Analysis of Tandem Repeat Protein Folding Using Nearest-Neighbor Models

2021 ◽  
Vol 50 (1) ◽  
Author(s):  
Mark Petersen ◽  
Doug Barrick
Keyword(s):  
Protein Folding ◽  
Tandem Repeat ◽  
Nearest Neighbor ◽  
Experimental System ◽  
Structural Features ◽  
Internal Symmetry ◽  
Statistical Thermodynamic ◽  
Annual Review ◽  
Publication Date ◽  
Repeat Proteins

Cooperativity is a hallmark of protein folding, but the thermodynamic origins of cooperativity are difficult to quantify. Tandem repeat proteins provide a unique experimental system to quantify cooperativity due to their internal symmetry and their tolerance of deletion, extension, and in some cases fragmentation into single repeats. Analysis of repeat proteins of different lengths with nearest-neighbor Ising models provides values for repeat folding (ΔGi) and inter-repeat coupling (Δ Gi-1, i). In this article, we review the architecture of repeat proteins and classify them in terms of Δ Gi and Δ Gi-1, i; this classification scheme groups repeat proteins according to their degree of cooperativity. We then present various statistical thermodynamic models, based on the 1D-Ising model, for analysis of different classes of repeat proteins. We use these models to analyze data for highly and moderately cooperative and noncooperative repeat proteins and relate their fitted parameters to overall structural features. Expected final online publication date for the Annual Review of Biophysics, Volume 50 is May 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Cold Shock Response in Bacteria

2021 ◽  
Vol 55 (1) ◽  
Author(s):  
Yan Zhang ◽  
Carol A. Gross
Keyword(s):  
Protein Folding ◽  
Cold Shock ◽  
Temperature Drop ◽  
Protein Translation ◽  
Annual Review ◽  
Publication Date ◽  
Molecular Response ◽  
Natural Habitats ◽  
Cold Shock Response ◽  
Shock Response

Bacteria often encounter temperature fluctuations in their natural habitats and must adapt to survive. The molecular response of bacteria to sudden temperature upshift or downshift is termed the heat shock response (HSR) or the cold shock response (CSR), respectively. Unlike the HSR, which activates a dedicated transcription factor that predominantly copes with heat-induced protein folding stress, the CSR is mediated by a diverse set of inputs. This review provides a picture of our current understanding of the CSR across bacteria. The fundamental aspects of CSR involved in sensing and adapting to temperature drop, including regulation of membrane fluidity, protein folding, DNA topology, RNA metabolism, and protein translation, are discussed. Special emphasis is placed on recent findings of a CSR circuitry in Escherichia coli mediated by cold shock family proteins and RNase R that monitors and modulates messenger RNA structure to facilitate global translation recovery during acclimation. Expected final online publication date for the Annual Review of Genetics, Volume 55 is November 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

scholarly journals Synonymous but not Silent: The Codon Usage Code for Gene Expression and Protein Folding

2021 ◽  
Vol 90 (1) ◽  
Author(s):  
Yi Liu ◽  
Qian Yang ◽  
Fangzhou Zhao
Keyword(s):  
Gene Expression ◽  
Protein Folding ◽  
Codon Usage ◽  
Protein Structures ◽  
Large Body ◽  
Annual Review ◽  
Publication Date ◽  
Translation Efficiency ◽  
Mrna Levels ◽  
Synonymous Mutations

Codon usage bias, the preference for certain synonymous codons, is found in all genomes. Although synonymous mutations were previously thought to be silent, a large body of evidence has demonstrated that codon usage can play major roles in determining gene expression levels and protein structures. Codon usage influences translation elongation speed and regulates translation efficiency and accuracy. Adaptation of codon usage to tRNA expression determines the proteome landscape. In addition, codon usage biases result in nonuniform ribosome decoding rates on mRNAs, which in turn influence the cotranslational protein folding process that is critical for protein function in diverse biological processes. Conserved genome-wide correlations have also been found between codon usage and protein structures. Furthermore, codon usage is a major determinant of mRNA levels through translation-dependent effects on mRNA decay and translation-independent effects on transcriptional and posttranscriptional processes. Here, we discuss the multifaceted roles and mechanisms of codon usage in different gene regulatory processes. Expected final online publication date for the Annual Review of Biochemistry, Volume 90 is June 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Dynamics of Ecological Communities Following Current Retreat of Glaciers

