Surbhi Sharma

All Publications

• New Minimotifs and their functions in the C-Terminome Journal of Proteomics & Bioinformatics Sharma, S., Novakovic, N., FitzHugh, Z., Bragg, A., Brooks, S., Wu, X., Schiller, M. R. 2022; 14 (12)
• The carboxy-terminus, a key regulator of protein function CRITICAL REVIEWS IN BIOCHEMISTRY AND MOLECULAR BIOLOGY Sharma, S., Schiller, M. R. 2019; 54 (2): 85–102

  Abstract

  All proteins end with a carboxyl terminus that has unique biophysical properties and is often disordered. Although there are examples of important C-termini functions, a more global role for the C-terminus is not yet established. In this review, we summarize research on C-termini, a unique region in proteins that cells exploit. Alternative splicing and proteolysis increase the diversity of proteins and peptides in cells with unique C-termini. The C-termini of proteins contain minimotifs, short peptides with an encoded function generally characterized as binding, posttranslational modifications, and trafficking. Many of these activities are specific to minimotifs on the C-terminus. Approximately 13% of C-termini in the human proteome have a known minimotif, and the majority, if not all of the remaining termini have conserved motifs inferring a function that remains to be discovered. C-termini, their predictions, and their functions are collated in the C-terminome, Proteus, and Terminus Oriented Protein Function INferred Database (TopFIND) database/web systems. Many C-termini are well conserved, and some have a known role in health and disease. We envision that this summary of C-termini will guide future investigation of their biochemical and physiological significance.

  View details for DOI 10.1080/10409238.2019.1586828

  View details for Web of Science ID 000469055800001

  View details for PubMedID 31106589

  View details for PubMedCentralID PMC6568268

• Minimotifs dysfunction is pervasive in neurodegenerative disorders. Alzheimer's & dementia (New York, N. Y.) Sharma, S., Young, R. J., Chen, J., Chen, X., Oh, E. C., Schiller, M. R. 2018; 4: 414-432

  Abstract

  Minimotifs are modular contiguous peptide sequences in proteins that are important for posttranslational modifications, binding to other molecules, and trafficking to specific subcellular compartments. Some molecular functions of proteins in cellular pathways can be predicted from minimotif consensus sequences identified through experimentation. While a role for minimotifs in regulating signal transduction and gene regulation during disease pathogenesis (such as infectious diseases and cancer) is established, the therapeutic use of minimotif mimetic drugs is limited. In this review, we discuss a general theme identifying a pervasive role of minimotifs in the pathomechanism of neurodegenerative diseases. Beyond their longstanding history in the genetics of familial neurodegeneration, minimotifs are also major players in neurotoxic protein aggregation, aberrant protein trafficking, and epigenetic regulation. Generalizing the importance of minimotifs in neurodegenerative diseases offers a new perspective for the future study of neurodegenerative mechanisms and the investigation of new therapeutics.

  View details for DOI 10.1016/j.trci.2018.06.005

  View details for PubMedID 30225339

  View details for PubMedCentralID PMC6139474

• The Functional Human C-Terminome PLOS ONE Sharma, S., Toledo, O., Hedden, M., Lyon, K. F., Brooks, S. B., David, R. P., Limtong, J., Newsome, J. M., Novakovic, N., Rajasekaran, S., Thapar, V., Williams, S. R., Schiller, M. R. 2016; 11 (4): e0152731

  Abstract

  All translated proteins end with a carboxylic acid commonly called the C-terminus. Many short functional sequences (minimotifs) are located on or immediately proximal to the C-terminus. However, information about the function of protein C-termini has not been consolidated into a single source. Here, we built a new "C-terminome" database and web system focused on human proteins. Approximately 3,600 C-termini in the human proteome have a minimotif with an established molecular function. To help evaluate the function of the remaining C-termini in the human proteome, we inferred minimotifs identified by experimentation in rodent cells, predicted minimotifs based upon consensus sequence matches, and predicted novel highly repetitive sequences in C-termini. Predictions can be ranked by enrichment scores or Gene Evolutionary Rate Profiling (GERP) scores, a measurement of evolutionary constraint. By searching for new anchored sequences on the last 10 amino acids of proteins in the human proteome with lengths between 3-10 residues and up to 5 degenerate positions in the consensus sequences, we have identified new consensus sequences that predict instances in the majority of human genes. All of this information is consolidated into a database that can be accessed through a C-terminome web system with search and browse functions for minimotifs and human proteins. A known consensus sequence-based predicted function is assigned to nearly half the proteins in the human proteome. Weblink: http://cterminome.bio-toolkit.com.

  View details for DOI 10.1371/journal.pone.0152731

  View details for Web of Science ID 000373603500051

  View details for PubMedID 27050421

  View details for PubMedCentralID PMC4822787