WW: An isolated three-stranded antiparallel beta-sheet domain that unfolds and refolds reversibly; evidence for a structured hydrophobic cluster in urea and GdnHCl and a disordered thermal unfolded state. (1/338)
The objective of this study was to evaluate the suitability of the WW domain as a desirable model system to understand the folding and stability of an isolated three-stranded antiparallel beta-sheet structure. The WW domain was subjected to thermal and chaotropic denaturation/reconstitution utilizing a variety of biophysical methods. This three-stranded sheet folds reversibly and cooperatively utilizing both urea and GdnHCl as denaturants; however, the denatured state retains structure in the form of a hydrophobic cluster involving at least one aromatic side chain. In contrast to chaotropic denaturation, thermal denaturation appears to be more complete and may be a two state process. The suitability of the WW domain for future studies aimed at understanding the kinetics and thermodynamics of antiparallel beta-sheet folding clearly emerges from this initial study. The most exciting and significant result in this manuscript is the finding that the chaotropic denatured state of WW has a hydrophobic cluster as discerned by near-UV CD evidence. The role that the denatured state plays in the folding and stability of a three-stranded beta-sheets, and its capacity for preventing aggregation may be particularly important and is the subject of ongoing studies. (+info)Detection of putative Zn(II) binding sites within Escherichia coli RNA polymerase: inconsistency between sequence-based prediction and 65Zn blotting. (2/338)
The availability of repeating 'Cys' and/or 'His' units in a particular order prompts the prediction of Zn(II) finger motifs in a protein. Escherichia coli RNA polymerase has two tightly bound Zn(II) per molecule of the enzyme as detected by atomic absorption spectroscopy. One Zn(II) was identified to be at the beta subunit, whereas the other putative Zn(II) binding site has recently been predicted to be at the N-terminal half of the beta' subunit, from primary sequence analysis. We show here that the beta' subunit has no ability to bind 65Zn(II). On the other hand, the N-terminal domain of the alpha subunit has strong Zn(II) binding ability with no obvious functional implications. (+info)Thiopental attenuates hypoxic changes of electrophysiology, biochemistry, and morphology in rat hippocampal slice CA1 pyramidal cells. (3/338)
BACKGROUND AND PURPOSE: Thiopental has been shown to protect against cerebral ischemic damage; however, it has undesirable side effects. We have examined how thiopental alters histological, physiological, and biochemical changes during and after hypoxia. These experiments should enable the discovery of agents that share some of the beneficial effects of thiopental. METHODS: We made intracellular recordings and measured ATP, sodium, potassium, and calcium concentrations from CA1 pyramidal cells in rat hippocampal slices subjected to 10 minutes of hypoxia with and without 600 micromol/L thiopental. RESULTS: Thiopental delayed the time until complete depolarization (21+/-3 versus 11+/-2 minutes for treated versus untreated slices, respectively) and attenuated the level of depolarization at 10 minutes of hypoxia (-33+/-6 versus -12+/-5 mV). There was improved recovery of the resting potential after 10 minutes of hypoxia in slices treated with thiopental (89% versus 31% recovery). Thiopental attenuated the changes in sodium (140% versus 193% of prehypoxic concentration), potassium (62% versus 46%), and calcium (111% versus 197%) during 10 minutes of hypoxia. There was only a small effect on ATP (18% versus 8%). The percentage of cells showing clear histological damage was decreased by thiopental (45% versus 71%), and thiopental improved protein synthesis after hypoxia (75% versus 20%). CONCLUSIONS: Thiopental attenuates neuronal depolarization, an increase in cellular sodium and calcium concentrations, and a decrease in cellular potassium and ATP concentrations during hypoxia. These effects may explain the reduced histological, protein synthetic, and electrophysiological damage to CA1 pyramidal cells after hypoxia with thiopental. (+info)Mitotic misregulation and human aging. (4/338)
