Abstract:
:Plots of free energy versus temperature are commonly called stability curves or Gibbs-Helmholtz curves, and they have proven to be extremely useful in protein folding and ligand-binding studies. Curvature in a Gibbs-Helmholtz or stability plot is indicative of a heat capacity change, and some of their primary uses in biochemistry over the past few decades have included determining ΔCp values and comparing ΔCp values between two related processes. This chapter describes basic approaches for analyzing curved Gibbs-Helmholtz plots, along with two specific extensions of standard Gibbs-Helmholtz plot analysis: (1) translating ΔG of folding versus temperature into ΔH and ΔS versus temperature for comparing mesophilic-thermophilic protein pairs, and (2) fitting Gibbs-Helmholtz plots to determine if ΔCp changes with temperature or not. Neither of these extensions is new, but they are infrequently used, and their use is particularly germane to certain molecular interpretations of thermodynamic information from ΔG versus temperature curves. It is shown that translating ΔG of folding into ΔH and ΔS of folding versus temperature for a mesophilic-thermophilic protein pair can immediately influence possible structural hypotheses for thermal stabilization of thermophilic proteins. It is also shown that very small temperature-dependent heat capacity changes (ΔΔCp values) can be obtained from extended fits to ΔG versus temperature plots, and that these very small ΔΔCp values can have serious consequences for any attempt to correlate ΔCp with ΔASA for some reactions.
journal_name
Methods Enzymoljournal_title
Methods in enzymologyauthors
LiCata VJ,Liu CCdoi
10.1016/B978-0-12-381268-1.00009-4subject
Has Abstractpub_date
2011-01-01 00:00:00pages
219-38eissn
0076-6879issn
1557-7988pii
B978-0-12-381268-1.00009-4journal_volume
488pub_type
杂志文章abstract::Apical caspases 8, 9, and 10 are only active as dimers. These dimers are unstable, and to characterize their activity they need to be maintained in vitro in a dimeric state. We provide updated methods for those looking to characterize various aspects of caspase function. We describe full methods for those looking to a...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/B978-0-12-417158-9.00007-8
更新日期:2014-01-01 00:00:00
abstract::Protein kinases transfer a phosphoryl group from ATP onto target proteins and play a critical role in signal transduction and other cellular processes. Here, we review the kinase kinetic and chemical mechanisms and their application in understanding kinase structure and function. Aberrant kinase activity has been impl...
journal_title:Methods in enzymology
pub_type: 杂志文章,评审
doi:10.1016/B978-0-12-397918-6.00001-X
更新日期:2014-01-01 00:00:00
abstract::The recalcitrance of the cell wall to enzymatic hydrolysis represents one of the greatest challenges for using biomass to replace the petroleum as a feedstock for fuels and chemicals. Cell walls are complex in architecture and composition, posing a biochemical challenge for the development of efficient enzymes to rele...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/B978-0-12-415931-0.00003-3
更新日期:2012-01-01 00:00:00
abstract::In eukaryotes, translation initiation involves recruitment of ribosomal subunits at either the 5' m7G cap structure or at an internal ribosome entry site (IRES). For most mRNAs, the initiation codon is located some distance downstream, necessitating ribosomal movement to this site. Although the mechanistic details of ...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/S0076-6879(07)29015-9
更新日期:2007-01-01 00:00:00
abstract::The qualitative detection, quantification, and structural characterization of analytes in biological systems are important requirements for objectives to be fulfilled in systems biology research. One analytical tool applied to a multitude of systems biology studies is mass spectrometry, particularly for the study of p...
journal_title:Methods in enzymology
pub_type: 杂志文章,评审
doi:10.1016/B978-0-12-385118-5.00002-5
更新日期:2011-01-01 00:00:00
abstract::Staphylococcus aureus is a Gram-positive major human pathogen involved in a wide range of human infectious diseases (from minor skin infections to septicemia, endocarditis or toxic shock syndrome). The treatment of S. aureus infections is very challenging due to the emergence of multiple antibiotic-resistant isolates....
