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Structure, Function and Evolution of Protein Domains

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A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Biology".

Deadline for manuscript submissions: closed (28 February 2022) | Viewed by 33330

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Prof. Dr. Sailen Barik

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3780 Pelham Drive, Mobile, AL 36619, USA
Interests: structure and function of proteins; structure and function of RNA; virology; parasitology; innate immunity; RNA interference

Special Issue Information

Dear Colleagues,

Beyond their amino acid sequences, essentially all biological proteins function by the use of specific domains that number in the hundreds, if not thousands. They have been recognized by their consensus sequence of various degrees of homology, higher order of structural features, and structure–function analyses. This Special Issue welcomes both original research articles and reviews on any aspect of protein domains, with special emphasis on their structure, function, potential evolutionary origins, and relationship with one another. We also encourage articles on sequence repeats of diverse lengths, of which there are many well-known examples, including (but not limited to) TPR/PPR, HEAT, Armadillo, WD40, Ankyrin, Kelch, and LRR (Leu-Rich Repeat). Several repeat families exhibit conservation of structure, such as an array of alpha-helices, or similarity of three-dimensional structures and folds, even though they may differ in amino acid sequence. How the structural and functional units have evolved to produce the larger repeats and complex domains with a distinct specificity for substrates and ligands remains an important unsolved mystery in molecular evolution. Finally, hitherto unrecognized domains and motifs that may be unraveled by novel strategies of sequence or structure alignment are also highly welcome, as well as genetic engineering studies to generate novel chimeric domains.

Prof. Dr. Sailen Barik
Guest Editor

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Keywords

domain
motif
scaffold
repeat
tetratricopeptide
structure
function
alpha-helix
beta-strand
homology
molecular evolution
protein folding

Published Papers (11 papers)

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Editorial

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4 pages, 179 KiB

Open AccessEditorial

Special Issue: Structure, Function and Evolution of Protein Domains

by Sailen Barik

Int. J. Mol. Sci. 2022, 23(11), 6201; https://doi.org/10.3390/ijms23116201 - 31 May 2022

Cited by 2 | Viewed by 1208

Abstract

Essentially, all proteins perform their biological roles through the use of specific domains that number in the hundreds, if not thousands [...] Full article

(This article belongs to the Special Issue Structure, Function and Evolution of Protein Domains)

Research

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13 pages, 3230 KiB

Open AccessArticle

Dimerization Activity of a Disordered N-Terminal Domain from Drosophila CLAMP Protein

by Evgeniya Tikhonova, Sofia Mariasina, Olga Arkova, Oksana Maksimenko, Pavel Georgiev and Artem Bonchuk

Int. J. Mol. Sci. 2022, 23(7), 3862; https://doi.org/10.3390/ijms23073862 - 31 Mar 2022

Cited by 7 | Viewed by 1789

Abstract

In Drosophila melanogaster, CLAMP is an essential zinc-finger transcription factor that is involved in chromosome architecture and functions as an adaptor for the dosage compensation complex. Most of the known Drosophila architectural proteins have structural N-terminal homodimerization domains that facilitate distance interactions. Because CLAMP performs architectural functions, we tested its N-terminal region for the presence of a homodimerization domain. We used a yeast two-hybrid assay and biochemical studies to demonstrate that the adjacent N-terminal region between 46 and 86 amino acids is capable of forming homodimers. This region is conserved in CLAMP orthologs from most insects, except Hymenopterans. Biophysical techniques, including nuclear magnetic resonance (NMR) and small-angle X-ray scattering (SAXS), suggested that this domain lacks secondary structure and has features of intrinsically disordered regions despite the fact that the protein structure prediction algorithms suggested the presence of beta-sheets. The dimerization domain is essential for CLAMP functions in vivo because its deletion results in lethality. Thus, CLAMP is the second architectural protein after CTCF that contains an unstructured N-terminal dimerization domain. Full article

(This article belongs to the Special Issue Structure, Function and Evolution of Protein Domains)