Messenger RNA levels were measured in actively dividing fibroblasts isolated from young, middle-age, and old-age humans and humans with progeria, a rare genetic disorder characterized by accelerated aging. Genes whose expression is associated with age-related phenotypes and diseases were identified. The data also suggest that an underlying mechanism of the aging process involves increasing errors in the mitotic machinery of dividing cells in the postreproductive stage of life. We propose that this dysfunction leads to chromosomal pathologies that result in misregulation of genes involved in the aging process. (+info)Oestrogen, progesterone, and androgen receptors in ovarian neoplasia: correlation between immunohistochemical and biochemical receptor analyses. (5/338)
AIM: To investigate the correlation between immunohistochemical and biochemical steroid receptor analyses by measurement of oestrogen, progesterone, and androgen receptor status in ovarian neoplasia. METHODS: Tissue samples were obtained from 27 ovarian neoplasms, including two borderline tumours. Immunohistochemical staining of the tissue slides was scored semiquantitatively, incorporating the intensity and percentage of positive staining (histo-score). Tumours with a histo-score of 10 or more were considered steroid receptor positive. The epithelial and stromal fractions of the tumours were analysed separately. To study the uniformity of receptor expression throughout a tumour, up to four samples were analysed. RESULTS: Immunohistochemical histo-scores of the oestrogen receptor in the epithelial fractions were significantly correlated with the biochemical oestrogen receptor values (r = 0.408). Androgen receptor status in the epithelial fraction was correlated with that in the stromal fraction (r = 0.741), while androgen receptor histo-scores in the epithelial fraction correlated with the biochemical assay values (r = 0.463). On biochemical analysis, 17 of the 27 ovarian tumours were oestrogen receptor positive and seven were progesterone receptor positive. On immunohistochemical analysis, eight tumours were oestrogen receptor positive and two were progesterone receptor positive. Biochemical analysis showed that 14 of the 26 tumours were slightly androgen receptor positive (10-50 fmol/mg protein), while all the others were negative. On immunohistochemical analysis, seven of the 26 tumours were androgen receptor positive. When two or more specimens from one tumour were analysed, marked differences in steroid status were found, especially in progesterone receptor and androgen receptor expression. Some parts of a tumour were steroid receptor positive, while other parts were negative owing to heterogeneity of expression. CONCLUSIONS: Immunohistochemical and biochemical analysis of steroid receptors in ovarian tumours correlated weakly or not at all. Heterogeneity of expression within a tumour and the presence of progesterone and androgen receptors in the stromal fraction partly accounted for this observation. Biochemical and immunohistochemical androgen receptor status was much lower than in previous reports. (+info)Trehalose effect on low temperature protein dynamics: fluctuation and relaxation phenomena. (6/338)
We performed spectral diffusion experiments in trehalose-enriched glycerol/buffer-glass on horseradish peroxidase where the heme was replaced by metal-free mesoporphyrin IX, and compared them with the respective behavior in a pure glycerol/buffer-glass (Schlichter et al., J. Chem. Phys. 2000, 112:3045-3050). Trehalose has a significant influence: spectral diffusion broadening speeds up compared to the trehalose-free glass. This speeding up is attributed to a shortening of the correlation time of the frequency fluctuations most probably by preventing water molecules from leaving the protein interior. Superimposed to the frequency fluctuation dynamics is a relaxation dynamics that manifests itself as an aging process in the spectral diffusion broadening. Although the trehalose environment speeds up the fluctuations, it does not have any influence on the relaxation. Both relaxation and fluctuations are governed by power laws in time. The respective exponents do not seem to change with the protein environment. From the spectral dynamics, the mean square displacement in conformation space can be determined. It is governed by anomalous diffusion. The associated frequency correlation time is incredibly long, demonstrating that proteins at low temperatures are truly nonergodic systems. (+info)A new method for mapping nucleic acid sequence homology by electron microscopy. (7/338)
