Erratum: “Environmental swap energy and role of configurational entropy in transfer of small molecules from water into alkanes” [J. Chem. Phys. 120, 1383 (2004)]

2005 ◽  
Vol 122 (22) ◽  
pp. 229902
Author(s):  
Pavel Smejtek ◽  
Robert C. Word
Keyword(s):  
Small Molecules ◽  
Configurational Entropy ◽  
Chem Phys

scholarly journals Role of SpoVA Proteins in Release of Dipicolinic Acid during Germination of Bacillus subtilis Spores Triggered by Dodecylamine or Lysozyme

2006 ◽  
Vol 189 (5) ◽  
pp. 1565-1572 ◽  
Author(s):  
Venkata Ramana Vepachedu ◽  
Peter Setlow
Keyword(s):  
Bacillus Subtilis ◽  
Small Molecules ◽  
Spore Germination ◽  
Dipicolinic Acid ◽  
Temperature Sensitive ◽  
Wild Type ◽  
Ph Optimum ◽  
Inner Membrane ◽  
Temperature Sensitive Mutants

ABSTRACT The release of dipicolinic acid (DPA) during the germination of Bacillus subtilis spores by the cationic surfactant dodecylamine exhibited a pH optimum of ∼9 and a temperature optimum of 60°C. DPA release during dodecylamine germination of B. subtilis spores with fourfold-elevated levels of the SpoVA proteins that have been suggested to be involved in the release of DPA during nutrient germination was about fourfold faster than DPA release during dodecylamine germination of wild-type spores and was inhibited by HgCl2. Spores carrying temperature-sensitive mutants in the spoVA operon were also temperature sensitive in DPA release during dodecylamine germination as well as in lysozyme germination of decoated spores. In addition to DPA, dodecylamine triggered the release of amounts of Ca2+ almost equivalent to those of DPA, and at least one other abundant spore small molecule, glutamic acid, was released in parallel with Ca2+ and DPA. These data indicate that (i) dodecylamine triggers spore germination by opening a channel in the inner membrane for Ca2+-DPA and other small molecules, (ii) this channel is composed at least in part of proteins, and (iii) SpoVA proteins are involved in the release of Ca2+-DPA and other small molecules during spore germination, perhaps by being a part of a channel in the spore's inner membrane.

ZERO AND FINITE TEMPERATURE STUDY OF SINGLE FULLERENE CAGES AND CARBON “ONIONS” — GEOMETRY AND SHAPE

1993 ◽  
Vol 07 (29n30) ◽  
pp. 1883-1895 ◽  
Author(s):  
A. MAITI ◽  
C.J. BRABEC ◽  
J. BERNHOLC
Keyword(s):  
Interatomic Potential ◽  
Critical Size ◽  
Tight Binding ◽  
Configurational Entropy ◽  
Electronic Structure Calculations ◽  
Carbon Onions ◽  
Three Body ◽  
Structure Calculations ◽  
Scaling Arguments

Scaling arguments are used to show that above a critical size of several thousand atoms, there is a stability crossover from single to multilayer cages. Conjugate gradient minimization using a classical three-body interatomic potential, as well as tight-binding electronic structure calculations yield ground-state configurations for large fullerene shells that are polyhedral with clearly faceted geometry. The structure, energetics and configurational entropy associated with low-energy defects are calculated and the number of defects estimated as a function of temperature. The role of these thermally generated defects on the shape of large fullerenes is investigated in order to explain the nearly spherical shapes of the newly discovered carbon “onions”.

Interactions of small molecules with TiO2(110) surfaces: The role of defects

1996 ◽  
Vol 14 (3) ◽  
pp. 1532-1538 ◽  
Author(s):  
Li‐Qiong Wang ◽  
A. N. Shultz ◽  
D. R. Baer ◽  
M. H. Engelhard
Keyword(s):  
Small Molecules

The Role of Membranes in the Transport of Small Molecules

2018 ◽  
pp. 1-52 ◽  
Author(s):  
J. E. Leonard ◽  
C. A. Lee ◽  
A. J. Apperson ◽  
S. S. Dills ◽  
M. H. Saier
Keyword(s):  
Small Molecules

scholarly journals Minimal mechanistic component of proteasome activation and prevention of impairment by pathological oligomers

2021 ◽  
Author(s):  
Janelle Chuah ◽  
Tifffany Thibaudeau ◽  
David Smith
Keyword(s):  
Small Molecules ◽  
Conformational Changes ◽  
Bound State ◽  
Proof Of Concept ◽  
Α Subunit ◽  
Gate Opening ◽  
Allosteric Mechanism ◽  
Dependent Mechanism ◽  
Degradation Of Peptides

