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Hire Dr. Sudeep K.

Finland

USD 50 /hr

Structural biologist with >9 years working in the areas of protein science

Profile Summary

I am a highly motivated and experienced research scientist in structural biology, protein biochemistry, biophysics, bioinformatics and molecular biology with 9+ years of experience in biomedical research. - Extensive working experience in the areas of molecular cloning, recombinant protein purification (bacterial and insect protein expression systems), x-ray crystallography, protein crystal data analysis and structure solution ( familiar with software like CCP4 suite, Pymol, Chimera, Phenix ) protein structure modeling, cryo-EM, bioinformatics, statistical analysis, small molecular screening and biophysical studies. - An excellent communicator and have a passion for protein science and science communication. Good scientific communication skills both verbally and in writing and published >3 peer-reviewed articles, presented in >10 national and international conferences, and successfully granted >€50000 funds. - Currently a postdoctoral researcher at the University of Helsinki, Finland. In my current project, I am trying to understand the role of the eukaryotic protein complexes present in the endoplasmic reticulum (ER) using advanced techniques in structural biology and molecular biology. In my Ph.D. work at University of Helsinki, I focused on understanding the molecular basis of the structure and function of protein complexes present in the brain and their role in the neuronal wiring of the brain.

Subject Matter Expertise

• ★ Structural Biology
• ★ Molecular Biology
• ☆ X-Ray Crystallography
• ☆ Biophysics
• ☆ Recombinant Protein Expression
• ☆ Bioinformatics

Services

• Writing
• Research
• Consulting
• Data & AI
• Product Development

Writing Technical Writing

Research Market Research, User Research, Gap Analysis, Gray Literature Search, Systematic Literature Review

Consulting Scientific and Technical Consulting

Data & AI Statistical Analysis, Data Processing

Product Development Formulation, Product Validation

Work Experience

University of Helsinki

- Present

Postdoctoral Researcher

University of Helsinki

March 2021 - Present

Laboratory Technician

University of Helsinki

January 2021 - February 2021

PhD. Researcher

University of Helsinki

February 2016 - December 2020

Education

University of Helsinki

- Present

PhD, Biochemistry

University of Helsinki

August 2016 - December 2020

Masters in Biology -Microbiology

University of Bergen

August 2013 - September 2015

Masters in molecular biosciences

University of Oslo

August 2010 - September 2012

Certifications

• LINXS workshop ISB 2nd Symposium

  Univeristy of Lund

  https://www.linxs.se/events/2019/10/9/linxs-event-isb-2nd-symposium

  October 2019 - October 2019

• Workshop on cryo-electron microscopy and CryoEM image re-construction

  University of Helsinki, Finalnd

  March 2019 - April 2019

• 14th International school of biophysics

  Croatian Biophysical Society

  http://school.ifs.hr/2018/

  August 2018 - September 2018

• iNEXT course X-ray and neutron diffraction studies of macromolecules: from data collection to structures

  University of Oulu, Finland

  April 2017 - April 2017

• RapidData 2017 - Course in Macromolecular X-Ray Diffraction

  Stanford University, USA

  March 2017 - April 2017

Publications

JOURNAL ARTICLE

Sudeep Karki, Jinhu Kim, Seungjoon Kim, Hyeonho Kim, In-Wook Hwang, Sungwon Bae, Dongwook Kim, Roberto Ogelman, Geul Bang, Jin Young Kim, et al.(2022). MDGA1 negatively regulates amyloid precursor protein–mediated synapse inhibition in the hippocampus . Proceedings of the National Academy of Sciences. 119. (4). p. e2115326119. Proceedings of the National Academy of Sciences

Jinhu Kim and Seungjoon Kim and Hyeonho Kim and In-Wook Hwang and Sungwon Bae and Sudeep Karki and Dongwook Kim and Roberto Ogelman and Geul Bang and Jin Young Kim and Tommi Kajander and Ji Won Um and Won Chan Oh and Jaewon Ko(2022). MDGA1 negatively regulates amyloid precursor protein–mediated synapse inhibition in the hippocampus . Proceedings of the National Academy of Sciences. 119. (4). p. e2115326119. Proceedings of the National Academy of Sciences

Sudeep Karki and Tommi Kajander(2022). Crystallization and low-resolution structure solution of the SALM3–PTPσ synaptic adhesion complex . Acta Crystallographica Section F Structural Biology Communications. 78. (1). p. 39--44. International Union of Crystallography ({IUCr})

Sudeep Karki, Tommi Antero Kajander(2021). Crystallization and low-resolution structure solution of the SALM3–PTPσ synaptic adhesion complex . Acta crystallographica section f-Structural biology communications. F78. p. 39--44. INT UNION CRYSTALLOGRAPHY

