scholarly journals Conformationally variable Rab protein surface regions mapped by limited proteolysis and homology modelling

1998 ◽  
Vol 336 (2) ◽  
pp. 461-469 ◽  
Author(s):  
Lydia NIKOLOVA ◽  
Kizhake SOMAN ◽  
Jeffry C. NICHOLS ◽  
D. Sundarsingh DANIEL ◽  
Burton F. DICKEY ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Peptide Mapping ◽  
Homology Modelling ◽  
Limited Proteolysis ◽  
Variable Region ◽  
Peptide Sequencing ◽  
Small Gtpases ◽  
Rab Proteins ◽  
Protein Protein Interactions ◽  
Rab Protein

Tryptic proteolysis of the small GTPases Rab4 and Rab5 is a multi-step, nucleotide-dependent process. Using N-terminal peptide sequencing, matrix-assisted laser desorption ionization–time-of-flight MS and molecular modelling, we identified the three initial sites of proteolysis in Rab5 as Arg-4, Arg-81 and Arg-197. Arg-4 and Arg-81 lie within regions previously implicated in Rab5 endocytic function, and Arg-197 lies in a region involved in membrane targeting. Topologically, Arg-81 lies within the conformationally variable Switch II region shown to be important for protein–protein interactions of other GTPases. Homology modelling studies on Rab5 indicate that the Arg-81 side chain is buried in the Rab5 GTP conformation, but is solvent-accessible in the GDP conformation, explaining the dependence of proteolysis on nucleotides. Peptide mapping of Rab4 was performed to take advantage of additional scissile bonds within Switch II to determine more precisely the limits of the nucleotide-dependent protease-accessible region. The Rab4 cleavage sites corresponded to Arg-81 and Pro-87 of Rab5, and taken together with the finding that Rab5 was not cleaved at Arg-91 this analysis defines an eight-residue surface-exposed conformationally variable region lying in the centre of Switch II. A sequence comparison of Rab proteins shows these eight residues to have a loosely conserved motif that we term Switch II(v) for its relative variability. C-terminal to Switch II(v) is a highly conserved Rab-specific YYRGA motif that we term Switch II(c) for its constant sequence. N-terminal to Switch II(v) is a sequence-invariant G-domain involved in nucleotide binding and hydrolysis. We propose that the Rab Switch II(v) region imparts specificity to nucleotide-dependent protein–protein interactions.

Exploring Proteomic Drug Targets, Therapeutic Strategies and Protein - Protein Interactions in Cancer: Mechanistic View

2019 ◽  
Vol 19 (6) ◽  
pp. 430-448 ◽  
Author(s):  
Khalid Bashir Dar ◽  
Aashiq Hussain Bhat ◽  
Shajrul Amin ◽  
Syed Anjum ◽  
Bilal Ahmad Reshi ◽  
...  
Keyword(s):  
Protein Interactions ◽  
High Throughput Screening ◽  
Critical Role ◽  
Cancer Therapeutics ◽  
Adaptor Proteins ◽  
Therapeutic Strategies ◽  
Small Gtpases ◽  
Beta Catenin ◽  
Protein Protein Interactions ◽  
Apoptosis Protein

Protein-Protein Interactions (PPIs) drive major signalling cascades and play critical role in cell proliferation, apoptosis, angiogenesis and trafficking. Deregulated PPIs are implicated in multiple malignancies and represent the critical targets for treating cancer. Herein, we discuss the key protein-protein interacting domains implicated in cancer notably PDZ, SH2, SH3, LIM, PTB, SAM and PH. These domains are present in numerous enzymes/kinases, growth factors, transcription factors, adaptor proteins, receptors and scaffolding proteins and thus represent essential sites for targeting cancer. This review explores the candidature of various proteins involved in cellular trafficking (small GTPases, molecular motors, matrix-degrading enzymes, integrin), transcription (p53, cMyc), signalling (membrane receptor proteins), angiogenesis (VEGFs) and apoptosis (BCL-2family), which could possibly serve as targets for developing effective anti-cancer regimen. Interactions between Ras/Raf; X-linked inhibitor of apoptosis protein (XIAP)/second mitochondria-derived activator of caspases (Smac/DIABLO); Frizzled (FRZ)/Dishevelled (DVL) protein; beta-catenin/T Cell Factor (TCF) have also been studied as prospective anticancer targets. Efficacy of diverse molecules/ drugs targeting such PPIs although evaluated in various animal models/cell lines, there is an essential need for human-based clinical trials. Therapeutic strategies like the use of biologicals, high throughput screening (HTS) and fragment-based technology could play an imperative role in designing cancer therapeutics. Moreover, bioinformatic/computational strategies based on genome sequence, protein sequence/structure and domain data could serve as competent tools for predicting PPIs. Exploring hot spots in proteomic networks represents another approach for developing targetspecific therapeutics. Overall, this review lays emphasis on a productive amalgamation of proteomics, genomics, biochemistry, and molecular dynamics for successful treatment of cancer.