We describe here a new method for the electron microscopic mapping of sequence homology in nucleic acids. Specific segments of the T7 chromosome have been isolated following digestion with the restriction endonuclease from Hemophilus aegyptious (Haey). Denatured segments are annealed to the l-strand of T7 DNA; treatment of the hybrid with glyoxal allows only guanosine residues in the single-chain region to the reacted, producing an adduct which will no longer hydrogen bond with its complement on the r-strand. When the segment is displaced and the glyoxalated l-strand allowed to renature with the r-strand, "H" shaped structures are produced in which the duplex region corresponds to the position of sequence homology with the segment. The conditions employed for glyoxalation do not detectably disrupt duplex regions as small as 400 base pairs. This procedure should be generally useful for observing sequence homology in more complex DNA molecules containing duplex regions which can be specifically enriched for and their arrangement determined by electron microscopy. (+info)A novel method to determine the topology of peroxisomal membrane proteins in vivo using the tobacco etch virus protease. (8/338)
Most proteins essential for the biogenesis of peroxisomes (peroxins) that are identified to date are associated with or are integral components of the peroxisomal membrane. A prerequisite in elucidating their function is to determine their topology in the membrane. We have developed a novel tool to analyze the topology of peroxisomal membrane proteins in the yeast Hansenula polymorpha in vivo using the 27-kDa NIa protease subunit from the tobacco etch virus (TEVp). TEVp specifically cleaves peptides containing the consensus sequence, EXXYXQ downward arrowS (tev). We show that cytosolic TEVp and peroxisomal TEVp.SKL are selectively active on soluble cytosolic and peroxisomal tev-containing proteins in vivo, respectively, without affecting the viability of the yeast cells. The tev sequence was introduced in between the primary sequence of the peroxisomal membrane proteins Pex3p or Pex10p and the reporter protein enhanced green fluorescent protein (eGFP). Co-synthesis of these functional tev-GFP tagged proteins with either cytosolic TEVp or peroxisomal TEVp.SKL revealed that the C termini of Pex3p and Pex10p are exposed to the cytosol. Additional applications of the TEV protease to study peroxisome biogenesis are discussed. (+info)Biochemical phenomena refer to the chemical processes and reactions that occur within living organisms. These phenomena are essential for the structure, function, and regulation of all cells and tissues in the body. They involve a wide range of molecular interactions, including enzyme-catalyzed reactions, signal transduction pathways, and gene expression regulatory mechanisms.
Biochemical phenomena can be studied at various levels, from individual molecules to complex biological systems. They are critical for understanding the underlying mechanisms of many physiological processes, as well as the basis of various diseases and medical conditions.
Examples of biochemical phenomena include:
1. Metabolism: the chemical reactions that occur within cells to maintain life, including the breakdown of nutrients to produce energy and the synthesis of new molecules.
2. Protein folding: the process by which a protein molecule assumes its three-dimensional structure, which is critical for its function.
3. Signal transduction: the molecular mechanisms by which cells respond to external signals, such as hormones or neurotransmitters, and convert them into intracellular responses.
4. Gene expression regulation: the complex network of molecular interactions that control the production of proteins from DNA, including transcription, RNA processing, and translation.
5. Cell-cell communication: the mechanisms by which cells communicate with each other to coordinate their functions and maintain tissue homeostasis.
6. Apoptosis: the programmed cell death pathway that eliminates damaged or unnecessary cells.
7. DNA repair: the molecular mechanisms that detect and correct damage to DNA, preventing mutations and maintaining genomic stability.