Structural basis of SALM3 dimerization and synaptic adhesion complex formation with PTPσ @article{3789b8342b8f4dcf90d8d6f321e8918a, title = "Structural basis of SALM3 dimerization and synaptic adhesion complex formation with PTPσ", abstract = "Synaptic adhesion molecules play an important role in the formation, maintenance and refinement of neuronal connectivity. Recently, several leucine rich repeat (LRR) domain containing neuronal adhesion molecules have been characterized including netrin G-ligands, SLITRKs and the synaptic adhesion-like molecules (SALMs). Dysregulation of these adhesion molecules have been genetically and functionally linked to various neurological disorders. Here we investigated the molecular structure and mechanism of ligand interactions for the postsynaptic SALM3 adhesion protein with its presynaptic ligand, receptor protein tyrosine phosphatase sigma (PTP sigma). We solved the crystal structure of the dimerized LRR domain of SALM3, revealing the conserved structural features and mechanism of dimerization. Furthermore, we determined the complex structure of SALM3 with PTP sigma using small angle X-ray scattering, revealing a 2:2 complex similar to that observed for SALM5. Solution studies unraveled additional flexibility for the complex structure, but validated the uniform mode of action for SALM3 and SALM5 to promote synapse formation. The relevance of the key interface residues was further confirmed by mutational analysis with cellular binding assays and artificial synapse formation assays. Collectively, our results suggest that SALM3 dimerization is a pre-requisite for the SALM3-PTP sigma complex to exert synaptogenic activity.", keywords = "1182 Biochemistry, cell and molecular biology, LAR-RPTPS, TRANSMEMBRANE PROTEINS, FAMILY, REFINEMENT, MOLECULES, INTERACTS, QUALITY", author = "Sudeep Karki and Shkumatov, {Alexander V.} and Sungwon Bae and Hyeonho Kim and Jaewon Ko and Tommi Kajander", note = "bioRxiv: doi: https://doi.org/10.1101/2020.01.09.893701 ", year = "2020", month = jul, day = "14", doi = "10.1038/s41598-020-68502-4", language = "English", volume = "10 ", journal = "Scientific Reports", issn = "2045-2322", publisher = "Nature Publishing Group", number = "1", } . Scientific Reports.

Inhibitor screening assay for neurexin-LRRTM adhesion protein interaction involved in synaptic maintenance and neurological disorders. @article{bae9ff7390504669906fec4c0178856b, title = "Inhibitor screening assay for neurexin-LRRTM adhesion protein interaction involved in synaptic maintenance and neurological disorders.", abstract = "Synaptic adhesion molecules, including presynaptic neurexins (NRXNs) and post-synaptic leucine-rich repeat transmembrane (LRRTM) proteins are important for development and maintenance of brain neuronal networks. NRXNs are probably the best characterized synaptic adhesion molecules, and one of the major presynaptic organizer proteins. The LRRTMs were found as ligands for NRXNs. Many of the synaptic adhesion proteins have been linked to neurological cognitive disorders, such as schizophrenia and autism spectrum disorders, making them targets of interest for both biological studies, and towards drug development. Therefore, we decided to develop a screening method to target the adhesion proteins, here the LRRTM-NRXN interaction, to find small molecule probes for further studies in cellular settings. To our knowledge, no potent small molecule compounds against the neuronal synaptic adhesion proteins are available. We utilized the AlphaScreen technology, and developed an assay targeting the NRXN-LRRTM2 interaction. We carried out screening of 2000 compounds and identified hits with moderate IC50-values. We also established an orthogonal in-cell Western blot assay to validate hits. This paves way for future development of specific high affinity compounds by further high throughput screening of larger compound libraries using the methods established here. The method could also be applied to screening other NRXN-ligand interactions.", keywords = "AlphaScreen, In-cell western blot, LRRTM, Neurexin, Synapse, Adhesion, Inhibitor assay, Neurological disorders, 1182 Biochemistry, cell and molecular biology, 3112 Neurosciences", author = "Sudeep Karki and Maksimainen, {Mirko M.} and Lari Lehti{\"o} and Tommi Kajander", year = "2019", month = dec, day = "15", doi = "10.1016/j.ab.2019.113463", language = "English", volume = "587", journal = "Analytical Biochemistry", issn = "0003-2697", publisher = "Elsevier", } . Analytical Biochemistry.

(2019). Inhibitor screening assay for neurexin-LRRTM adhesion protein interaction involved in synaptic maintenance and neurological disorders . Analytical Biochemistry.

