Structural Bio Overview Book

Understanding Life and Disease I N AT O M I C D E TA I L

DEPARTMENT OF STRUCTURAL BIOLOGY | 1

CONTENTS

A view of the state-of-the-art Biomolecular NMR Center

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4

Mission

8

Main Developments

10

Faculty Research

24 Beyond the Department 30 Center of Excellence for Data-Driven Discovery 32

Culture

34 Resources and Space

36

TECHNOLOGY CORE CENTERS

38 Biomolecular NMR Center 40 Biomolecular X-Ray Crystallography Center 42 Computational Structural Biology Center 44 Cryo-EM Center 46 Protein Technologies Center 48 Single-Molecule Imaging Center

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Cutting-edge biomolecular visualization is made possible through singlemolecule imaging techniques.

MISSION The Department of Structural Biology has currently 11 faculty members and over 200 trainees and employees, working to decipher the biophysical principles and molecular mechanisms underlying key biological processes.

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Charalampos Babis Kalodimos, PhD, Structural Biology Chair, in the Biomolecular NMR Center

Charalampos Babis Kalodimos, PhD, joined St. Jude in 2017 as the new Structural Biology chair, and he brought with him a clear mission: to understand health and disease in atomic detail. His vision for the department led to the launch of the technology centers, which allow researchers to study biology at its most fundamental level using state-ofthe-art technology: X-ray crystallography, nuclear magnetic resonance (NMR) spectroscopy, cryo-electron microscopy and tomography, single-molecule imaging, mass spectrometry and computational structural biology.

Dr. Kalodimos also identified and recruited faculty investigating research topics at the forefront of structural biology that had previously been underrepresented within the department. These include exploring membrane protein complexes, studying large macromolecular assemblies using single-molecule spectroscopy and cryoEM/single particle analysis, and integrating structural information and diverse data types (functional, genetic, genomic, etc.) through computational approaches.

St. Jude Structural Biology department continues to evolve and expand, but it remains steadfast in its mission, while building an open and collaborative environment and nurturing the next generation of structural biologists.

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A close-up view of the NMR spectrometer

St. Jude Structural Biology department has established six technology core centers focused on advanced techniques: X-ray crystallography, NMR, cryo-EM, protein technologies, single-molecule imaging and computational structural biology. Staffed by expert scientists, these centers offer cuttingedge technology and training, empowering integrative structural biology and drawing researchers at various career stages.

The department’s strategy for advancement involves recruiting accomplished scientists as well as emerging researchers, fostering a diverse range of expertise and addressing previous gaps within the field.

MAIN

DEVELOPMENTS

SC IE N TIF IC AC HIE V E M E N TS The department has been highly productive: since 2017, its researchers have contributed to 250+ primary research articles in peer-reviewed journals and 60+ secondary research articles (reviews, commentaries, book chapters).

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Meiqin Jiang, PhD, Postdoc in Structural Biology Department, preparing a grid for cryo-electron microscopy

FAC U LT Y RESEARCH

Scan to learn more about the Structural Biology Faculty Research

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M. MADAN BABU

SCOTT BLANCHARD

PhD, FRS, FRSC, FMedSci

PhD

Uses a multidisciplinary approach in biomedical data science to address fundamental questions with translational impact.

Focuses on developing methodological approaches to gain direct, quantitative insights into the timing and role of conformational changes in biomolecular complexes and how they govern function and regulation.

His recent work, “Predicting evolutionary outcomes through the probability of accessing sequence variants,” published in Science Advances, uses data science approaches to determine the probability of accessing different sequence variants from a starting sequence, thereby enabling the prediction of evolutionary trajectories and outcomes.

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His recent work, “mRNA decoding in human is kinetically and structurally distinct from bacteria,” published in Nature, combines single-molecule imaging and cryo-EM methods to examine the molecular basis of human ribosome fidelity.

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CHARALAMPOS G. KALODIMOS MARIO HALIC PhD Uses cryo-electron microscopy to research chromatin processes and gene expression regulation.