Rab22a affects the morphology and function of the endocytic pathway

2001 ◽  
Vol 114 (22) ◽  
pp. 4041-4049 ◽  
Author(s):  
Rosana Mesa ◽  
Cristina Salomón ◽  
Marcelo Roggero ◽  
Philip D. Stahl ◽  
Luis S. Mayorga
Keyword(s):  
Fluorescent Protein ◽  
Fluid Phase ◽  
Small Gtpases ◽  
Endocytic Pathway ◽  
Site Directed Mutagenesis ◽  
Rab Proteins ◽  
Rab Protein ◽  
Late Endosomes ◽  
And Function ◽  
Negative Mutant

Soon after endocytosis, internalized material is sorted along different pathways in a process that requires the coordinated activity of several Rab proteins. Although abundant information is available about the subcellular distribution and function of some of the endocytosis-specific Rabs (e.g. Rab5 and Rab4), very little is known about some other members of this family of proteins. To unveil some of the properties of Rab22a, one of the less studied endosome-associated small GTPases, we have expressed the protein tagged with the green fluorescent protein in CHO cells. The results indicate that Rab22a associates with early and late endosomes (labeled by a 5 minute rhodamine-transferrin uptake and the cation-independent mannose 6-phosphate receptor, respectively) but not with lysosomes (labeled by 1 hour rhodamine horseradish peroxidase uptake followed by 1 hour chase). Overexpression of the protein causes a prominent morphological enlargement of the early and late endosomes. Two mutants were generated by site-directed mutagenesis, a negative mutant (Rab22aS19N, with reduced affinity for GTP) and a constitutively active mutant (Rab22aQ64L, with reduced endogenous GTPase activity). The distribution of the negative mutant was mostly cytosolic, whereas the positive mutant associated with early and late endosomes and, interestingly also with lysosomes and autophagosomes (labeled with monodansylcadaverine). Cells expressing Rab22a wild type and Rab22aS19N displayed decreased endocytosis of a fluid phase marker. Conversely, overexpression of Rab22aQ64L, which strongly affects the morphology of endosomes, did not inhibit bulk endocytosis. Our results show that Rab22a has a unique distribution along the endocytic pathway that is not shared by any other Rab protein, and that it strongly affects the morphology and function of endosomes.

scholarly journals The structural evolution of host-pathogen protein interactions: an integrative approach

2019 ◽  
Author(s):  
Anderson F. Brito ◽  
John W. Pinney
Keyword(s):  
Protein Interactions ◽  
Homology Modelling ◽  
Structural Evolution ◽  
Integrative Approach ◽  
Binding Affinities ◽  
Protein Protein Interactions ◽  
Host Pathogen ◽  
Cell Membrane Proteins ◽  
Pathogen Protein ◽  
History Of

ABSTRACTThe evolution of protein-protein interactions (PPIs) is directly influenced by the evolutionary histories of the genes and the species encoding the interacting proteins. When it comes to PPIs of host-pathogen systems, the complexity of their evolution is much higher, as two independent, but biologically associated entities, are involved. In this work, an integrative approach combining phylogenetics, tree reconciliations, ancestral sequence reconstructions, and homology modelling is proposed for studying the evolution of host-pathogen PPIs. As a case study, we analysed the evolution of interactions between herpesviral glycoproteins gD/gG and the cell membrane proteins nectins. By modelling the structures of more than 12,000 ancestral states of these virus-host complexes it was found that in early times of their evolution, these proteins were unable to interact, most probably due to electrostatic incompatibilities between their interfaces. After the event of gene duplication that gave rise to a paralog of gD (known as gG), both protein lineages evolved following distinct functional constraints, with most gD reaching high binding affinities towards nectins, while gG lost such ability, most probably due to a process of neofunctionalization. Based on their favourable interaction energies (negative ΔG), it is possible to hypothesize that apart from nectins 1 and 2, some alphaherpesviruses might also use nectins 3 and 4 as cell receptors. These findings show that the proposed integrative method is suitable for modelling the evolution of host-pathogen protein interactions, and useful for raising new hypotheses that broaden our understanding about the evolutionary history of PPIs, and their molecular functioning.