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Processes5
- Category G contains an extensive array of terms for biological, chemical, physical processes and phenomena. (nih.gov)
- The phenomenon of catalysis makes possible biochemical reactions necessary for all life processes. (worthington-biochem.com)
- Synaptic plasticity is a complex phenomenon involving multiple biochemical processes that operate on different timescales. (biorxiv.org)
- These species permit detailed physiological, pharmacological, and biochemical investigations, but are limited by the current lack of available techniques to allow precise and systematic alterations in their genetic composition and, thus, to precisely define the contributions of specific genes and/or their encoded proteins in cardiovascular disease processes. (nih.gov)
- We use cell biological, biochemical, genetic and structural approaches to dissect cytoskeletal processes with the aim of understanding how they work in molecular detail. (hopkinsmedicine.org)
Biophysical Phenomena1
- Cryobiology encompasses an enormous range of physical and biophysical phenomena, and as such is a field rich in interesting, tractable, and non-contrived problems that span a large range of applied mathematical techniques. (gmu.edu)
Metabolism2
- Physiological and biochemical studies of T. mathranii, including extraction of intracellular metabolites and enzymes of the pentose phosphate pathway and glycolysis, revealed several bottlenecks in the D-xylose metabolism. (osti.gov)
- The living cell is the site of tremendous biochemical activity called metabolism. (worthington-biochem.com)
Pathways4
- The plan calls for research into the biochemical pathways and other physiological phenomenon of pregnancy and preterm birth, ultimately to find ways to prevent preterm birth. (nih.gov)
- But pain is a much more complicated phenomenon than can be captured by simple biochemical pathways. (insidescience.org)
- In fact, we don't actually know what biochemical pathways detect that sensation and send that signal to your brain. (insidescience.org)
- In parallel, we also try to understand how cell morphology affects biochemical pathways inside cells. (hopkinsmedicine.org)
Transport phenomena1
- In biology and chemistry complex biochemical networks displaced far from equilibrium coupled with transport phenomena maintain the NESA structures. (confex.com)
Mathematical1
- This algorithm, designed previously within the François research group, randomly generates mathematical models of biochemical networks. (sciencedaily.com)
Biological1
- Advances in numerous areas of the biological and medical sciences will continue to require a quantitative understanding of the complex network of biochemical interactions underlying biological phenomena. (nih.gov)
Characterization1
- Leite AET, Briganti L, de Ara?jo EA, Pellegrini VOA, Camilo CM, Polikarpov I. Low-resolution molecular shape, biochemical characterization and emulsification properties of a halotolerant esterase from Bacillus licheniformis. (ucdenver.edu)
Reactions4
- The greatest majority of these biochemical reactions do not take place spontaneously. (worthington-biochem.com)
- The catalysts of biochemical reactions are enzymes and are responsible for bringing about almost all of the chemical reactions in living organisms. (worthington-biochem.com)
- The facilitation of biochemical reactions with the aid of naturally occurring catalysts such as ENZYMES. (ucdenver.edu)
- An indiscriminate usage of the concepts and terminology borrowed from the systems control theory obscures the fundamental fact that intracellular functionality is nothing else than a vast system of interconnecting biochemical reactions between billions of molecules belonging to tens of thousands of molecular species. (springeropen.com)
Occurs2
- The scientific study of the chemical and biochemical phenomena that occurs in natural places. (citizendium.org)
- From these findings it can be concluded that in vivo DDIs for CYP3A4 can be predicted from in vitro data, even when more than one biochemical phenomenon occurs simultaneously. (aspetjournals.org)
Concepts1
- The Eagen Lab combines concepts and approaches from structural biology and biochemistry with methods and analytical tools from molecular biology and genomics to determine the structural and biochemical basis of chromatin folding and chromosome condensation. (nih.gov)
Molecular2
- Molecular electrostatic potentials: an effective tool for the elucidation of biochemical phenomena. (nih.gov)
- Here's another real-world example that shows how dropout works: A biochemical company wants to design a new molecular structure that will enable it to produce a revolutionary form of plastic. (techtarget.com)
Adaptation1
- The researchers' computer simulations yielded a surprisingly simple solution related to the well-known phenomenon of biochemical adaptation -- a general biochemical mechanism that enable organisms to cope with varying environmental conditions. (sciencedaily.com)
Complex1
- Complex cellular and biochemical phenomena are involved in the process. (com.sa)