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19 pages, 3496 KiB

Open AccessArticle

Allosteric Inter-Domain Contacts in Bacterial Hsp70 Are Located in Regions That Avoid Insertion and Deletion Events

by Michal Gala, Peter Pristaš and Gabriel Žoldák

Int. J. Mol. Sci. 2022, 23(5), 2788; https://doi.org/10.3390/ijms23052788 - 3 Mar 2022

Cited by 1 | Viewed by 2115

Abstract

Heat shock proteins 70 (Hsp70) are chaperones consisting of a nucleotide-binding domain (NBD) and a substrate-binding domain (SBD), the latter of which binds protein clients. After ATP binds to the NBD, the SBD α/β subdomains’ shared interface opens, and the open SBD docks to the NBD. Such allosteric effects are stabilized by the newly formed NBD-SBD interdomain contacts. In this paper, we examined how such an opening and formation of subdomain interfaces is affected during the evolution of Hsp70. In particular, insertion and deletion events (indels) can be highly disruptive for the mechanical events since such changes introduce a collective shift in the pairing interactions at communicating interfaces. Based on a multiple sequence alignment analysis of data collected from Swiss-Prot/UniProt database, we find several indel-free regions (IFR) in Hsp70. The two largest IFRs are located in interdomain regions that participate in allosteric structural changes. We speculate that the reason why the indels have a lower likelihood of occurrence in these regions is that indel events in these regions cause dysfunction in the protein due to perturbations of the mechanical balance. Thus, the development of functional allosteric machines requires including in the rational design a concept of the balance between structural elements. Full article

(This article belongs to the Special Issue Structure, Function and Evolution of Protein Domains)

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25 pages, 31041 KiB

Open AccessArticle

The KRAB Domain of ZNF10 Guides the Identification of Specific Amino Acids That Transform the Ancestral KRAB-A-Related Domain Present in Human PRDM9 into a Canonical Modern KRAB-A Domain

by Peter Lorenz, Felix Steinbeck, Ludwig Krause and Hans-Jürgen Thiesen

Int. J. Mol. Sci. 2022, 23(3), 1072; https://doi.org/10.3390/ijms23031072 - 19 Jan 2022

Cited by 4 | Viewed by 2765

Abstract

Krüppel-associated box (KRAB) zinc finger proteins are a large class of tetrapod transcription factors that usually exert transcriptional repression through recruitment of TRIM28/KAP1. The evolutionary root of modern KRAB domains (mKRAB) can be traced back to an ancestral motif (aKRAB) that occurs even in invertebrates. Here, we first stratified three subgroups of aKRAB sequences from the animal kingdom (PRDM9, SSX and coelacanth KZNF families) and defined ancestral subdomains for KRAB-A and KRAB-B. Using human ZNF10 mKRAB-AB as blueprints for function, we then identified the necessary amino acid changes that transform the inactive aKRAB-A of human PRDM9 into an mKRAB domain capable of mediating silencing and complexing TRIM28/KAP1 in human cells when employed as a hybrid with ZNF10-B. Full gain of function required replacement of residues KR by the conserved motif MLE (positionsA32-A34), which inserted an additional residue, and exchange of A9/S for F, A20/M for L, and A27/R for V. AlphaFold2 modelling documented an evolutionary conserved L-shaped body of two α-helices in all KRAB domains. It is transformed into a characteristic spatial arrangement typical for mKRAB-AB upon the amino acid replacements and in conjunction with a third helix supplied by mKRAB-B. Side-chains pointing outward from the core KRAB 3D structure may reveal a protein-protein interaction code enabling graded binding of TRIM28 to different KRAB domains. Our data provide basic insights into structure-function relationships and emulate transitions of KRAB during evolution. Full article

(This article belongs to the Special Issue Structure, Function and Evolution of Protein Domains)

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15 pages, 4948 KiB

Open AccessArticle

The Distinct Properties of the Consecutive Disordered Regions Inside or Outside Protein Domains and Their Functional Significance

by Huqiang Wang, Haolin Zhong, Chao Gao, Jiayin Zang and Dong Yang

Int. J. Mol. Sci. 2021, 22(19), 10677; https://doi.org/10.3390/ijms221910677 - 1 Oct 2021