Rab GTPases and microtubule motors

2011 ◽  
Vol 39 (5) ◽  
pp. 1202-1206 ◽  
Author(s):  
Conor P. Horgan ◽  
Mary W. McCaffrey
Keyword(s):  
Protein Interactions ◽  
Intracellular Trafficking ◽  
Cytoplasmic Dynein ◽  
Small Gtpases ◽  
Transport Processes ◽  
Effector Proteins ◽  
Rab Proteins ◽  
Rab Gtpases ◽  
Microtubule Motor ◽  
Rab Effector

Rab proteins are a family of small GTPases which, since their initial identification in the late 1980s, have emerged as master regulators of all stages of intracellular trafficking processes in eukaryotic cells. Rabs cycle between distinct conformations that are dependent on their guanine-nucleotide-bound status. When active (GTP-bound), Rabs are distributed to the cytosolic face of specific membranous compartments where they recruit downstream effector proteins. Rab–effector complexes then execute precise intracellular trafficking steps, which, in many cases, include vesicle motility. Microtubule-based kinesin and cytoplasmic dynein motor complexes are prominent among the classes of known Rab effector proteins. Additionally, many Rabs associate with microtubule-based motors via effectors that act as adaptor molecules that can simultaneously associate with the GTP-bound Rab and specific motor complexes. Thus, through association with motor complexes, Rab proteins can allow for membrane association and directional movement of various vesicular cargos along the microtubule cytoskeleton. In this mini-review, we highlight the expanding repertoire of Rab/microtubule motor protein interactions, and, in doing so, present an outline of the multiplicity of transport processes which result from such interactions.

scholarly journals Time-lapsed proteomics reveals a role for the novel protein, SNED1, in modulating ECM composition and protein folding

2022 ◽  
Author(s):  
Fred Lee ◽  
Xinhao Shao ◽  
Yu Gao ◽  
Alexandra Naba
Keyword(s):  
Protein Interactions ◽  
Dynamic Range ◽  
Structural Information ◽  
Limited Proteolysis ◽  
The Novel ◽  
Protein Protein Interactions ◽  
Sequence Coverage ◽  
Post Translational Modifications ◽  
Ecm Proteins ◽  
Broad Dynamic Range

The extracellular matrix (ECM) is a complex and dynamic meshwork of proteins providing structural support to cells. It also provides biochemical signals governing cellular processes including proliferation and migration. Alterations of ECM structure and/or composition has been shown to lead to, or accompany, many pathological processes including cancer and fibrosis. To understand how the ECM contributes to diseases, we first need to obtain a comprehensive characterization of the ECM of tissues and of its changes during disease progression. Over the past decade, mass-spectrometry-based proteomics has become the state-of-the-art method to profile the protein composition of ECMs. However, existing methods do not fully capture the broad dynamic range of protein abundance in the ECM, nor do they permit to achieve the high coverage needed to gain finer biochemical information, including the presence of isoforms or post-translational modifications. In addition, broadly adopted proteomic methods relying on extended trypsin digestion do not provide structural information on ECM proteins, yet, gaining insights into ECM protein structure is critical to better understanding protein functions. Here, we present the optimization of a time-lapsed proteomic method using limited proteolysis of partially denatured samples and the sequential release of peptides to achieve superior sequence coverage as compared to standard ECM proteomic workflow. Exploiting the spatio-temporal resolution of this method, we further demonstrate how 3-dimensional time-lapsed peptide mapping can identify protein regions differentially susceptible to trypsin and can thus identify sites of post-translational modifications, including protein-protein interactions. We further illustrate how this approach can be leveraged to gain insight on the role of the novel ECM protein SNED1 in ECM homeostasis. We found that the expression of SNED1 expression by mouse embryonic fibroblasts results in the alteration of overall ECM composition and the sequence coverage of certain ECM proteins, raising the possibility that SNED1 could modify accessibility to trypsin by engaging in protein-protein interactions.

scholarly journals Conservation of co-evolving protein interfaces bridges prokaryote-eukaryote homologies in the twilight zone

2016 ◽  
Author(s):  
Juan Rodriguez-Rivas ◽  
Simone Marsili ◽  
David Juan ◽  
Alfonso Valencia
Keyword(s):  
Protein Interactions ◽  
Homology Modelling ◽  
Accurate Information ◽  
Sequence Information ◽  
Evolutionary Analysis ◽  
Interacting Proteins ◽  
Protein Protein Interactions ◽  
Sequence Alignments ◽  
Multiple Sequence ◽  
Protein Interfaces

