Domain Interactions Determine the Conformational Ensemble of the Periplasmic Chaperone SurA
This article is protected by copyright. All rights reserved. (Source: Protein Science)
Source: Protein Science - August 3, 2020 Category: Biochemistry Authors: Dagan C. Marx, Mathis J. Leblanc, Ashlee M. Plummer, Susan Krueger, Karen G. Fleming Tags: Article Source Type: research

Doses for experiments with microbeams and microcrystals: Monte Carlo simulations in RADDOSE ‐3D
This article is protected by copyright. All rights reserved. (Source: Protein Science)
Source: Protein Science - July 30, 2020 Category: Biochemistry Authors: Joshua L. Dickerson, Elspeth F. Garman Tags: Tools for Protein Science Source Type: research

The Bio3D Packages for Structural Bioinformatics
This article is protected by copyright. All rights reserved. (Source: Protein Science)
Source: Protein Science - July 30, 2020 Category: Biochemistry Authors: Barry J. Grant, Lars Skj ærven, Xin‐Qiu Yao Tags: Tools for Protein Science Source Type: research

Crystal structure of a GH1 β‐glucosidase from Hamamotoa singularis
This article is protected by copyright. All rights reserved. (Source: Protein Science)
Source: Protein Science - July 26, 2020 Category: Biochemistry Authors: Ryo Uehara, Riki Iwamoto, Sayaka Aoki, Takuya Yoshizawa, Kazufumi Takano, Hiroyoshi Matsumura, Shun ‐ichi Tanaka Tags: Protein Structure Reports Source Type: research

Flying Blind, or Just Flying Under the Radar? The Underappreciated Power of de novo Methods of Mass Spectrometric Peptide Identification
This article is protected by copyright. All rights reserved. (Source: Protein Science)
Source: Protein Science - July 26, 2020 Category: Biochemistry Authors: Isabelle O'Bryon, Sarah C. Jenson, Eric D. Merkley Tags: Review Source Type: research

Structure and function of the juxtamembrane GAF domain of potassium biosensor KdpD
This article is protected by copyright. All rights reserved. (Source: Protein Science)
Source: Protein Science - July 26, 2020 Category: Biochemistry Authors: Shivesh Kumar, Richard E. Gillilan, Dinesh A. Yernool Tags: Protein Structure Reports Source Type: research

Structure ‐guided evolution of Green2 towards photostability and quantum yield enhancement by F145Y substitution
This article is protected by copyright. All rights reserved. (Source: Protein Science)
Source: Protein Science - July 26, 2020 Category: Biochemistry Authors: Tingting Sun, Tianpeng Li, Ke Yi, Xiaolian Gao Tags: Article Source Type: research

Tumorigenic p53 Mutants Undergo Common Structural Disruptions Including Conversion to α‐Sheet Structure
This article is protected by copyright. All rights reserved. (Source: Protein Science)
Source: Protein Science - July 26, 2020 Category: Biochemistry Authors: Dennis Bromley, Valerie Daggett Tags: Article Source Type: research

Using physical features of protein core packing to distinguish real proteins from decoys
This article is protected by copyright. All rights reserved. (Source: Protein Science)
Source: Protein Science - July 25, 2020 Category: Biochemistry Authors: Alex T. Grigas, Zhe Mei, John D. Treado, Zachary A. Levine, Lynne Regan, Corey S. O'Hern Tags: Article Source Type: research

Drivers of recombinant soluble influenza A virus hemagglutinin and neuraminidase expression in mammalian cells
This article is protected by copyright. All rights reserved. (Source: Protein Science)
Source: Protein Science - July 25, 2020 Category: Biochemistry Authors: Roosmarijn Woude, Hannah L. Turner, Ilhan Tomris, Kim M. Bouwman, Andrew B. Ward, Robert P. Vries Tags: Full ‐Length Papers Source Type: research

In This Issue
Protein Science, Volume 29, Issue 8, Page 1697-1697, August 2020. (Source: Protein Science)
Source: Protein Science - July 24, 2020 Category: Biochemistry Tags: In This Issue Source Type: research

