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Journal Proteins

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Computational backbone design enables soluble engineering of transferrin receptor apical domain.

Dick J Sjöström, Sarah A Berger, Gustav Oberdorfer, Sinisa Bjelic,

Supply of iron into human cells is achieved by iron carrier protein transferrin and its receptor, that upon complex formation get internalized by endocytosis. Similarly, the iron needs to be delivered into the brain, and necessitates the transport across the blood-brain barrier. While there are still unanswered questions about these ... Read more >>

Proteins (Proteins)
[2020, :]

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Structural dynamics of pentapeptide repeat proteins.

Shenyuan Xu, Michael A Kennedy,

Pentapeptide repeat proteins (PRPs) represent a large superfamily with more than 38 000 sequences in nearly 3500 species, the majority belonging to cyanobacteria but represented among all branches of life. PRPs contain at least eight consecutive pentapeptide repeats with the consensus (A/C/S/V/T/L/I)(D/N/S/K/E/I/R)(L/F)(S/T/R/E/Q/K/V/D)(G/D/E/N/R/Q/K). PRPs fold into right-handed quadrilateral β helices, also ... Read more >>

Proteins (Proteins)
[2020, :]

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Evolutionary relationships and sequence-structure determinants in human SARS coronavirus-2 spike proteins for host receptor recognition.

Lalitha Guruprasad,

Coronavirus disease 2019 (COVID-19) is a pandemic infectious disease caused by novel Severe Acute Respiratory Syndrome coronavirus-2 (SARS CoV-2). The SARS CoV-2 is transmitted more rapidly and readily than SARS CoV. Both, SARS CoV and SARS CoV-2 via their glycosylated spike proteins recognize the human angiotensin converting enzyme-2 (ACE-2) receptor. ... Read more >>

Proteins (Proteins)
[2020, :]

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β-Strand-mediated interactions of protein domains.

Archana S Bhat, Lisa N Kinch, Nick V Grishin,

Protein domains exist by themselves or in combination with other domains to form complex multi-domain proteins. Defining domain boundaries in proteins is essential for understanding their evolution and function but is not trivial. More specifically, partitioning domains that interact by forming a single β-sheet is known to be particularly troublesome ... Read more >>

Proteins (Proteins)
[2020, :]

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Investigating dual Ca2+ modulation of the ryanodine receptor 1 by molecular dynamics simulation.

Wenjun Zheng, Han Wen,

The ryanodine receptors (RyR) are essential to calcium signaling in striated muscles. A deep understanding of the complex Ca2+ -activation/inhibition mechanism of RyRs requires detailed structural and dynamic information for RyRs in different functional states (e.g., with Ca2+ bound to activating or inhibitory sites). Recently, high-resolution structures of the RyR ... Read more >>

Proteins (Proteins)
[2020, :]

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Dimerization of Aβ40 inside dipalmitoylphosphatidylcholine bilayer and its effect on bilayer integrity: Atomistic simulation at three temperatures.

Faezeh Kargar, Saeed Emadi, Hossein Fazli,

Amyloid-beta (Aβ) protein is related to Alzheimer's disease (AD), and various experiments have shown that oligomers as small as dimers are cytotoxic. Recent studies have concluded that interactions of Aβ with neuronal cell membranes lead to disruption of membrane integrity, toxicity and play a key role in the development of ... Read more >>

Proteins (Proteins)
[2020, :]

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Structural Compliance - A New Metric for Protein Flexibility.

Domenico Scaramozzino, Pranav M Khade, Robert L Jernigan, Giuseppe Lacidogna, Alberto Carpinteri,

Proteins are the active players in performing essential molecular activities throughout biology, and their dynamics has been broadly demonstrated to relate to their mechanisms. The intrinsic fluctuations have often been used to represent their dynamics and then compared to the experimental B-factors. However, proteins do not move in a vacuum ... Read more >>

Proteins (Proteins)
[2020, :]

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Citius, Altius, Fortius.

J Lange, G Vriend,

2020 is a leap year. That means that we have one day extra and, if the Olympic games had survived the corona crisis, we would all be watching television and ask the eternal question whether Olympic records will for ever be broken and broken again, or that there are limits ... Read more >>

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[2020, :]

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Distinctive Communication Networks in Inactive States of β2 -Adrenergic Receptor: Mutual Information and Entropy Transfer Analysis.