AbstractProtein-protein interactions are fundamental for the proper functioning of the cell. As a result, protein interaction surfaces are subject to strong evolutionary constraints. Recent developments have shown that residue co-evolution provides accurate predictions of heterodimeric protein interfaces from sequence information. So far these approaches have been limited to the analysis of families of prokaryotic complexes for which large multiple sequence alignments of homologous sequences can be compiled. We explore the hypothesis that co-evolution points to structurally conserved contacts at protein-protein interfaces, which can be reliably projected to homologous complexes with distantly related sequences. We introduce a novel domain-centred protocol to study the interplay between residue co-evolution and structural conservation of protein-protein interfaces. We show that sequence-based co-evolutionary analysis systematically identifies residue contacts at prokaryotic interfaces that are structurally conserved at the interface of their eukaryotic counterparts. In turn, this allows the prediction of conserved contacts at eukaryotic protein-protein interfaces with high confidence using solely mutational patterns extracted from prokaryotic genomes. Even in the context of high divergence in sequence, where standard homology modelling of protein complexes is unreliable, our approach provides sequence-based accurate information about specific details of protein interactions at the residue level. Selected examples of the application of prokaryotic co-evolutionary analysis to the prediction of eukaryotic interfaces further illustrates the potential of this novel approach.Significance statementInteracting proteins tend to co-evolve through interdependent changes at the interaction interface. This phenomenon leads to patterns of coordinated mutations that can be exploited to systematically predict contacts between interacting proteins in prokaryotes. We explore the hypothesis that co-evolving contacts at protein interfaces are preferentially conserved through long evolutionary periods. We demonstrate that co-evolving residues in prokaryotes identify inter-protein contacts that are particularly well conserved in the corresponding structure of their eukaryotic homologues. Therefore, these contacts have likely been important to maintain protein-protein interactions during evolution. We show that this property can be used to reliably predict interacting residues between eukaryotic proteins with homologues in prokaryotes even if they are very distantly related in sequence.

scholarly journals GRASP and IPCEF Promote ARF-to-Rac Signaling and Cell Migration by Coordinating the Association of ARNO/cytohesin 2 with Dock180

2010 ◽  
Vol 21 (4) ◽  
pp. 562-571 ◽  
Author(s):  
David T. White ◽  
Katie M. McShea ◽  
Myriam A. Attar ◽  
Lorraine C. Santy
Keyword(s):  
Cell Migration ◽  
Protein Interactions ◽  
Cell Shape ◽  
Coiled Coil ◽  
Small Gtpases ◽  
Accessory Proteins ◽  
Protein Protein Interactions ◽  
Coiled Coil Domain ◽  
The Many ◽  
Dependent Processes

ARFs are small GTPases that regulate vesicular trafficking, cell shape, and movement. ARFs are subject to extensive regulation by a large number of accessory proteins. The many different accessory proteins are likely specialized to regulate ARF signaling during particular processes. ARNO/cytohesin 2 is an ARF-activating protein that promotes cell migration and cell shape changes. We report here that protein–protein interactions mediated by the coiled-coil domain of ARNO are required for ARNO induced motility. ARNO lacking the coiled-coil domain does not promote migration and does not induce ARF-dependent Rac activation. We find that the coiled-coil domain promotes the assembly of a multiprotein complex containing both ARNO and the Rac-activating protein Dock180. Knockdown of either GRASP/Tamalin or IPCEF, two proteins known to bind to the coiled-coil of ARNO, prevents the association of ARNO and Dock180 and prevents ARNO-induced Rac activation. These data suggest that scaffold proteins can regulate ARF dependent processes by biasing ARF signaling toward particular outputs.