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/bs.mie.2018.08.022
更新日期:2018-01-01 00:00:00
abstract::The combined use of rotating-frame relaxation methods, temperature-dependent measurements of line shapes and magnetization transfer experiments allows in favorable cases the examination in some detail of exchange processes that occur on the millisecond time scale. It is possible to determine not only the rate constant...
journal_title:Methods in enzymology
pub_type: 杂志文章,评审
doi:10.1016/s0076-6879(94)39023-1
更新日期:1994-01-01 00:00:00
abstract::We describe the methodologies for the design of artificial enzymes with genetically encoded unnatural amino acids. Genetically encoded unnatural amino acids offer great promise for constructing artificial enzymes with novel activities. In our studies, the designs of artificial enzyme were divided into two steps. First...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/bs.mie.2016.06.005
更新日期:2016-01-01 00:00:00
abstract::Structural approaches have provided insight into the mechanisms of circadian clock oscillators. This review focuses upon the myriad structural methods that have been applied to the molecular architecture of cyanobacterial circadian proteins, their interactions with each other, and the mechanism of the KaiABC posttrans...
journal_title:Methods in enzymology
pub_type: 杂志文章,评审
doi:10.1016/bs.mie.2014.10.004
更新日期:2015-01-01 00:00:00
abstract::A significant proportion of RNA decay in eukaryotes takes place in the nucleus. In addition to targeting nongenic RNAs such as products of processing and spurious transcription events, nuclear RNA decay also removes aberrant transcripts from regular genes. Moreover, a small list of genes utilizes nuclear RNA turnover ...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/S0076-6879(08)02410-5
更新日期:2008-01-01 00:00:00
abstract::Chemokines are essential mediators of leukocyte movement in vivo. In vitro assays of leukocyte migration cannot mimic the complex interactions with other cell types and matrix needed for cells to extravasate and migrate into tissues. Therefore, in vivo strategies to study the effects and potential relevance of chemoki...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/bs.mie.2015.09.015
更新日期:2016-01-01 00:00:00
abstract::Molecular mechanisms of dark-to-light state transitions in flavoprotein photoreceptors have been the subject of intense investigation. Blue-light sensing flavoproteins fall into three general classes that share aspects of their activation processes: LOV domains, BLUF proteins, and cryptochromes. In all cases, light-in...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/bs.mie.2019.03.023
更新日期:2019-01-01 00:00:00
abstract::Inducible expression systems represent the founding technology for the emergence of synthetic biology in mammalian cells. The core molecules in these systems are bacterial regulator proteins that bind to or dissociate from a cognate DNA operator sequence in response to an exogenous stimulus like a small-molecule induc...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/B978-0-12-385075-1.00011-1
更新日期:2011-01-01 00:00:00
abstract::Human embryonic stem cells (hESCs) are derived from preimplantation embryos. Approximately 60% of human embryos are blocked during in vitro development. Although statistics are inconclusive, experience demonstrates that hESCs are more effectively derived from high-quality embryos. In this way, optimal human embryo cul...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/S0076-6879(06)20001-6
更新日期:2006-01-01 00:00:00
abstract::Enveloped virus particles select their lipid-protein components and egress by budding from the host cell membranes. The matrix protein of many enveloped viruses has been proposed as a crucial element for viral budding; however, molecular mechanisms behind membrane remodeling by the matrix protein are yet to be unravel...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/S0076-6879(09)64004-0
更新日期:2009-01-01 00:00:00
abstract::Isotopic enrichment of biomacromolecules is a widely used technique that enables the investigation of the structural and dynamic properties to provide information not accessible with natural abundance isotopic composition. This study reports an approach for deuterium incorporation into bacterial cellulose. A media for...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/bs.mie.2015.08.031
更新日期:2015-01-01 00:00:00
abstract::Complex RNA structures regulate many biological processes but are often too large for structure determination by nuclear magnetic resonance (NMR) methods. We determined the solution structure of domain II of the hepatitis C viral internal ribosome entry site (HCV IRES), a 25-kDa RNA, using a novel NMR approach. Conven...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/S0076-6879(05)94016-0
更新日期:2005-01-01 00:00:00
abstract::The lung is composed of two major anatomically distinct regions-the conducting airways and gas-exchanging airspaces. From a cell biology standpoint, the conducting airways can be further divided into two major compartments, the tracheobronchial and bronchiolar airways, while the alveolar regions of the lung make up th...