Nuray Sogunmez, E Demet Akten,

Mutual information and entropy transfer analysis employed on two inactive states of human beta-2 adrenergic receptor (β2 -AR) unraveled distinct communication pathways. Previously, a so-called "highly" inactive state of the receptor was observed during 1.5 μs long MD simulation where the largest intracellular loop (ICL3) was swiftly packed onto G-protein ... Read more >>

Proteins (Proteins)
[2020, :]

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A shift of dynamic equilibrium between the KIT active and inactive states causes drug resistance.

Sanjay K Srikakulam, Tomas Bastys, Olga V Kalinina,

Tyrosine phosphorylation, a highly regulated post-translational modification, is carried out by the enzyme tyrosine kinase (TK). TKs are important mediators in signaling cascades, facilitating diverse biological processes in response to stimuli. TKs may acquire mutations leading to malignancy and are viable targets for anti-cancer drugs. Mast/stem cell growth factor receptor ... Read more >>

Proteins (Proteins)
[2020, :]

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Ligand-protein interactions in lysozyme investigated through a dual-resolution model.

Raffaele Fiorentini, Kurt Kremer, Raffaello Potestio,

A fully atomistic (AT) modeling of biological macromolecules at relevant length- and time-scales is often cumbersome or not even desirable, both in terms of computational effort required and a posteriori analysis. This difficulty can be overcome with the use of multiresolution models, in which different regions of the same system ... Read more >>

Proteins (Proteins)
[2020, :]

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cnnAlpha: Protein Disordered Regions Prediction by Reduced Amino Acid Alphabets and Convolutional Neural Networks.

Mauricio Oberti, Iosif I Vaisman,

Intrinsically disordered regions (IDR) play an important role in key biological processes and are closely related to human diseases. IDRs have great potential to serve as targets for drug discovery, most notably in disordered binding regions. Accurate prediction of IDRs is challenging because their genome wide occurrence and a low ... Read more >>

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[2020, :]

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C1188D mutation abolishes specific recognition between MLL1-CXXC domain and CpG site by inducing conformational switch of flexible N- terminal.

Jiawen Chen, Yanping Qi, Yong Duan, Mojie Duan, Minghui Yang,

Mixed lineage leukemia protein (MLL1 protein) recognizes CpG site via its CXXC domain and is frequently associated with leukemia. The specific recognition is abolished by C1188D mutation which also prevents MLL-related leukemia. In this paper, multiple molecular dynamic simulations were performed to investigate the mechanism of recognition and influences of ... Read more >>

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[2020, :]

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Dynamic aspects of pressure and temperature-stabilized intermediates of outer surface protein A.

Takuro Wakamoto, Soichiro Kitazawa, Tomoshi Kameda, Ryo Kitahara,

Structural characterization of alternatively folded and partially disordered protein conformations remains challenging. Outer surface protein A (OspA) is a pivotal protein in Borrelia infection, which is the etiological agent of Lyme disease. OspA exists in equilibrium with intermediate conformations, in which the central and the C-terminal regions of the protein ... Read more >>

Proteins (Proteins)
[2020, :]

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New Facets of Larger Nest Motifs in Proteins.

Debnath Pal, Subhankar Sahu, Raja Banerjee,

The Nest is a concave-shaped structural motif in proteins formed by consecutive enantiomeric left-handed (L) and right-handed (R) helical conformation of the backbone. This important motif subsumes many turn and helix capping structures and binds electron-rich ligands. Simple Nests are either RL or LR. Larger Nests (>2 residues long) may ... Read more >>

Proteins (Proteins)
[2020, :]

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Conformational changes in a Vernier zone region: implications for antibody dual specificity.

Merve Arslan, Dilara Karadag, Sibel Kalyoncu,

Understanding determinants of antibody specificity is one of the challenging tasks in antibody development. Mono-specific antibodies are still dominant in approved antibody therapeutics but there is a significant body of work to show that multispecific antibodies can increase overall therapeutic effect. Dual specific or "Two-in-One" antibodies can bind to two ... Read more >>

Proteins (Proteins)
[2020, :]

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Numerous severely twisted N-acetylglucosamine conformations found in the protein databank.

Johann Hendrickx, Vinh Tran, Yves-Henri Sanejouand,

Taking advantage of the known planarity of the N-acetyl group of N-acetylglucosamine, an analysis of the quality of carbohydrate structures found in the protein databank was performed. Few obvious defects of the local geometry of the carbonyl group were observed. However, the N-acetyl group was often found in the less ... Read more >>

Proteins (Proteins)
[2020, :]

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The actin cytoskeleton orchestra in Entamoeba histolytica.