Issue information
Protein Science, Volume 29, Issue 8, Page 1693-1696, August 2020. (Source: Protein Science)
Source: Protein Science - July 24, 2020 Category: Biochemistry Tags: Issue information Source Type: research

Cumulative deamidations of the major lens protein γS‐crystallin increase its aggregation during unfolding and oxidation
This article is protected by copyright. All rights reserved. (Source: Protein Science)
Source: Protein Science - July 22, 2020 Category: Biochemistry Authors: Calvin J. Vetter, David C. Thorn, Samuel G. Wheeler, Charlie Mundorff, Kate Halverson, Thomas E. Wales, Ujwal Shinde, John R. Engen, Larry L. David, John A. Carver, Kirsten J. Lampi Tags: Article Source Type: research

A Humanized Antibody Inhibitor for Cathepsin L
This article is protected by copyright. All rights reserved. (Source: Protein Science)
Source: Protein Science - July 19, 2020 Category: Biochemistry Authors: Xiaojing Shi, Yong Zhang Tags: Article Source Type: research

Solution structure of the zinc finger domain of human RNF144A ubiquitin ligase
In this study, the solution structure of RNF144A RING was determined using n uclear magnetic resonance. Moreover, using a metallochromic indicator, we spectrophotometrically determined the stoichiometry of zinc ions and elucidated that RNF144A RING binds two zinc atoms. This structural analysis provided the position and range of the active site of RNF144A RING at the atomic level, which contributes to the creation of artificial RING fingers having the specific ubiquitin‐conjugating enzyme (E2)‐binding capability. (Source: Protein Science)
Source: Protein Science - July 13, 2020 Category: Biochemistry Authors: Kazuhide Miyamoto, Kaori Migita, Kazuki Saito Tags: Protein Structure Reports Source Type: research

Progress toward Alzheimer's disease treatment: Leveraging the Achilles' heel of A β oligomers?
AbstractAfter three decades of false hopes and failures, a pipeline of therapeutic drugs that target the actual root cause of Alzheimer's disease (AD) is now available. Challenging the old paradigm that focused on β‐amyloid peptide (Aβ) aggregation in amyloid plaques, these compounds are designed to prevent the neurotoxicity of Aβ oligomers that form Ca2+ permeable pores in the membranes of brain cells. By triggering an intracellular Ca2+ overdose, A β oligomers induce a cascade of neurotoxic events including oxidative stress, tau hyperphosphorylation, and neuronal loss. Targeting any post‐Ca2+ entr...
Source: Protein Science - July 13, 2020 Category: Biochemistry Authors: Jacques Fantini, Henri Chahinian, Nouara Yahi Tags: Review Source Type: research

Architecture and self ‐assembly of the SARS‐CoV‐2 nucleocapsid protein
This article is protected by copyright. All rights reserved. (Source: Protein Science)
Source: Protein Science - July 12, 2020 Category: Biochemistry Authors: Qiaozhen Ye, Alan M.V. West, Steve Silletti, Kevin D. Corbett Tags: Full ‐Length Papers Source Type: research

Structural Investigation of 2 ‐Naphthyl Phenyl Ether Inhibitors Bound to WT and Y181C Reverse Transcriptase Highlights Key Features of the NNRTI Binding Site
This article is protected by copyright. All rights reserved. (Source: Protein Science)
Source: Protein Science - July 8, 2020 Category: Biochemistry Authors: Vincent N. Duong, Joseph A. Ippolito, Albert H. Chan, Won ‐Gil Lee, Krasimir A. Spasov, William L. Jorgensen, Karen S. Anderson Tags: Article Source Type: research

An allosteric pathway explains beneficial fitness in yeast for long ‐range mutations in an essential TIM barrel enzyme
This article is protected by copyright. All rights reserved. (Source: Protein Science)
Source: Protein Science - July 8, 2020 Category: Biochemistry Authors: Yvonne H. Chan, Konstantin B. Zeldovich, C. Robert Matthews Tags: Article Source Type: research

