Specific features of a scaffolding antibody light chain
AbstractThe antigen-binding sites in conventional antibodies are formed by hypervariable complementarity-determining regions (CDRs) from both heavy chains (HCs) and light chains (LCs). A deviation from this paradigm is found in a subset of bovine antibodies that bind antigens via an ultra-long CDR. The HCs bearing ultra-long CDRs pair with a restricted set of highly conserved LCs that convey stability to the antibody. Despite the importance of these LCs, their specific features remained unknown. Here, we show that the conserved bovine LC found in antibodies with ultra-long CDRs exhibits a distinct combination of favorable ...
Source: Protein Science - April 13, 2024 Category: Biochemistry Authors: Johanna Trommer,
Florian Lesniowski,
Johannes Buchner,
Hristo L. Svilenov Tags: RESEARCH ARTICLE Source Type: research
Retromer ‐mediated recruitment of the WASH complex involves discrete interactions between VPS35, VPS29, and FAM21
AbstractEndosomal trafficking ensures the proper distribution of lipids and proteins to various cellular compartments, facilitating intracellular communication, nutrient transport, waste disposal, and the maintenance of cell structure. Retromer, a peripheral membrane protein complex, plays an important role in this process by recruiting the associated actin-polymerizing WASH complex to establish distinct sorting domains. The WASH complex is recruited through the interaction of the VPS35 subunit of retromer with the WASH complex subunit FAM21. Here, we report the identification of two separate fragments of FAM21 that intera...
Source: Protein Science - April 12, 2024 Category: Biochemistry Authors: Miguel Romano ‐Moreno,
Elsa N. Astorga‐Simón,
Adriana L. Rojas,
Aitor Hierro Tags: RESEARCH ARTICLE Source Type: research
Lipid exchange of apolipoprotein A ‐I amyloidogenic variants in reconstituted high‐density lipoprotein with artificial membranes
AbstractHigh-density lipoproteins (HDLs) are responsible for removing cholesterol from arterial walls, through a process known as reverse cholesterol transport. The main protein in HDL, apolipoprotein A-I (ApoA-I), is essential to this process, and changes in its sequence significantly alter HDL structure and functions. ApoA-I amyloidogenic variants, associated with a particular hereditary degenerative disease, are particularly effective at facilitating cholesterol removal, thus protecting carriers from cardiovascular disease. Thus, it is conceivable that reconstituted HDL (rHDL) formulations containing ApoA-I proteins wit...
Source: Protein Science - April 12, 2024 Category: Biochemistry Authors: Yubexi Correa,
Mathilde Ravel,
Marie Imbert,
Sarah Waldie,
Luke Clifton,
Ann Terry,
Felix Roosen ‐Runge,
Jens O. Lagerstedt,
Michael Moir,
Tamim Darwish,
Marité Cárdenas,
Rita Del Giudice Tags: RESEARCH ARTICLE Source Type: research
How hydrophobicity, side chains, and salt affect the dimensions of disordered proteins
AbstractDespite the generally accepted role of the hydrophobic effect as the driving force for folding, many intrinsically disordered proteins (IDPs), including those with hydrophobic content typical of foldable proteins, behave nearly as self-avoiding random walks (SARWs) under physiological conditions. Here, we tested how temperature and ionic conditions influence the dimensions of the N-terminal domain of pertactin (PNt), an IDP with an amino acid composition typical of folded proteins. While PNt contracts somewhat with temperature, it nevertheless remains expanded over 10 –58°C, with a Flory exponent,ν,>0.50. Bo...
Source: Protein Science - April 12, 2024 Category: Biochemistry Authors: Michael C. Baxa,
Xiaoxuan Lin,
Cedrick D. Mukinay,
Srinivas Chakravarthy,
Joseph R. Sachleben,
Sarah Antilla,
Nina Hartrampf,
Joshua A. Riback,
Isabelle A. Gagnon,
Bradley L. Pentelute,
Patricia L. Clark,
Tobin R. Sosnick Tags: RESEARCH ARTICLE Source Type: research
Engineering bio ‐brick protein scaffolds for organizing enzyme assemblies
This study introduces a novel family of engineered SCAffolding Bricks, named SCABs, utilizing the consensus tetratricopeptide repeat (CTPR) domain for organized multi-enzyme systems. Two SCAB systems are developed, one employing head-to-tail interactions with reversible covalent disulfide bonds, the other relying on non-covalent metal-driven assembly via engineered metal coordinating interfaces. Enzymes are directly fused to SCAB modules, triggering assembly in a non-reducing environment or by metal presence. A proof-of-concept with formate dehydrogenase (FDH) and L-alanine dehydrogenase (AlaDH) shows enhanced specific pro...