Mechanisms3
- Biochemical mechanisms of cadmium -induced anemia. (cdc.gov)
- The biochemical mechanisms underlying those phenomena are not well understood. (cdc.gov)
- fruit, and now there is increasing interest in the biochemical mechanisms responsible for this phenomenon. (biomedcentral.com)
Biology1
- In particular, we show that burstiness, a well-known phenomenon in the biology of gene expression, is a natural consequence of high dimensionality coupled with high nonlinearity. (springeropen.com)
Chemical2
- Life is not an information phenomenon, but a bio-chemical one. (uncommondescent.com)
- In the area of Asopos, Greece , there is an interesting polluting phenomenon: some industries dump directly to the water bed chemical waste while few hundred yards further, the farmers use bore wholes to pump out water to cultivate food tubers. (thepressproject.gr)
Metabolic1
- Taken together these biochemical data indicate the metabolic poise of A. socius is only partly explained by hypoxia in early development, and that the atypical set points are also intrinsic features of this ontogenetic period in the life cycle. (biologists.com)
Intracellular2
- Two major approaches are known in the field of stochastic dynamics of intracellular biochemical networks. (springeropen.com)
- High-dimensional biochemical networks are the integral parts of intracellular organization. (springeropen.com)
Occur2
- It seems probable that the phenomena described in these animal models occur in human knees with subfracture injury. (medscape.com)
- Successful cryopreservation of cells and tissues offers a host of benefits to a broad spectrum of fundamental sciences and agricultural and medical industries, but the path to and from -190 degrees Celsius requires a complete and accurate model of the biophysical and biochemical phenomena that occur as cells and tissues are frozen and thawed. (gmu.edu)
Investigations1
- To support their conclusion, the authors cite several investigations that have suggested similar short- to intermediate-term biochemical progression-free survival rates with RP and RT. (cancernetwork.com)
Clinical2
- However, biochemical failure is a -heterogeneous phenomenon and a poor surrogate for clinical endpoints. (cancernetwork.com)
- The clinical and biochemical features of this cohort are described within. (stanford.edu)
Principles1
- New insights into the mechanism of electron bifurcation provide a foundation to establish the unifying principles and essential elements of this fascinating biochemical phenomenon. (usu.edu)
Data1
- By excluding irrelevant data upfront, this biochemical company's AI model avoids a phenomenon known as overfitting . (techtarget.com)
Networks2
- In this work, the focus of attention is placed on the dynamical stability of biochemical networks. (springeropen.com)
- First, we show that stringent requirements of dynamical stability have very little chance to be satisfied in the biochemical networks of sufficiently high order. (springeropen.com)
Research1
- He discusses the value of scaling laws in physics as a means for understanding biochemical phenomena, and he describes the numerous ways that the NIH provides an ideal environment for research. (aip.org)
General1
- Therefore, studying general properties of such large biochemical systems is of primary importance for understanding functionality of the cell. (springeropen.com)
Process1
- The first one places the focus of attention on the fact that many biochemical constituents vitally important for the network functionality may be present only in small quantities within the cell, and therefore the regulatory process is essentially discrete and prone to relatively big fluctuations. (springeropen.com)
Techniques1
- Inhibition of AR signaling in CRPC could be advanced using state-of-the-art biophysical and biochemical techniques. (nih.gov)
Analysis2
- As secondary aims, the study also included measurements of cardiac function and structure by ultrasound and MRI, evaluation of atherosclerosis by ultrasound and MRI, 7 day food intake recordings, detailed ECG analysis, cardiovascular autonomic function, body composition by DXA, DNA analysis and lung function, as well as a number of biochemical markers. (gu.se)
- Logically, such a subdivision serves as a way of compartmentalizing a big biochemical system into relatively independent parts for the simplification of analysis. (springeropen.com)
Force1
- In order to be a stabilizing force, a biochemical "controller" should first be stable itself. (springeropen.com)
Model1
- Therefore, our aECM model system is well suited to unveil the role of biophysical and biochemical determinants of physiologically relevant cell migration phenomena. (nih.gov)
Understand1
- To better understand the interplay of biophysical and biochemical effectors in controlling three-dimensional cell migration, a poly(ethylene glycol)-based aECM platform was used in this study to explore the influence of matrix cross-linking density, represented here by stiffness, on cell migration in vitro and in vivo. (nih.gov)