Discriminating changes in protein structure using tyrosine conjugation
This study demonstrates a new use of tyrosine conjugation using PTAD as an analytic tool able to distinguish the conformational states of a protein. (Source: Protein Science)
Source: Protein Science - July 6, 2020 Category: Biochemistry Authors: Mahta Moinpour, Natalie K. Barker, Lindsay E. Guzman, John C. Jewett, Paul R. Langlais, Jacob C. Schwartz Tags: Article Source Type: research

PyXlinkViewer: A flexible tool for visualization of protein chemical crosslinking data within the PyMOL molecular graphics system
AbstractChemical crosslinking ‐mass spectrometry (XL‐MS) is a valuable technique for gaining insights into protein structure and the organization of macromolecular complexes. XL‐MS data yield inter‐residue restraints that can be compared with high‐resolution structural data. Distances greater than the crosslinker space r‐arm can reveal lowly populated “excited” states of proteins/protein assemblies, or crosslinks can be used as restraints to generate structural models in the absence of structural data. Despite increasing uptake of XL‐MS, there are few tools to enable rapid and facile mapping of XL...
Source: Protein Science - July 3, 2020 Category: Biochemistry Authors: Bob Schiffrin, Sheena E. Radford, David J. Brockwell, Antonio N. Calabrese Tags: TOOLS FOR PROTEIN SCIENCE Source Type: research

Cryo ‐electron microscopy structure of CLHM1 ion channel from Caenorhabditis elegans
AbstractCalcium homeostasis modulators (CALHMs/CLHMs) comprise a family of pore ‐forming protein complexes assembling into voltage‐gated, Ca2+‐sensitive, nonselective channels. These complexes contain an ion‐conduction pore sufficiently wide to permit the passing of ATP molecules serving as neurotransmitters. While their function and structure information is accumulating, the precise mechanisms of these channel complexes remain to be full understood. Here, we present the structure of theCaenorhabditis elegans CLHM1 channel in its open state solved through single ‐particle cryo‐electron microscopy at 3.7‐&Arin...
Source: Protein Science - June 30, 2020 Category: Biochemistry Authors: Weixin Yang, Youwang Wang, Jianli Guo, Lingli He, Ye Zhou, Hui Zheng, Zhenfeng Liu, Ping Zhu, Xuejun C. Zhang Tags: ARTICLE Source Type: research

Homodimerization of a glycoside hydrolase family GH1 β‐glucosidase suggests distinct activity of enzyme different states
This article is protected by copyright. All rights reserved. (Source: Protein Science)
Source: Protein Science - June 29, 2020 Category: Biochemistry Authors: Felipe Akihiro Melo Otsuka, Rafael Siqueira Chagas, Vitor Medeiros Almeida, Sandro Roberto Marana Tags: Article Source Type: research

These motors were made for walking
AbstractKinesins are a diverse group of adenosine triphosphate (ATP) ‐dependent motor proteins that transport cargos along microtubules (MTs) and change the organization of MT networks. Shared among all kinesins is a ~40 kDa motor domain that has evolved an impressive assortment of motility and MT remodeling mechanisms as a result of subtle tweaks and edits withi n its sequence. Several elegant studies of different kinesin isoforms have exposed the purpose of structural changes in the motor domain as it engages and leaves the MT. However, few studies have compared the sequences and MT contacts of these kinesins sy...
Source: Protein Science - June 26, 2020 Category: Biochemistry Authors: Byron Hunter, John S. Allingham Tags: Review Source Type: research

The long form of pVHL is artifactually modified by serine protease inhibitor AEBSF
Abstractvon Hippel –Lindau protein (pVHL) is the tumor suppressor responsible for ubiquitylating the hypoxia‐inducible factor (HIF) family of transcription factors for degradation under normoxic conditions. There are two major pVHL isoforms with the shorter isoform (pVHL19) lacking the acidic domain present in the N ‐terminus of the longer isoform (pVHL30). Although both isoforms can degrade HIF and suppress tumor formation in experimental systems, previous research suggests that pVHL30 can undergo posttranslational modifications (PTM) and interact with unique proteins. Indeed, pVHL30 has long been observed to mi...
Source: Protein Science - June 25, 2020 Category: Biochemistry Authors: Daniel Tarade, Shelley He, Jonathan St ‐Germain, Avi Petroff, Anya Murphy, Brian Raught, Michael Ohh Tags: For The Record Source Type: research