2021 ◽  
Vol 52 (1) ◽  
Author(s):  
Gentile Francesco Ficetola ◽  
Silvio Marta ◽  
Alessia Guerrieri ◽  
Mauro Gobbi ◽  
Roberto Ambrosini ◽  
...  
Keyword(s):  
Community Dynamics ◽  
Abiotic Factors ◽  
Empirical Studies ◽  
Experimental System ◽  
Theoretical Models ◽  
Glacier Retreat ◽  
Community Formation ◽  
Annual Review ◽  
Publication Date ◽  
Ecological Communities

Glaciers are retreating globally, and the resulting ice-free areas provide an experimental system for understanding species colonization patterns, community formation, and dynamics. The last several years have seen crucial advances in our understanding of biotic colonization after glacier retreats, resulting from the integration of methodological innovations and ecological theories. Recent empirical studies have demonstrated how multiple factors can speed up or slow down the velocity of colonization and have helped scientists develop theoretical models that describe spatiotemporal changes in community structure. There is a growing awareness of how different processes (e.g., time since glacier retreat, onset or interruption of surface processes, abiotic factors, dispersal, biotic interactions) interact to shape community formation and, ultimately, their functional structure through succession. Here, we examine how these studies address key theoretical questions about community dynamics and show how classical approaches are increasingly being combined with environmental DNA metabarcoding and functional trait analysis to document the formation of multitrophic communities, revolutionizing our understanding of the biotic processes that occur following glacier retreat. Expected final online publication date for the Annual Review of Ecology, Evolution, and Systematics, Volume 52 is November 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Protein Structure Prediction with Mass Spectrometry Data

2021 ◽  
Vol 73 (1) ◽  
Author(s):  
Sarah E. Biehn ◽  
Steffen Lindert
Keyword(s):  
Mass Spectrometry ◽  
Protein Structure ◽  
Protein Structure Prediction ◽  
Structure Prediction ◽  
Limited Proteolysis ◽  
Structural Features ◽  
Mass Spectrometry Data ◽  
Computational Techniques ◽  
Annual Review ◽  
Publication Date

Knowledge of protein structure is crucial to our understanding of biological function and is routinely used in drug discovery. High-resolution techniques to determine the three-dimensional atomic coordinates of proteins are available. However, such methods are frequently limited by experimental challenges such as sample quantity, target size, and efficiency. Structural mass spectrometry (MS) is a technique in which structural features of proteins are elucidated quickly and relatively easily. Computational techniques that convert sparse MS data into protein models that demonstrate agreement with the data are needed. This review features cutting-edge computational methods that predict protein structure from MS data such as chemical cross-linking, hydrogen–deuterium exchange, hydroxyl radical protein footprinting, limited proteolysis, ion mobility, and surface-induced dissociation. Additionally, we address future directions for protein structure prediction with sparse MS data. Expected final online publication date for the Annual Review of Physical Chemistry, Volume 73 is April 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Chaperonin Mechanisms: Multiple and (Mis)Understood?

2022 ◽  
Vol 51 (1) ◽  
Author(s):  
Amnon Horovitz ◽  
Tali Haviv Reingewertz ◽  
Jorge Cuéllar ◽  
José María Valpuesta
Keyword(s):  
Escherichia Coli ◽  
Protein Folding ◽  
Reaction Mechanism ◽  
Reaction Mechanisms ◽  
Online Publication ◽  
Annual Review ◽  
Folding Pathway ◽  
Publication Date ◽  
T Complex ◽  
Key Aspects

