depth Range ◽  
Dislocation Loops ◽  
Force Microscopy ◽  
Pile Up ◽  
Out Of Plane ◽  
Scanning Force ◽  
Dynamics Simulations

AbstractThe pile up patterns arising in nanoindentation are shown to be indicative of the sample crystal symmetry. To explain and interpret these patterns, complementary molecular dynamics simulations and experiments have been performed to determine the atomistic mechanisms of the nanoindentation process in single crystal Fe{110}. The simulations show that dislocation loops start from the tip and end on the crystal surface propagating outwards along the four in-plane <111> directions. These loops carry material away from the indenter and form bumps on the surface along these directions separated from the piled-up material around the indenter hole. Atoms also move in the two out-of-plane <111> directions causing propagation of subsurface defects and pile-up around the hole. This finding is confirmed by scanning force microscopy mapping of the imprint, the piling-up pattern proving a suitable indicator of the surface crystallography. Experimental force-depth curves over the depth range of a few nanometers do not appear smooth and show distinct pop-ins. On the sub-nanometer scale these pop-ins are also visible in the simulation curves and occur as a result of the initiation of the dislocation loops from the tip.

Molecular Basis of Glucose Transport Mechanism in Plants

2019 ◽  
Author(s):  
Balaji Selvam ◽  
Ya-Chi Yu ◽  
Liqing Chen ◽  
Diwakar Shukla
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Molecular Dynamics Simulations ◽  
Conformational Changes ◽  
Transport Mechanism ◽  
Conformational Dynamics ◽  
Site Directed Mutagenesis ◽  
Free Energy Barrier ◽  
Transport Cycle ◽  
Dynamics Simulations

<p>The SWEET family belongs to a class of transporters in plants that undergoes large conformational changes to facilitate transport of sugar molecules across the cell membrane. However, the structures of their functionally relevant conformational states in the transport cycle have not been reported. In this study, we have characterized the conformational dynamics and complete transport cycle of glucose in OsSWEET2b transporter using extensive molecular dynamics simulations. Using Markov state models, we estimated the free energy barrier associated with different states as well as 1 for the glucose the transport mechanism. SWEETs undergoes structural transition to outward-facing (OF), Occluded (OC) and inward-facing (IF) and strongly support alternate access transport mechanism. The glucose diffuses freely from outside to inside the cell without causing major conformational changes which means that the conformations of glucose unbound and bound snapshots are exactly same for OF, OC and IF states. We identified a network of hydrophobic core residues at the center of the transporter that restricts the glucose entry to the cytoplasmic side and act as an intracellular hydrophobic gate. The mechanistic predictions from molecular dynamics simulations are validated using site-directed mutagenesis experiments. Our simulation also revealed hourglass like intermediate states making the pore radius narrower at the center. This work provides new fundamental insights into how substrate-transporter interactions actively change the free energy landscape of the transport cycle to facilitate enhanced transport activity.</p>

Definitions and concepts of reproductive biology of diatoms (terminological glossary)

2017 ◽  
Vol 51 ◽  
pp. 71-105 ◽  
Author(s):  
N. A. Davidovich
Keyword(s):  
Mating System ◽  
Sexual Reproduction ◽  
Reproductive Biology ◽  
World Literature ◽  
Russian Literature ◽  
Life Cycles ◽  
Transfer Of Knowledge ◽  
Research Experience ◽  
Key Terms

The absence of a conceptual terminology, sufficiently developed and widely accepted in the Russian literature, significantly hinders progress in the field of reproductive biology of diatoms, restricts communication and debate, prevents training and transfer of knowledge. The present work is an attempt, based on world literature and our own research experience, to summarize, systematize, add, and clarify the existing terms, concepts and definitions related to research which are focused on sex and sexual reproduction in diatoms. A glossary of key terms (more than 200, including synonyms) is provided. Terms refer to diatom reproductive biology, life cycles, fertilization, mating system, gender (including inheritance and determination of sex, as well as inheritance associated with sex). Contradictions between possible interpretations of certain terms are briefly discussed.

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