An accurate classification of native and non-native protein-protein interactions using supervised and semi-supervised learning approaches

ABSTRACT CheY-like phosphoacceptor (or receiver [REC]) domain is a common module in a variety of response regulators of the bacterial signal transduction systems. In this work, 4,610 response regulators, encoded in complete genomes of 200 bacterial and archaeal species, were identified and classified by their domain architectures. Previously uncharacterized output domains were analyzed and, in some cases, assigned to known domain families. Transcriptional regulators of the OmpR, NarL, and NtrC families were found to comprise almost 60% of all response regulators; transcriptional regulators with other DNA-binding domains (LytTR, AraC, Spo0A, Fis, YcbB, RpoE, and MerR) account for an additional 6%. The remaining one-third is represented by the stand-alone REC domain (∼14%) and its combinations with a variety of enzymatic (GGDEF, EAL, HD-GYP, CheB, CheC, PP2C, and HisK), RNA-binding (ANTAR and CsrA), protein- or ligand-binding (PAS, GAF, TPR, CAP_ED, and HPt) domains, or newly described domains of unknown function. The diversity of domain architectures and the abundance of alternative domain combinations suggest that fusions between the REC domain and various output domains is a widespread evolutionary mechanism that allows bacterial cells to regulate transcription, enzyme activity, and/or protein-protein interactions in response to environmental challenges. The complete list of response regulators encoded in each of the 200 analyzed genomes is available online at http://www.ncbi.nlm.nih.gov/Complete_Genomes/RRcensus.html .

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Synthesis of Epitope-Targeting Antibody Based on Native Protein–Protein Interactions for Ftsz Filamentation Suppressor

10.21203/rs.3.rs-757826/v1 ◽

2021 ◽

Author(s):

Hikaru Nakazawa ◽

Taiji Katsuki ◽

Takashi Matsui ◽

Atsushi Tsugita ◽

Takeshi Yokoyama ◽

...

Keyword(s):

Molecular Evolution ◽

Phage Display ◽

Protein Interactions ◽

Selection Process ◽

Evolutionary Engineering ◽

Temperature Sensitive ◽

Native Protein ◽

Protein Protein Interactions ◽

Division Rate ◽

Evolution Approach

Abstract Phage display and biopanning is a powerful tool for generating binding molecules for a specific target. However, the selection process based on binding affinity provides no assurance for the antibody’s affinity to the target epitope. In this study, we propose a molecular-evolution approach guided by native protein–protein interactions to generate epitope-targeting antibodies. The binding-site sequence in a native protein was grafted into a complementarity-determining region (CDR) in the antibody, and a nonrelated CDR loop (in the grafted antibody) was randomized by phage display techniques. In this construction of antibodies by integrating graft and evolution technology (CAnIGET method), suitable grafting of the functional sequence weakly functionalized the antibody, and the molecular-evolution approach enhanced the binding function to inhibit the native protein–protein interactions. Antibody fragments with an affinity for filamenting temperature-sensitive mutant Z (FtsZ) were constructed and completely inhibited the polymerization of FtsZ. Consequently, the expression of these fragments drastically decreased the cell division rate. We demonstrate the potential of the CAnIGET method with the use of native protein–protein interactions for steady epitope-specific evolutionary engineering.

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Modified Potential Functions Result in Enhanced Predictions of a Protein Complex by All-Atom MD Simulations, Confirming a Step-wise Association Process for Native PPIs

10.1101/241810 ◽

2018 ◽

Cited By ~ 1

Author(s):

Zhen-lu Li ◽

Matthias Buck

Keyword(s):

Electrostatic Interaction ◽

Protein Interactions ◽

Protein Complex ◽

Complex Structure ◽

Md Simulations ◽

Potential Functions ◽

Amino Acid Side Chain ◽

Native Protein ◽

Protein Protein Interactions ◽

Steering Mechanism

ABSTRACTNative protein-protein interactions (PPIs) are the cornerstone for understanding the structure, dynamics and mechanisms of function of protein complexes. In this study, we investigate the association of the SAM domains of the EphA2 receptor and SHIP2 enzyme by performing a combined total of 48 μs all-atom molecular dynamics (MD) simulations. While the native SAM heterodimer is only predicted at a low rate of 6.7% with the original CHARMM36 force field, the yield is increased to 16.7% and to 18.3% by scaling the vdW solute-solvent interactions (better fitting the solvation free energy of amino acid side chain analogues) and by an increase of vdW radius of guanidinium interactions, and thus a dramatic reduction of electrostatic interaction between Arg and Glu/Asn in CHARMM36m, respectively. These modifications effectively improve the overly sticky association of proteins, such as ubiquitin, using the original potential function. By analyzing the 25 native SAM complexes formed in the simulations, we find that their formation involves a pre-orientation guided by electrostatic interaction, consistent with an electrostatic steering mechanism. The complex could then transform to the native protein interaction surfaces directly from a well pre-orientated position (Δinterface-RMSD < 5Å). In other cases, modest (< 90°) orientational and/or translational adjustments are needed (5 Å <Δi-RMSD <10 Å) to the native complex. Although the tendency for non-native complexes to dissociate has nearly doubled with the modified potential functions, a re-association to the correct complex structure is still rare. Instead a most non-native complexes are undergoing configurational changes/surface searching, which do not lead to native structures on a timescale of 250 ns. These observations provide a rich picture on mechanisms of protein-protein complex formation, and suggest that computational predictions of native complex protein-protein interactions could be improved further.

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