Source: Protein Science - April 12, 2024 Category: Biochemistry Authors: Alba Ledesma ‐Fernandez,
Susana Velasco‐Lozano,
Pedro Campos‐Muelas,
Ricardo Madrid,
Fernando López‐Gallego,
Aitziber L. Cortajarena Tags: RESEARCH ARTICLE Source Type: research
Disruption of Ca2+/calmodulin:KSR1 interaction lowers ERK activation
In this study, we set out to generate a KSR1 point mutant with reduced Ca2+/CaM binding in order to unravel the functional implications of their interaction. To do so, we solved the structural determinants of complex formation. Using purified fragments of KSR1, we showed that Ca2+/CaM binds to the CA3 domain of KSR1. We then used in silico molecular modeling to predict contact residues for binding. This approach identified two possible modes of interaction: (1) binding of extended Ca2+/CaM to a globular conformation of KSR1-CA3 via electrostatic interactions or (2) binding of collapsed Ca2+/CaM to α-helical KSR1-CA3 via h...
Source: Protein Science - April 10, 2024 Category: Biochemistry Authors: Louise Thines,
Hyunbum Jang,
Zhigang Li,
Samar Sayedyahossein,
Ryan Maloney,
Ruth Nussinov,
David B. Sacks Tags: RESEARCH ARTICLE Source Type: research
Myxococcus xanthus translesion DNA synthesis protein ImuA is an ATPase enhanced by DNA
AbstractTranslesion DNA synthesis pathways are necessary to ensure bacterial replication in the presence of DNA damage. Translesion DNA synthesis carried out by the PolV mutasome is well-studied inEscherichia coli, but ~one third of bacteria use a functionally homologous protein complex, consisting of ImuA, ImuB, and ImuC (also called DnaE2). Numerous in vivo studies have shown that all three proteins are required for translesion DNA synthesis and that ImuC is the error-prone polymerase, but the roles of ImuA and ImuB are unclear. Here we carry out biochemical characterization of ImuA and a truncation of ImuB fromMyxococcu...
Source: Protein Science - April 9, 2024 Category: Biochemistry Authors: Kristi Lichimo,
Dana J. Sowa,
Andriana Tetenych,
Monica M. Warner,
Caitlin Doubleday,
Harman S. Dev,
Catie Luck,
Sara N. Andres Tags: RESEARCH ARTICLE Source Type: research
Disentangling the formation, mechanism, and evolvement of the covalent methanesulfonyl fluoride acetylcholinesterase adduct: Insights into an aged ‐like inactive complex susceptible to reactivation by a combination of nucleophiles
AbstractChemical warfare nerve agents and pesticides, known as organophosphorus compounds inactivate cholinesterases (ChEs) by phosphorylating the serine hydroxyl group located at the active site of ChEs. Over the course of time, phosphorylation is followed by loss of an organophosphate-leaving group and the bond with ChEs becomes irreversible, a process known as aging. Differently, structurally related irreversible catalytic poisons bearing sulfur instead of phosphorus convert ChEs in its aged form only by covalently binding to the key catalytic serine. Kinetic and crystallographic studies of the interaction betweenTorped...