Abstract Impairment of proteasomal function has been implicated in neurodegenerative diseases, justifying the need to understand how the proteasome is activated for protein degradation. Here, using biochemical and structural (cryo-EM) strategies in both archaeal and mammalian proteasomes, we further determine the HbYX(-motif)-dependent mechanism of proteasomal activation used by multiple proteasome-activating complexes including the 19S Particle. We identify multiple proteasome α subunit residues involved in HbYX-dependent activation, a point mutation that activates the proteasome by partially mimicking a HbYX-bound state, and conformational changes involved in gate-opening with a 2.0A structure. Through an iterative process of peptide synthesis, we successfully design a HbYX-like dipeptide mimetic as a robust tool to elucidate how the motif autonomously activates the proteasome. The mimetic induces near complete gate-opening at saturating concentration, activating mammalian proteasomal degradation of peptides and proteins. Findings using our peptide mimetic suggest the HbYX-dependent mechanism requires cooperative binding in at least two intersubunit pockets of the α ring. Collectively, the results presented here unambiguously demonstrate the lone role of the HbYX tyrosine in the allosteric mechanism of proteasome activation and offer proof of concept for the robust potential of HbYX-like small molecules to activate the proteasome.

scholarly journals Causal role of L-glutamine in sickle cell disease painful crises: a Mendelian randomization analysis

2019 ◽  
Author(s):  
Yann Iboudo ◽  
Melanie E. Garrett ◽  
Pablo Bartolucci ◽  
Carlo Brugnara ◽  
Clary B. Clish ◽  
...  
Keyword(s):  
Sickle Cell Disease ◽  
Small Molecules ◽  
Causal Relationship ◽  
Sickle Cell ◽  
Drug Targets ◽  
Mendelian Randomization ◽  
Cell Disease ◽  
Aseptic Necrosis ◽  
Randomization Analysis

ABSTRACTIn a recent clinical trial, the metabolite L-glutamine was shown to reduce painful crises in sickle cell disease (SCD) patients. To confirm this observation and identify other metabolites implicated in SCD clinical heterogeneity, we profiled 129 metabolites in the plasma of 705 SCD patients. We tested correlations between metabolite levels and six SCD-related complications (painful crises, cholecystectomy, retinopathy, leg ulcer, priapism, aseptic necrosis) or estimated glomerular filtration rate (eGFR), and used Mendelian randomization (MR) to assess causality. We found a causal relationship between L-glutamine levels and painful crises (N=1,278, odds ratio (OR) [95% confidence interval] = 0.68 [0.52 – 0.89], P=0.0048). In two smaller SCD cohorts (N=299 and 406), the protective effect of L-glutamine was observed (OR=0.82 [0.50-1.34]), although the MR result was not significant (P=0.44). We identified 66 significant correlations between the levels of other metabolites and SCD-related complications or eGFR. We tested these correlations for causality using MR analyses and found no significant causal relationship. The baseline levels of quinolinic acid was associated with prospectively ascertained survival in SCD patients, and this effect was dependent on eGFR. Metabolomics provide a promising approach to prioritize small molecules that may serve as biomarkers or drug targets in SCD.

scholarly journals PET Imaging Radiotracers of Chemokine Receptors

Molecules ◽  
2021 ◽  
Vol 26 (17) ◽  
pp. 5174
Author(s):  
Santosh R. Alluri ◽  
Yusuke Higashi ◽  
Kun-Eek Kil
Keyword(s):  
Small Molecules ◽  
Chemokine Receptors ◽  
Brain Disorders ◽  
Infectious Agents ◽  
Cardiovascular Research ◽  
Critical Signal ◽  
Inflammatory Reactions ◽  
Positron Emission

Chemokines and chemokine receptors have been recognized as critical signal components that maintain the physiological functions of various cells, particularly the immune cells. The signals of chemokines/chemokine receptors guide various leukocytes to respond to inflammatory reactions and infectious agents. Many chemokine receptors play supportive roles in the differentiation, proliferation, angiogenesis, and metastasis of diverse tumor cells. In addition, the signaling functions of a few chemokine receptors are associated with cardiac, pulmonary, and brain disorders. Over the years, numerous promising molecules ranging from small molecules to short peptides and antibodies have been developed to study the role of chemokine receptors in healthy states and diseased states. These drug-like candidates are in turn exploited as radiolabeled probes for the imaging of chemokine receptors using noninvasive in vivo imaging, such as positron emission tomography (PET). Recent advances in the development of radiotracers for various chemokine receptors, particularly of CXCR4, CCR2, and CCR5, shed new light on chemokine-related cancer and cardiovascular research and the subsequent drug development. Here, we present the recent progress in PET radiotracer development for imaging of various chemokine receptors.

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