Pragyan Parimita Rath, Samudrala Gourinath,

Years of evolution have kept actin conserved throughout various clades of life. It is an essential protein starring in many cellular processes. In a primitive eukaryote named Entamoeba histolytica, actin directs the process of phagocytosis. A finely tuned coordination between various actin-binding proteins (ABPs) choreographs this process and forms one ... Read more >>

Proteins (Proteins)
[2020, :]

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Using Restraints in EROS-Dock Improves Model Quality in Pairwise and Multicomponent Protein Docking.

Maria Elisa Ruiz Echartea, David W Ritchie, Isaure Chauvot de Beauchêne,

Protein docking algorithms aim to predict the 3D structure of a protein complex from the structures of its separated components. In the past, most docking algorithms focused on docking pairs of proteins to form dimeric complexes. However, attention is now turning towards the more difficult problem of using docking methods ... Read more >>

Proteins (Proteins)
[2020, :]

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Engineering the specificity of Streptococcus pyogenes sortase A by loop grafting.

Magdalena Wójcik, Kamil Szala, Ronald van Merkerk, Wim J Quax, Ykelien L Boersma,

Sortases are a group of enzymes displayed on the cell-wall of Gram-positive bacteria. They are responsible for the attachment of virulence factors onto the peptidoglycan in a transpeptidation reaction through recognition of a pentapeptide substrate. Most housekeeping sortases recognize one specific pentapeptide motif; however, Streptococcus pyogenes sortase A (SpSrtA WT) ... Read more >>

Proteins (Proteins)
[2020, :]

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Performance of human and server prediction in CAPRI rounds 38-45.

Rui Duan, Liming Qiu, Xianjin Xu, Zhiwei Ma, Benjamin Ryan Merideth, Chi-Ren Shyu, Xiaoqin Zou,

CAPRI challenges offer a variety of blind tests for protein-protein interaction prediction. In CAPRI Rounds 38-45, we generated a set of putative binding modes for each target with an FFT-based docking algorithm, and then scored and ranked these binding modes with a proprietary scoring function, ITScorePP. We have also developed ... Read more >>

Proteins (Proteins)
[2020, :]

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Identification of biochemically neutral positions in liver pyruvate kinase.

Tyler A Martin, Tiffany Wu, Qingling Tang, Larissa L Dougherty, Daniel J Parente, Liskin Swint-Kruse, Aron W Fenton,

Understanding how each residue position contributes to protein function has been a long-standing goal in protein science. Substitution studies have historically focused on conserved protein positions. However, substitutions of nonconserved positions can also modify function. Indeed, we recently identified nonconserved positions that have large substitution effects in human liver pyruvate ... Read more >>

Proteins (Proteins)
[2020, :]

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Cumulative hydropathic topology of a voltage-gated sodium channel at atomic resolution.

Markos N Xenakis, Dimos Kapetis, Yang Yang, Jordi Heijman, Stephen G Waxman, Giuseppe Lauria, Catharina G Faber, Hubert J Smeets, Ronald L Westra, Patrick J Lindsey,

Voltage-gated sodium channels (NavChs) are biological pores that control the flow of sodium ions through the cell membrane. In humans, mutations in genes encoding NavChs can disrupt physiological cellular activity thus leading to a wide spectrum of diseases. Here, we present a topological connection between the functional architecture of a ... Read more >>

Proteins (Proteins)
[2020, :]

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Multicopper oxidases: modular structure, sequence space, and evolutionary relationships.

Maike Gräff, Patrick C F Buchholz, Marilize Le Roes-Hill, Jürgen Pleiss,

Multicopper oxidases (MCOs) use copper ions as cofactors to oxidize a variety of substrates while reducing oxygen to water. MCOs have been identified in various taxa, with notable occurrences in fungi. The role of these fungal MCOs in lignin degradation sparked an interest due to their potential for application in ... Read more >>

Proteins (Proteins)
[2020, :]

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Enhancing the promiscuity of a member of the Caspase protease family by rational design.

Christoph Öhlknecht, Drazen Petrov, Petra Engele, Christina Kröß, Bernhard Sprenger, Andreas Fischer, Nico Lingg, Rainer Schneider, Chris Oostenbrink,

The N-terminal cleavage of fusion tags to restore the native N-terminus of recombinant proteins is a challenging task and up to today, protocols need to be optimized for different proteins individually. Within this work, we present a novel protease that was designed in-silico to yield enhanced promiscuity toward different N-terminal ... Read more >>

Proteins (Proteins)
[2020, :]

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