High ‐resolution structures of transient receptor potential vanilloid channels: Unveiling a functionally diverse group of ion channels
AbstractTransient receptor potential vanilloid (TRPV) channels are part of the superfamily of TRP ion channels and play important roles in widespread physiological processes including both neuronal and non ‐neuronal pathways. Various diseases such as skeletal abnormalities, chronic pain, and cancer are associated with dysfunction of a TRPV channel. In order to obtain full understanding of disease pathogenesis and create opportunities for therapeutic intervention, it is essential to unravel how these channels function at a molecular level. In the past decade, incredible progress has been made in biochemical sample prepara...
Source: Protein Science - June 24, 2020 Category: Biochemistry Authors: Mark K. Goor, Leanne Jager, Yifan Cheng, Jenny Wijst Tags: REVIEW Source Type: research

Erratum
Protein Science, Volume 29, Issue 7, Page 1692-1692, July 2020. (Source: Protein Science)
Source: Protein Science - June 24, 2020 Category: Biochemistry Tags: ERRATUM Source Type: research

Issue information
Protein Science, Volume 29, Issue 7, Page 1555-1557, July 2020. (Source: Protein Science)
Source: Protein Science - June 24, 2020 Category: Biochemistry Tags: Issue information Source Type: research

In This Issue
Protein Science, Volume 29, Issue 7, Page 1558-1558, July 2020. (Source: Protein Science)
Source: Protein Science - June 24, 2020 Category: Biochemistry Tags: In This Issue Source Type: research

Chaperone action of a cofactor in protein folding
AbstractPreviously, we have reported that ATP accelerates the folding and unfolding ofEscherichia coli glyceraldehyde ‐3‐phosphate dehydrogenase (GAPDH), which is a glycolytic enzyme utilizing NAD+ as a cofactor. Because ATP and NAD+ share the ADP moiety, we hypothesized that NAD+ also accelerates the folding of GAPDH and that the common structural motif between ATP and NAD+ is responsible for the chaperone activity. After confirming that NAD+ indeed accelerates the folding of GAPDH, we examined the chaperone activity of the structural fragments of NAD+ (ADP, AMP, adenosine, and nicotinamide monophosphate). Our finding...
Source: Protein Science - June 24, 2020 Category: Biochemistry Authors: Chen Chen, Chiwook Park Tags: ARTICLE Source Type: research

High affinity between CREBBP/p300 and NCOA evolved in vertebrates
AbstractThe interaction between the transcriptional coactivators CREBBP/p300 and NCOA is governed by two intrinsically disordered domains called NCBD and CID, respectively. The CID domain emerged within the NCOA protein in deuterostome animals (including vertebrates) after their split from the protostomes (molluscs, worms, and arthropods). However, it has not been clear at which point a high affinity interaction evolved within the deuterostome clade and whether all present ‐day deuterostome animals have a high affinity NCBD:CID interaction. We have here expressed and measured affinity for NCBD and CID domains from animal...
Source: Protein Science - June 24, 2020 Category: Biochemistry Authors: Elin Karlsson, Amanda Lindberg, Eva Andersson, Per Jemth Tags: FOR THE RECORD Source Type: research

X ‐ray crystal structure localizes the mechanism of inhibition of an IL‐36R antagonist monoclonal antibody to interaction with Ig1 and Ig2 extra cellular domains
We report here the molecular structure of a complex between an extracellular portion of human IL‐36R and a Fab derived from a high affinity anti‐IL‐36R neutralizing monoclonal antibody at 2.3 Å resolution. This stru cture, the first of IL‐36R, reveals similarities with other structurally characterized IL‐1R family members and elucidates the molecular determinants leading to the high affinity binding of the monoclonal antibody. The structure of the complex reveals that the epitope recognized by the Fab is re mote from both the putative ligand and accessory protein binding interfaces on IL‐36R, suggesting t...
Source: Protein Science - June 24, 2020 Category: Biochemistry Authors: Eric T. Larson, Debra L. Brennan, Eugene R. Hickey, Raj Ganesan, Rachel Kroe ‐Barrett, Neil A. Farrow Tags: PROTEIN STRUCTURE REPORTS Source Type: research