Cited by 8 | Viewed by 3997

Abstract

The consecutive disordered regions (CDRs) are the basis for the formation of intrinsically disordered proteins, which contribute to various biological functions and increasing organism complexity. Previous studies have revealed that CDRs may be present inside or outside protein domains, but a comprehensive analysis of the property differences between these two types of CDRs and the proteins containing them is lacking. In this study, we investigated this issue from three viewpoints. Firstly, we found that in-domain CDRs are more hydrophilic and stable but have less stickiness and fewer post-translational modification sites compared with out-domain CDRs. Secondly, at the protein level, we found that proteins with only in-domain CDRs originated late, evolved rapidly, and had weak functional constraints, compared with the other two types of CDR-containing proteins. Proteins with only in-domain CDRs tend to be expressed spatiotemporal specifically, but they tend to have higher abundance and are more stable. Thirdly, we screened the CDR-containing protein domains that have a strong correlation with organism complexity. The CDR-containing domains tend to be evolutionarily young, or they changed from a domain without CDR to a CDR-containing domain during evolution. These results provide valuable new insights about the evolution and function of CDRs and protein domains. Full article

(This article belongs to the Special Issue Structure, Function and Evolution of Protein Domains)

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31 pages, 9223 KiB

Open AccessArticle

Conservative and Atypical Ferritins of Sponges

by Kim I. Adameyko, Anton V. Burakov, Alexander D. Finoshin, Kirill V. Mikhailov, Oksana I. Kravchuk, Olga S. Kozlova, Nicolay G. Gornostaev, Alexander V. Cherkasov, Pavel A. Erokhov, Maria I. Indeykina, Anna E. Bugrova, Alexey S. Kononikhin, Andrey V. Moiseenko, Olga S. Sokolova, Artem N. Bonchuk, Irina V. Zhegalova, Anton A. Georgiev, Victor S. Mikhailov, Natalia E. Gogoleva, Guzel R. Gazizova, Elena I. Shagimardanova, Oleg A. Gusev and Yulia V. Lyupina Show full author list Hide full author list

Int. J. Mol. Sci. 2021, 22(16), 8635; https://doi.org/10.3390/ijms22168635 - 11 Aug 2021

Cited by 8 | Viewed by 7156

Abstract

Ferritins comprise a conservative family of proteins found in all species and play an essential role in resistance to redox stress, immune response, and cell differentiation. Sponges (Porifera) are the oldest Metazoa that show unique plasticity and regenerative potential. Here, we characterize the ferritins of two cold-water sponges using proteomics, spectral microscopy, and bioinformatic analysis. The recently duplicated conservative HdF1a/b and atypical HdF2 genes were found in the Halisarca dujardini genome. Multiple related transcripts of HpF1 were identified in the Halichondria panicea transcriptome. Expression of HdF1a/b was much higher than that of HdF2 in all annual seasons and regulated differently during the sponge dissociation/reaggregation. The presence of the MRE and HRE motifs in the HdF1 and HdF2 promotor regions and the IRE motif in mRNAs of HdF1 and HpF indicates that sponge ferritins expression depends on the cellular iron and oxygen levels. The gel electrophoresis combined with specific staining and mass spectrometry confirmed the presence of ferric ions and ferritins in multi-subunit complexes. The 3D modeling predicts the iron-binding capacity of HdF1 and HpF1 at the ferroxidase center and the absence of iron-binding in atypical HdF2. Interestingly, atypical ferritins lacking iron-binding capacity were found in genomes of many invertebrate species. Their function deserves further research. Full article

(This article belongs to the Special Issue Structure, Function and Evolution of Protein Domains)

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11 pages, 2496 KiB

Open AccessArticle

Virtual Evolution of HVEM Segment for Checkpoint Inhibitor Discovery

by Mingjia Yu, Huimin Zhao, Yuhui Miao, Shi-Zhong Luo and Song Xue

Int. J. Mol. Sci. 2021, 22(12), 6638; https://doi.org/10.3390/ijms22126638 - 21 Jun 2021