Source: Protein Science - April 9, 2024 Category: Biochemistry Authors: Jure Stojan,
Alessandro Pesaresi,
An že Meden,
Doriano Lamba Tags: RESEARCH ARTICLE Source Type: research
Computational and experimental identification of keystone interactions in Ebola virus matrix protein VP40 dimer formation
This study sheds light on the structural origins of VP40 dimer formation and may inform the design of a small molecule that can disrupt VP40 dimer stability. (Source: Protein Science)
Source: Protein Science - April 9, 2024 Category: Biochemistry Authors: Yogesh Narkhede,
Roopashi Saxena,
Tej Sharma,
Jacob P. Conarty,
Valentina Toro Ramirez,
Balindile B. Motsa,
Souad Amiar,
Sheng Li,
Prem P. Chapagain,
Olaf Wiest,
Robert V. Stahelin Tags: RESEARCH ARTICLE Source Type: research
Diverse crystalline protein scaffolds through metal ‐dependent polymorphism
AbstractAs protein crystals are increasingly finding diverse applications as scaffolds, controlled crystal polymorphism presents a facile strategy to form crystalline assemblies with controllable porosity with minimal to no protein engineering. Polymorphs of consensus tetratricopeptide repeat proteins with varying porosity were obtained through co-crystallization with metal salts, exploiting the innate metal ion geometric requirements. A single structurally exposed negative amino acid cluster was responsible for metal coordination, despite the abundance of negatively charged residues. Density functional theory calculations...
Source: Protein Science - April 9, 2024 Category: Biochemistry Authors: Mantas Liutkus,
Ivan R. Sasselli,
Adriana L. Rojas,
Aitziber L. Cortajarena Tags: RESEARCH ARTICLE Source Type: research
Proteasome ‐dependent degradation of histone H1 subtypes is mediated by its C‐terminal domain
AbstractHistone H1 is involved in chromatin compaction and dynamics. In human cells, the H1 complement is formed by different amounts of somatic H1 subtypes, H1.0-H1.5 and H1X. The amount of each variant depends on the cell type, the cell cycle phase, and the time of development and can be altered in disease. However, the mechanisms regulating H1 protein levels have not been described. We have analyzed the contribution of the proteasome to the degradation of H1 subtypes in human cells using two different inhibitors: MG132 and bortezomib. H1 subtypes accumulate upon treatment with both drugs, indicating that the proteasome ...
Source: Protein Science - April 9, 2024 Category: Biochemistry Authors: D. Garc ía‐Gomis,
J. López,
A. Calderón,
M. Andrés,
I. Ponte,
A. Roque Tags: RESEARCH ARTICLE Source Type: research
Transient interdomain interactions in free USP14 shape its conformational ensemble
AbstractThe deubiquitinase (DUB) ubiquitin-specific protease 14 (USP14) is a dual domain protein that plays a regulatory role in proteasomal degradation and has been identified as a promising therapeutic target. USP14 comprises a conserved USP domain and a ubiquitin-like (Ubl) domain separated by a 25-residue linker. The enzyme activity of USP14 is autoinhibited in solution, but is enhanced when bound to the proteasome, where the Ubl and USP domains of USP14 bind to the Rpn1 and Rpt1/Rpt2 units, respectively. No structure of full-length USP14 in the absence of proteasome has yet been presented, however, earlier work has de...
Source: Protein Science - April 9, 2024 Category: Biochemistry Authors: Johannes Salomonsson,
Bj örn Wallner,
Linda Sjöstrand,
Pádraig D'Arcy,
Maria Sunnerhagen,
Alexandra Ahlner Tags: RESEARCH ARTICLE Source Type: research
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(Source: Protein Science)
Source: Protein Science - April 8, 2024 Category: Biochemistry Tags: Cover Image Source Type: research
Issue information
(Source: Protein Science)
Source: Protein Science - April 8, 2024 Category: Biochemistry Tags: Issue Information Source Type: research
Protein structure –function continuum model: Emerging nexuses between specificity, evolution, and structure
AbstractThe rationale for replacing the old binary of structure –function with the trinity of structure, disorder, and function has gained considerable ground in recent years. A continuum model based on the expanded form of the existing paradigm can now subsume importance of both conformational flexibility and intrinsic disorder in protein function. The disord er is actually critical for understanding the protein–protein interactions in many regulatory processes, formation of membrane-less organelles, and our revised notions of specificity as amply illustrated by moonlighting proteins. While its importance in formation...
Source: Protein Science - March 27, 2024 Category: Biochemistry Authors: Munishwar Nath Gupta,
Vladimir N. Uversky Tags: REVIEW ARTICLE Source Type: research