Structural and chemical trapping of flavin ‐oxide intermediates reveals substrate‐directed reaction multiplicity
AbstractThough reactive flavin ‐N5/C4α‐oxide intermediates can be spectroscopically profiled for some flavin‐assisted enzymatic reactions, their exact chemical configurations are hardly visualized. Structural systems biology and stable isotopic labelling techniques were exploited to correct this stereotypical view. Three t ransition‐like complexes, the α‐ketoacid…N5‐FMNox complex (I), the FMNox‐N5‐aloxyl‐C′α−‐C4α+ zwitterion (II), and the FMN ‐N5‐ethenol‐N5‐C4α‐epoxide (III), were determined from mandelate oxidase (Hmo) or its mutant Y128F (mono...
Source: Protein Science - June 24, 2020 Category: Biochemistry Authors: Kuan ‐Hung Lin, Syue‐Yi Lyu, Hsien‐Wei Yeh, Yi‐Shan Li, Ning‐Shian Hsu, Chun‐Man Huang, Yung‐Lin Wang, Hao‐Wei Shih, Zhe‐Chong Wang, Chang‐Jer Wu, Tsung‐Lin Li Tags: ARTICLE Source Type: research

Deuteration of nonexchangeable protons on proteins affects their thermal stability, side ‐chain dynamics, and hydrophobicity
AbstractWe have investigated the effect of deuteration of non ‐exchangeable protons on protein global thermal stability, hydrophobicity, and local flexibility using well‐known thermostable model systems such as the villin headpiece subdomain (HP36) and the third immunoglobulin G‐binding domain of protein G (GB3). Reversed‐phase high‐performance liqui d chromatography (RP‐HPLC) measurements as a function of temperature probe global thermal stability in the presence of acetonitrile, while differential scanning calorimetry determines thermal stability in solution. Both indicate small but measurable changes in the ...
Source: Protein Science - June 24, 2020 Category: Biochemistry Authors: Parker J. Nichols, Isaac Falconer, Aaron Griffin, Colin Mant, Robert Hodges, Christopher J. McKnight, Beat V ögeli, Liliya Vugmeyster Tags: ARTICLE Source Type: research

Oligomerization of a symmetric β‐trefoil protein in response to folding nucleus perturbation
We describe the targeted mutation of the carboxyl ‐terminal region of the (internally located) FN of the de novo designed purely‐symmetric β‐trefoil protein Symfoil‐4P. This mutation involves wholesale replacement of a repeating trefoil‐fold motif with a “blade” motif from a β‐propeller protein, and postulated to trap that region of the Symfoil‐4P FN in a nonproductive folding intermediate. The resulting protein (termed “Bladefoil”) is shown to be cooperatively folding, but as a trimeric oligomer. The results illustrate how symmetric protein architectures have potentially div...
Source: Protein Science - June 24, 2020 Category: Biochemistry Authors: Connie A. Tenorio, Joseph B. Parker, Michael Blaber Tags: ARTICLE Source Type: research

Comparison of metal ‐bound and unbound structures of aminopeptidase B proteins from Escherichia coli and Yersinia pestis
AbstractProtein degradation by aminopeptidases is involved in bacterial responses to stress.Escherichia coli produces two metal ‐dependent M17 family leucine aminopeptidases (LAPs), aminopeptidase A (PepA) and aminopeptidase B (PepB). Several structures have been solved for PepA as well as other bacterial M17 peptidases. Herein, we report the first structures of a PepB M17 peptidase. TheE. coli PepB protein structure was determined at a resolution of 2.05 and 2.6 Å. One structure has both Zn2+ and Mn2+, while the second structure has two Zn2+ ions bound to the active site. A 2.75  Å apo structure is al...
Source: Protein Science - June 24, 2020 Category: Biochemistry Authors: George Minasov, Matthew R. Lam, Monica Rosas ‐Lemus, Joanna Sławek, Magdalena Woinska, Ivan G. Shabalin, Ludmilla Shuvalova, Bernhard Ø. Palsson, Adam Godzik, Wladek Minor, Karla J. F. Satchell Tags: FULL ‐LENGTH PAPERS Source Type: research