Cited by 6 | Viewed by 2640

Abstract

Immune therapy has emerged as an effective treatment against cancers. Inspired by the PD-1/PD-L1 antibodies, which have achieved great success in clinical, other immune checkpoint proteins have drawn increasing attention in cancer research. B and T lymphocyte attenuator (BTLA) and herpes virus entry mediator (HVEM) are potential targets for drug development. The co-crystal structure of BTLA/HVEM have revealed that HVEM (26–38) fragment is the core sequence which directly involved on the interface. Herein, we conducted virtual evolution with this sequence by using saturation mutagenesis in silico and mutants with lower binding energy were selected. Wet-lab experiments confirmed that several of them possessed higher affinity with BTLA. Based on the best mutant of the core sequence, extended peptides with better efficacy were obtained. Furthermore, the mechanism of the effects of mutations was revealed by computational analysis. The mutated peptide discovered here can be a potent inhibitor to block BTLA/HVEM interaction and its mechanism may extend people’s view on inhibitor discovery for the checkpoint pair. Full article

(This article belongs to the Special Issue Structure, Function and Evolution of Protein Domains)

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Review

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12 pages, 2024 KiB

Open AccessReview

Diffracted X-ray Tracking Method for Measuring Intramolecular Dynamics of Membrane Proteins

by Shoko Fujimura, Kazuhiro Mio, Tatsunari Ohkubo, Tatsuya Arai, Masahiro Kuramochi, Hiroshi Sekiguchi and Yuji C. Sasaki

Int. J. Mol. Sci. 2022, 23(4), 2343; https://doi.org/10.3390/ijms23042343 - 20 Feb 2022

Cited by 5 | Viewed by 2122

Abstract

Membrane proteins change their conformations in response to chemical and physical stimuli and transmit extracellular signals inside cells. Several approaches have been developed for solving the structures of proteins. However, few techniques can monitor real-time protein dynamics. The diffracted X-ray tracking method (DXT) is an X-ray-based single-molecule technique that monitors the internal motion of biomolecules in an aqueous solution. DXT analyzes trajectories of Laue spots generated from the attached gold nanocrystals with a two-dimensional axis by tilting (θ) and twisting (χ). Furthermore, high-intensity X-rays from synchrotron radiation facilities enable measurements with microsecond-timescale and picometer-spatial-scale intramolecular information. The technique has been applied to various membrane proteins due to its superior spatiotemporal resolution. In this review, we introduce basic principles of DXT, reviewing its recent and extended applications to membrane proteins and living cells, respectively. Full article

(This article belongs to the Special Issue Structure, Function and Evolution of Protein Domains)

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13 pages, 18887 KiB

Open AccessReview

Conserved Structure and Evolution of DPF Domain of PHF10—The Specific Subunit of PBAF Chromatin Remodeling Complex

by Anton O. Chugunov, Nadezhda A. Potapova, Natalia S. Klimenko, Victor V. Tatarskiy, Sofia G. Georgieva and Nataliya V. Soshnikova

Int. J. Mol. Sci. 2021, 22(20), 11134; https://doi.org/10.3390/ijms222011134 - 15 Oct 2021

Cited by 6 | Viewed by 2769

Abstract

Transcription activation factors and multisubunit coactivator complexes get recruited at specific chromatin sites via protein domains that recognize histone modifications. Single PHDs (plant homeodomains) interact with differentially modified H3 histone tails. Double PHD finger (DPF) domains possess a unique structure different from PHD and are found in six proteins: histone acetyltransferases MOZ and MORF; chromatin remodeling complex BAF (DPF1–3); and chromatin remodeling complex PBAF (PHF10). Among them, PHF10 stands out due to the DPF sequence, structure, and functions. PHF10 is ubiquitously expressed in developing and adult organisms as four isoforms differing in structure (the presence or absence of DPF) and transcription regulation functions. Despite the importance of the DPF domain of PHF10 for transcription activation, its structure remains undetermined. We performed homology modeling of the human PHF10 DPF domain and determined common and distinct features in structure and histone modifications recognition capabilities, which can affect PBAF complex chromatin recruitment. We also traced the evolution of DPF1–3 and PHF10 genes from unicellular to vertebrate organisms. The data reviewed suggest that the DPF domain of PHF10 plays an important role in SWI/SNF-dependent chromatin remodeling during transcription activation. Full article