The structure of SALM5 suggests a dimeric assembly for the presynaptic RPTP ligand recognition. @article{262771f55a8d46e3a05d06fa2539360b, title = "The structure of SALM5 suggests a dimeric assembly for the presynaptic RPTP ligand recognition.", abstract = "Synaptic adhesion molecules play a crucial role in the regulation of synapse development and maintenance. Recently, several families of leucine-rich repeat (LRR) domain-containing neuronal adhesion molecules have been characterised, including netrin-G ligands, LRRTMs and the synaptic adhesion-like molecule (SALM) family proteins. Most of these are expressed at the excitatory glutamatergic synapses, and dysfunctions of these genes are genetically linked with cognitive disorders, such as autism spectrum disorders and schizophrenia. The SALM family proteins SALM3 and SALM5, similar to SLITRKs, have been shown to bind to the presynaptic receptor protein tyrosine phosphatase (RPTP) family ligands. Here, we present the 3.1 {\AA} crystal structure of the SALM5 LRR-Ig-domain construct and biophysical studies that verify the crystallographic results. We show that SALM1, SALM3 and SALM5 form similar dimeric structures, in which the LRR domains form the dimer interface. Both SALM3 and SALM5 bind to RPTP immunoglobulin domains with micromolar affinity. SALM3 shows a clear preference for the RPTP ligands with the meB splice insert. Our structural studies and sequence conservation analysis suggests a ligand-binding site and mechanism for RPTP binding via the dimeric LRR domain region.", keywords = "adhesion, crystal structure, leucine-rich repeat, SALM, synapse, EXCITATORY SYNAPSE DEVELOPMENT, PROTEIN-TYROSINE PHOSPHATASES, ADHESION-LIKE MOLECULES, NERVOUS-SYSTEM, PTP-SIGMA, LAR-RPTPS, FAMILY, COMPLEX, REPLACEMENT, REFINEMENT, 1182 Biochemistry, cell and molecular biology", author = "Sudeep Karki and Prodeep Paudel and Sele, {Celeste Paula Eloise} and Shkumatov, {Alexander V.} and Kajander, {Tommi Antero}", year = "2018", month = may, doi = "10.1093/protein/gzy012", language = "English", volume = "31", pages = "147--157", journal = "Protein Engineering, Design and Selection", issn = "1741-0126", publisher = "Oxford University Press", number = "5", } . Protein Engineering, Design and Selection.

DISSERTATION THESIS

STRUCTURAL AND FUNCTIONAL CHARACTERIZATION OF LEUCINE-RICH REPEAT SYNAPTIC ADHESION MOLECULES @phdthesis{4926786d26194405b929b8d2ac75ed88, title = "STRUCTURAL AND FUNCTIONAL CHARACTERIZATION OF LEUCINE-RICH REPEAT SYNAPTIC ADHESION MOLECULES", abstract = "Synaptic adhesion molecules play a key role in the regulation of synapse development and maintenance. Several families of leucine-rich repeat (LRR) domain containing synaptic adhesion molecules have been characterized, including synaptic adhesion-like molecules (SALMs), and the LRR transmembrane (LRRTM) proteins. These proteins localize mostly in postsynaptic neurons in excitatory synapses and interact with presynaptic adhesion protein families; neurexin (NRXN) and leukocyte common antigen-related protein tyrosine phosphatases (LAR-RPTPs). Dysfunction of the synaptic adhesion molecules is linked to cognitive disorders, such as autism spectrum disorders and schizophrenia. This thesis work comprises the structural and functional study of SALM3 and SALM5 proteins from the SALM family, and their interaction with PTPσ from the LAR-RPTPs family. In addition, this thesis includes the work on the development of an inhibitory screening assay for synaptic adhesion molecules interactions, here targeting the LRRTM2-NRXN interaction. The SALM family proteins include five members, SALM1-5. We have solved the crystal structures of the mouse SALM5 LRR-Ig, and SALM3 LRR constructs at 3.1 {\AA} and 2.8 {\AA} resolution, respectively. Both the structures show the LRR domain mediating the dimerization, also verified by biophysical studies. We determined the binding affinity of SALM3 and SALM5 as 2-23 µM towards PTPσ, and solved the solution structure of the SALM3-PTPσ complex using small-angle X-ray scattering (SAXS), revealing a 2:2 complex formation similar to that observed for SALM5 and PTP. Based on our structure-function studies, SALM3 dimerization is vital for the SALM3-PTPσ complex to exert synaptogenic activity. We also developed an inhibitor screening method for the adhesion proteins interactions, focusing on the LRRTM2-NRXN interaction. We utilized the AlphaScreen technology to identify inhibitors with moderate IC50-values and established an orthogonal in-cell western blot assay to verify the obtained hits. This paves the way for the future development of high affinity compounds by further high throughput screening of larger compound libraries. The studies conducted in this thesis and the results have contributed to a better understanding of the role of SALM proteins in synapse formation, and possibly these structure-based studies will help to understand their implications in disease. The inhibitor screening assay developed can be adapted towards other synaptic adhesion interactions, and the inhibitors obtained could be used for functional studies, or towards drug discovery.", keywords = "1182 Biochemistry, cell and molecular biology", author = "Sudeep Karki", year = "2020", month = dec, day = "17", language = "English", isbn = "978-951-51-6827-6", publisher = "Helsingin yliopisto", address = "Finland", school = "University of Helsinki", } . null.

OTHER

Sudeep Karki, Alexander V. Shkumatov, Sungwon Bae, Jaewon Ko, Tommi Kajander(2020). Structural basis of SALM3 dimerization and synaptic adhesion complex formation with PTPσ . Cold Spring Harbor Laboratory