Two fatty acid ‐binding proteins expressed in the intestine interact differently with endocannabinoids
AbstractTwo different members of the fatty acid ‐binding protein (FABP) family are found in enterocyte cells of the gastrointestinal system, namely liver‐type and intestinal fatty acid‐binding proteins (LFABP and IFABP, also called FABP1 and FABP2, respectively). Striking phenotypic differences have been observed in knockout mice for either protein, for example, high fat‐fed IFABP‐null mice remained lean, whereas LFABP‐null mice were obese, correlating with differences in food intake. This finding prompted us to investigate the role each protein plays in directing the specificity of binding to ligands involved ...
Source: Protein Science - June 24, 2020 Category: Biochemistry Authors: May Poh Lai, Francine S. Katz, C édric Bernard, Judith Storch, Ruth E. Stark Tags: ARTICLE Source Type: research

Crystal structure of Nsp15 endoribonuclease NendoU from SARS ‐CoV‐2
AbstractSevere Acute Respiratory Syndrome coronavirus 2 (SARS ‐CoV‐2) is rapidly spreading around the world. There is no existing vaccine or proven drug to prevent infections and stop virus proliferation. Although this virus is similar to human and animal SARS‐CoVs and Middle East Respiratory Syndrome coronavirus (MERS‐CoVs), the detailed information a bout SARS‐CoV‐2 proteins structures and functions is urgently needed to rapidly develop effective vaccines, antibodies, and antivirals. We applied high‐throughput protein production and structure determination pipeline at the Center for Structural Genomics of I...
Source: Protein Science - June 24, 2020 Category: Biochemistry Authors: Youngchang Kim, Robert Jedrzejczak, Natalia I. Maltseva, Mateusz Wilamowski, Michael Endres, Adam Godzik, Karolina Michalska, Andrzej Joachimiak Tags: ARTICLE Source Type: research

Erratum
Protein Science, Volume 29, Issue 7, Page 1692-1692, July 2020. (Source: Protein Science)
Source: Protein Science - June 24, 2020 Category: Biochemistry Tags: ERRATUM Source Type: research

Issue information
Protein Science, Volume 29, Issue 7, Page 1555-1557, July 2020. (Source: Protein Science)
Source: Protein Science - June 24, 2020 Category: Biochemistry Tags: Issue information Source Type: research

In This Issue
Protein Science, Volume 29, Issue 7, Page 1558-1558, July 2020. (Source: Protein Science)
Source: Protein Science - June 24, 2020 Category: Biochemistry Tags: In This Issue Source Type: research

Harnessing Synthetic Biology to Enhance Heterologous Protein Expression
This article is protected by copyright. All rights reserved. (Source: Protein Science)
Source: Protein Science - June 22, 2020 Category: Biochemistry Authors: Shlomo Zarzhitsky, Alex Jiang, Elizabeth Stanley, Michael Hecht Tags: Accelerated Communication Source Type: research

Progress toward Alzheimer's disease treatment: Leveraging the Achilles ’ heel of Aβ oligomers ?
This article is protected by copyright. All rights reserved. (Source: Protein Science)
Source: Protein Science - June 21, 2020 Category: Biochemistry Authors: Jacques Fantini, Henri Chahinian, Nouara Yahi Tags: Review Source Type: research

A mechanistic view of enzyme evolution
This article is protected by copyright. All rights reserved. (Source: Protein Science)
Source: Protein Science - June 19, 2020 Category: Biochemistry Authors: Gloria Yang, Charlotte Miton, Nobuhiko Tokuriki Tags: Review Source Type: research