The chaperonins are ubiquitous and essential nanomachines that assist in protein folding in an ATP-driven manner. They consist of two back-to-back stacked oligomeric rings with cavities in which protein (un)folding can take place in a shielding environment. This review focuses on GroEL from Escherichia coli and the eukaryotic chaperonin-containing t-complex polypeptide 1, which differ considerably in their reaction mechanisms despite sharing a similar overall architecture. Although chaperonins feature in many current biochemistry textbooks after being studied intensively for more than three decades, key aspects of their reaction mechanisms remain under debate and are discussed in this review. In particular, it is unclear whether a universal reaction mechanism operates for all substrates and whether it is passive, i.e., aggregation is prevented but the folding pathway is unaltered, or active. It is also unclear how chaperonin clients are distinguished from nonclients and what are the precise roles of the cofactors with which chaperonins interact. Expected final online publication date for the Annual Review of Biophysics, Volume 51 is May 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Materials Properties, Oral Processing, and Sensory Analysis of Eating Meat and Meat Analogs

2021 ◽  
Vol 13 (1) ◽  
Author(s):  
Jovan Ilić ◽  
Ilija Djekic ◽  
Igor Tomasevic ◽  
Filip Oosterlinck ◽  
Marco A. van den Berg
Keyword(s):  
Sensory Perception ◽  
Holistic Approach ◽  
Structural Features ◽  
Annual Review ◽  
Food Science ◽  
Publication Date ◽  
Eating Meat ◽  
Oral Processing ◽  
Number Of Publications ◽  
Made In

To increase the appeal of plant protein–based meat analogs, further progress needs to be made in their sensory perception. Given the limited number of studies on meat analogs, this review focuses on structure, oral processing, and sensory perception of meat and subsequently translates the insights to meat analogs. An extensive number of publications has built the current understanding of meat mechanical and structural properties, but inconsistencies concerning terminology and methodology execution as well as the wide variety in terms of natural origin limit solid conclusions about the control parameters for oral processing and sensory perception. Consumer-relevant textural aspects such as tenderness and juiciness are not directly correlated to single structural features but depend on an interplay of multiple factors and thus require a holistic approach. We discuss the differences in mastication and disintegration of meat and meat analogs and provide an outlook toward converting skeptical consumers into returning customers. Expected final online publication date for the Annual Review of Food Science and Technology, Volume 13 is March 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

scholarly journals It's Better To Be Lucky Than Smart

2021 ◽  
Vol 90 (1) ◽  
Author(s):  
H.R. Kaback
Keyword(s):  
Energy Source ◽  
Active Transport ◽  
Experimental System ◽  
Membrane Vesicles ◽  
Solute Concentration ◽  
Annual Review ◽  
Publication Date ◽  
Experimental Conditions ◽  
Intact Cells ◽  
Transport Vesicles

Bacterial cytoplasmic membrane vesicles provide a unique experimental system for studying active transport. Vesicles are prepared by lysis of osmotically sensitized cells (i.e., protoplasts or spheroplasts) and comprise osmotically intact, unit-membrane-bound sacs that are approximately 0.5–1.0 μm in diameter and devoid of internal structure. Their metabolic activities are restricted to those provided by the enzymes of the membrane itself, and each vesicle is functional. The energy source for accumulation of a particular substrate can be determined by studying which compounds or experimental conditions drive solute accumulation, and metabolic conversion of the transported substrate or the energy source is minimal. These properties of the vesicle system constitute a considerable advantage over intact cells, as the system provides clear definition of the reactions involved in the transport process. This discussion is not intended as a general review but is concerned with respiration-dependent active transport in membrane vesicles from Escherichia coli. Emphasis is placed on experimental observations demonstrating that respiratory energy is converted primarily into work in the form of a solute concentration gradient that is driven by a proton electrochemical gradient, as postulated by the chemiosmotic theory of Peter Mitchell. Expected final online publication date for the Annual Review of Biochemistry, Volume 90 is June 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Endogenous Retroviruses Drive Resistance and Promotion of Exogenous Retroviral Homologs

2020 ◽  
Vol 9 (1) ◽  
Author(s):  
Elliott S. Chiu ◽  
Sue VandeWoude
Keyword(s):  
Immune Modulation ◽  
Viral Infections ◽  
Viral Evolution ◽  
Endogenous Retroviruses ◽  
Annual Review ◽  
Publication Date ◽  
Biological Functions ◽  
Self Tolerance ◽  
Vertebrate Hosts ◽  
Insight Into