(This article belongs to the Special Issue Structure, Function and Evolution of Protein Domains)

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14 pages, 2110 KiB

Open AccessReview

Human FoxP Transcription Factors as Tractable Models of the Evolution and Functional Outcomes of Three-Dimensional Domain Swapping

by Pablo Villalobos, César A. Ramírez-Sarmiento, Jorge Babul and Exequiel Medina

Int. J. Mol. Sci. 2021, 22(19), 10296; https://doi.org/10.3390/ijms221910296 - 24 Sep 2021

Cited by 2 | Viewed by 2468

Abstract

The association of two or more proteins to adopt a quaternary complex is one of the most widespread mechanisms by which protein function is modulated. In this scenario, three-dimensional domain swapping (3D-DS) constitutes one plausible pathway for the evolution of protein oligomerization that exploits readily available intramolecular contacts to be established in an intermolecular fashion. However, analysis of the oligomerization kinetics and thermodynamics of most extant 3D-DS proteins shows its dependence on protein unfolding, obscuring the elucidation of the emergence of 3D-DS during evolution, its occurrence under physiological conditions, and its biological relevance. Here, we describe the human FoxP subfamily of transcription factors as a feasible model to study the evolution of 3D-DS, due to their significantly faster dissociation and dimerization kinetics and lower dissociation constants in comparison to most 3D-DS models. Through the biophysical and functional characterization of FoxP proteins, relevant structural aspects highlighting the evolutionary adaptations of these proteins to enable efficient 3D-DS have been ascertained. Most biophysical studies on FoxP suggest that the dynamics of the polypeptide chain are crucial to decrease the energy barrier of 3D-DS, enabling its fast oligomerization under physiological conditions. Moreover, comparison of biophysical parameters between human FoxP proteins in the context of their minute sequence differences suggests differential evolutionary strategies to favor homoassociation and presages the possibility of heteroassociations, with direct impacts in their gene regulation function. Full article

(This article belongs to the Special Issue Structure, Function and Evolution of Protein Domains)

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17 pages, 3744 KiB

Open AccessReview

An Analytical Review of the Structural Features of Pentatricopeptide Repeats: Strategic Amino Acids, Repeat Arrangements and Superhelical Architecture

by Sailen Barik

Int. J. Mol. Sci. 2021, 22(10), 5407; https://doi.org/10.3390/ijms22105407 - 20 May 2021

Cited by 1 | Viewed by 2255

Abstract

Tricopeptide repeats are common in natural proteins, and are exemplified by 34- and 35-residue repeats, known respectively as tetratricopeptide repeats (TPRs) and pentatricopeptide repeats (PPRs). In both classes, each repeat unit forms an antiparallel bihelical structure, so that multiple such units in a polypeptide are arranged in a parallel fashion. The primary structures of the motifs are nonidentical, but amino acids of similar properties occur in strategic positions. The focus of the present work was on PPR, but TPR, its better-studied cousin, is often included for comparison. The analyses revealed that critical amino acids, namely Gly, Pro, Ala and Trp, were placed at distinct locations in the higher order structure of PPR domains. While most TPRs occur in repeats of three, the PPRs exhibited a much greater diversity in repeat numbers, from 1 to 30 or more, separated by spacers of various sequences and lengths. Studies of PPR strings in proteins showed that the majority of PPR units are single, and that the longer tandems (i.e., without space in between) occurred in decreasing order. The multi-PPR domains also formed superhelical vortices, likely governed by interhelical angles rather than the spacers. These findings should be useful in designing and understanding the PPR domains. Full article

(This article belongs to the Special Issue Structure, Function and Evolution of Protein Domains)

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