journal_title:Methods in enzymology
pub_type: 杂志文章,评审
doi:10.1016/S0076-6879(06)19012-6
更新日期:2006-01-01 00:00:00
abstract::Gene regulatory grids (GRGs) encompass the space of all the possible transcription factor (TF)-target gene interactions that regulate gene expression, with gene regulatory networks (GRNs) representing a temporal and spatial manifestation of a portion of the GRG, essential for the specification of gene expression. Thus...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/bs.mie.2016.03.003
更新日期:2016-01-01 00:00:00
abstract::Membrane-initiated steroid signaling (MISS) involves rapid second messenger based intracellular signaling without coupling to transcription or translation. MISS activates important cellular signaling cascades such as mitogen-activated protein kinase (MAPK) or adenylate cyclase pathways. Despite its vital role in signa...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/bs.mie.2020.02.018
更新日期:2020-01-01 00:00:00
abstract::Complex I is the major entry point in the bacterial and mitochondrial respiratory chain. Structural knowledge of the enzyme is still limited because of its large size and complicated architecture. Only the structure of the hydrophilic domain of a bacterial Complex I has been solved to high resolution by X-ray crystall...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/S0076-6879(08)04401-7
更新日期:2009-01-01 00:00:00
abstract::Crystallographic studies on flavodiiron proteins (FDPs) have revealed that the common sequence core ( approximately 400 residues) that defines this protein family comprises two structural domains. The N-terminal domain (of approximately 250 residues) displays a metallo-beta-lactamase-like-fold, being indeed structural...
journal_title:Methods in enzymology
pub_type: 杂志文章,评审
doi:10.1016/S0076-6879(07)37001-8
更新日期:2008-01-01 00:00:00
abstract::Ecological samples of fungal associations pose particular challenges for nucleic acid extraction due to the presence of several genomes. Thorough examination of the samples prior to extraction is important to assess the risks of contamination. If manual separation of symbionts or their axenic cultivation is not feasib...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/S0076-6879(05)95004-0
更新日期:2005-01-01 00:00:00
abstract::The above methodology has been used to prepare a variety of PE-immunotoxins. These reagents are potent cytotoxic agents for cells in culture that bind the appropriate antibody and nontoxic when cells do not bind the antibody. PE-immunotoxins can be used to select for mutant cultured cells which lack the target of the ...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/s0076-6879(87)51015-1
更新日期:1987-01-01 00:00:00
abstract::The aminocoumarin antibiotics novobiocin, clorobiocin and coumermycin A(1) are formed by different Streptomyces strains and are potent inhibitors of bacterial gyrase. Their biosynthetic gene clusters have been analyzed in detail by genetic and biochemical investigations. Heterologous expression of these gene clusters ...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/S0076-6879(09)04618-7
更新日期:2009-01-01 00:00:00
abstract::The method presented here is intended as a compromise between finding a good overall alignment and the time taken to do so. Many multiple alignment algorithms spend an excessively large amount of effort trying to find the best global alignment. This time is often ill spent because the results of the standard dynamic p...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/0076-6879(90)83031-4
更新日期:1990-01-01 00:00:00
abstract::Autophagy is a catabolic process that is crucial for cellular homeostasis and adaptive response to changing environments. Importantly, autophagy has been shown to be induced in many longevity-associated scenarios and to be required to maintain lifespan extension. Notably, autophagy is a highly conserved cellular proce...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/bs.mie.2016.09.086
更新日期:2017-01-01 00:00:00
abstract::Nonnative protein aggregation has been classically treated as an amorphous process occurring by colloidal coagulation kinetics and proceeding to an essentially irreversible endpoint often ascribed to a chaotic tangle of unfolded chains. However, some nonnative aggregates, particularly amyloid fibrils, exhibit ordered ...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/S0076-6879(06)13003-7
更新日期:2006-01-01 00:00:00
abstract::Although many players of the DNA damage response and DNA repair have been identified in several systems their biochemical role is still poorly understood. The use of the Xenopus laevis egg extract cell-free system allowed biochemical dissection of DNA replication and cell cycle events in a complex biological context. ...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/bs.mie.2017.03.018
更新日期:2017-01-01 00:00:00
abstract::Interactions between chemokines and glycosaminoglycans (GAGs) are crucial for the physiological and pathophysiological activities of chemokines. GAGs are therefore commonly designated as chemokine coreceptors which are deeply involved in the chemokine-signaling network. Studying the interaction of chemokines with GAGs...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/bs.mie.2015.09.018
更新日期:2016-01-01 00:00:00