Endogenous retroviruses (ERVs) serve as markers of ancient viral infections and provide invaluable insight into host and viral evolution. ERVs have been exapted to assist in performing basic biological functions, including placentation, immune modulation, and oncogenesis. A subset of ERVs share high nucleotide similarity to circulating horizontally transmitted exogenous retrovirus (XRV) progenitors. In these cases, ERV–XRV interactions have been documented and include ( a) recombination to result in ERV–XRV chimeras, ( b) ERV induction of immune self-tolerance to XRV antigens, ( c) ERV antigen interference with XRV receptor binding, and ( d) interactions resulting in both enhancement and restriction of XRV infections. Whereas the mechanisms governing recombination and immune self-tolerance have been partially determined, enhancement and restriction of XRV infection are virus specific and only partially understood. This review summarizes interactions between six unique ERV–XRV pairs, highlighting important ERV biological functions and potential evolutionary histories in vertebrate hosts. Expected final online publication date for the Annual Review of Animal Biosciences, Volume 9 is February 16, 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Advancing Socioeconomic Rights Through Interdisciplinary Factfinding: Opportunities and Challenges

2021 ◽  
Vol 17 (1) ◽  
Author(s):  
Sarah Knuckey ◽  
Joshua D. Fisher ◽  
Amanda M. Klasing ◽  
Tess Russo ◽  
Margaret L. Satterthwaite
Keyword(s):  
Human Rights ◽  
Mixed Methods ◽  
Social Science ◽  
Science Volume ◽  
Lessons Learned ◽  
Limited Resources ◽  
Annual Review ◽  
Publication Date ◽  
Socioeconomic Rights ◽  
Human Rights Movement

The human rights movement is increasingly using interdisciplinary, multidisciplinary, mixed-methods, and quantitative factfinding. There has been too little analysis of these shifts. This article examines some of the opportunities and challenges of these methods, focusing on the investigation of socioeconomic human rights. By potentially expanding the amount and types of evidence available, factfinding's accuracy and persuasiveness can be strengthened, bolstering rights claims. However, such methods can also present significant challenges and may pose risks in individual cases and to the human rights movement generally. Interdisciplinary methods can be costly in human, financial, and technical resources; are sometimes challenging to implement; may divert limited resources from other work; can reify inequalities; may produce “expertise” that disempowers rightsholders; and could raise investigation standards to an infeasible or counterproductive level. This article includes lessons learned and questions to guide researchers and human rights advocates considering mixed-methods human rights factfinding. Expected final online publication date for the Annual Review of Law and Social Science, Volume 17 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Conversation and Culture

2021 ◽  
Vol 50 (1) ◽  
Author(s):  
Simeon Floyd
Keyword(s):  
Conversation Analysis ◽  
Quantitative Methods ◽  
Sequential Analysis ◽  
Contemporary Literature ◽  
Annual Review ◽  
Publication Date ◽  
Face To Face ◽  
Qualitative And Quantitative Methods ◽  
Language Studies ◽  
Speech Communities

Conversation analysis is a method for the systematic study of interaction in terms of a sequential turn-taking system. Research in conversation analysis has traditionally focused on speakers of English, and it is still unclear to what extent the system observed in that research applies to conversation more generally around the world. However, as this method is now being applied to conversation in a broader range of languages, it is increasingly possible to address questions about the nature of interactional diversity across different speech communities. The approach of pragmatic typology first applies sequential analysis to conversation from different speech communities and then compares interactional patterns in ways analogous to how traditional linguistic typology compares morphosyntax. This article discusses contemporary literature in pragmatic typology, including single-language studies and multilanguage comparisons reflecting both qualitative and quantitative methods. This research finds that microanalysis of face-to-face interaction can identify both universal trends and culture-specific interactional tendencies. Expected final online publication date for the Annual Review of Anthropology, Volume 50 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

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