Interrelationships Between the Complement System and the Coagulation Kinin-Forming and Fibrinolytic Systems

1979 ◽  
Author(s):  
Neil R. Cooper
Keyword(s):  
Protein Interactions ◽  
Serine Proteases ◽  
Limited Proteolysis ◽  
Factor Xa ◽  
Systematic Investigation ◽  
Factor Xii ◽  
Protein Protein Interactions ◽  
Contact Activation ◽  
Calcium Dependent ◽  
Single Polypeptide Chain

During contact activation, the coagulation, kinin-forming and fibrinolytic systems are initiated following the attachment of Factor XII to a surface by a complex series of protein-protein interactions that lead to the activation of serine proteases by limited proteolysis. The activation processes are modulated by protein cofactors and by inhibitors. These molecular processes are similar to those involved in triggering of the complement (C) system, another major plasma effector system. Multiple interrelationships of these four plasma effector systems that have been suggested will be summarized and their functional significance considered.We have begun a systematic investigation of such potential relationships employing highly purified proteins of the four systems. Initial efforts have been directed at determining whether plasma kallikrein, plasmin, thrombin or Factor Xa activate the first reacting component of the classical C pathway, Cl (C) is a calcium-dependent complex of three proteins: CIq , involved in binding ta antibody or other activators, generally on a surface; and Clr and Cls, zymogens of serine proteases. Both kallikrein and plasmin directly activate Clr and also Cls while thrombin and Factor Xa do not. Kallikrein and plasmin cleave the single polypeptide chain of Cls at a site near to or identical to that attacked by and also cleave Cls at another, distant site. These evolving studies confirm and extend earlier work and indicate that the four plasma effector systems are closely interrelated.

A role for Rab27b in NF-E2-dependent pathways of platelet formation

Blood ◽  
2003 ◽  
Vol 102 (12) ◽  
pp. 3970-3979 ◽  
Author(s):  
Sanjay Tiwari ◽  
Joseph E. Italiano ◽  
Duarte C. Barral ◽  
Emilie H. Mules ◽  
Edward K. Novak ◽  
...  
Keyword(s):  
Small Gtpases ◽  
Organelle Transport ◽  
Rab Proteins ◽  
Dense Granules ◽  
Rab Protein ◽  
Normal Expression ◽  
Specific Effector ◽  
Proplatelet Formation ◽  
Effector Pathways

Abstract Megakaryocytes release platelets by reorganizing the cytoplasm into proplatelet extensions. Fundamental to this process is the need to coordinate transport of products and organelles in the appropriate abundance to nascent platelets. The importance of the Rab family of small GTPases (guanosine 5′-triphosphatases) in platelet biogenesis is revealed in gunmetal (gm/gm) mice, which show deficient Rab isoprenylation and macrothrombocytopenia with few granules and abnormal megakaryocyte morphology. Although some Rab proteins are implicated in vesicle and organelle transport along microtubules or actin, the role of any Rab protein in platelet biogenesis is unknown. The limited number of Rab proteins with defective membrane association in gm/gm megakaryocytes prominently includes Rab27a and Rab27b. Normal expression of Rab27b is especially increased with terminal megakaryocyte differentiation and dependent on nuclear factor-erythroid 2 (NF-E2), a transcription factor required for thrombopoiesis. Chromatin immunoprecipitation demonstrates recruitment of NF-E2 to the putative Rab27B promoter. Inhibition of endogenous Rab27 function in primary megakaryocytes causes severe quantitative and qualitative defects in proplatelet formation that mimic findings in gm/gm cells. Rab27b localizes to alpha and dense granules in megakaryocytes. These results establish a role for Rab27 in platelet synthesis and suggest that Rab27b in particular may coordinate proplatelet formation with granule transport, possibly by recruiting specific effector pathways.

Cross-linking/MS analysis of TBEV and neuroblastoma cells v1

2021 ◽  
Author(s):  
Sarah Barrass ◽  
Lauri I. A. Pulkkinen ◽  
Olli Vapalahti ◽  
Suvi H. Kuivanen ◽  
Maria Anastasina ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Protein Interactions ◽  
Internal Control ◽  
Limited Proteolysis ◽  
Neuroblastoma Cells ◽  
Host Protein ◽  
Cross Linking ◽  
Protein Protein Interactions ◽  
Cross Links ◽  
Using Data

Virus-host protein-protein interactions are central to viral infection, but are challenging to identify and characterise, especially in complex systems involving intact viruses and cells. Here, we describe a proteome-wide approach to identify virus-host interactions using chemical cross-linking coupled with mass spectrometry. We adsorbed tick-borne encephalitis virus onto metabolically-stalled neuroblastoma cells, covalently cross-linked interacting virus-host proteins, and performed limited proteolysis to release primarily the surface-exposed proteins for analysis by mass spectrometry. Proteins in the sample were identified using data-dependent acquisition mass spectrometry and cross-linked peptides were identified using the software pLink2. Cross-links are validated using the intraviral cross-links as an internal control.

Sign in / Sign up

Export Citation Format

Share Document