His recent work, “Histone modifications regulate pioneer transcription factor cooperativity,” published in Nature, uses cryoEM to explore how binding of OCT4 transcription factor induces changes to the nucleosome structure, repositions the nucleosomal DNA and facilitates cooperative binding of additional OCT4 and SOX2 to their internal binding sites.

PhD Structural Biology Chair

Focuses his research on understanding the structure and dynamics of protein kinases and molecular chaperones by combining high-resolution NMR spectroscopy and other structural approaches.

His recent work, “Mechanism for the activation of the anaplastic lymphoma kinase receptor”, published in Nature, uses an integrated structural biology approach to obtain valuable insights into how endogenous ligands bind and activate ALK, an important target for cancer drug development.

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ELIZABETH KELLOGG PhD

RICHARD W. KRIWACKI PhD

Uses structural biology, genetics and protein design approaches to explore the mechanisms used

by CRISPR-associated transposons (CASTs) to identify and integrate into their target sites.

Explores how proteins that form aberrant cellular compartments contribute to a variety of pediatric cancers.

Her recent work, “Structures of

in Cancer Discovery uses biophysics

the holo CRISPR RNA-guided transposon integration complex,” published in Nature, reveals how the components of the

His work, “Phase separation mediates NUP98 fusion oncoprotein leukemic transformation,” published and cellular imaging approaches to study the role of phase separation in leukemogenesis by NUP98 fusion oncoproteins.

transpososome interact with each other and with DNA. This research enhances the understanding of CAST systems and suggests ways to engineer them for precision genome-editing applications.

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CHIA-HSUEH LEE

TANJA MITTAG

PhD

PhD

Studies the structure and function of membrane transporters and enzymes to understand how these macromolecular machines transmit information across the membrane, and how their dysfunction can lead to diseases.

Focuses on understanding the molecular interactions underlying the formation of membrane-less organelles, or so-called biomolecular condensates, and how they give rise to function and disease.

Her recent work, “Higher-order

His recent work, “Structural and

SPOP assembly reveals a basis for

functional insights into Spns2-

cancer mutant dysregulation,”

mediated transport of sphingosine-

published in Molecular Cell,

1-phosphate,” published in Cell, uses

uncovers molecular mechanisms

cryo-EM and functional assays to shed

underlying the dysregulation

light on Spns2-mediated S1P transport

of speckle-type POZ protein

and can aid in developing advanced

(SPOP) function.

Spns2 inhibitors.

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JUNMIN PENG

BRENDA SCHULMAN

PhD

PhD

Integrates mass spectrometry–based proteomics and genetics approaches to explore the molecular mechanisms at play in cancer and neurodegenerative diseases.

Studies the structural basis for post-translational modification by ubiquitin and ubiquitin-like proteins.

His recent work, “Alzheimer’s

substrate fidelity,” published in

disease-associated U1 snRNP splicing dysfunction causes neuronal hyperexcitability and cognitive impairment”, published in Nature Aging, reveals a novel

Her recent work, “E3 ligase autoinhibition by C-degron mimicry maintains C-degron Molecular Cell, examines how a cullin-RING ligase discriminates bona fide substrates from other proteins that have degron-like sequences.

mechanism by which RNA splicing defects contribute to Alzheimer’s disease.

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JI SUN PhD Leverages structural biology and biophysics expertise to dissect the function of enzymes and signaling molecules at the membrane interface.

His recent work, “Human IFT-A complex structures provide molecular insights into ciliary transport,” published in Cell Research, reveals Intraflagellar transport (IFT)-A architecture, sheds light on ciliary transport and IFT train formation and enables the rationalization of disease mutations in ciliopathies.

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Zoe Watson, PhD, Postdoc, Department of Structural Biology operates a Titan Krios electron microscope.

B E YO ND

T H E D E PA R T M E N T In addition to delving into individual research projects, department members participate in collaborative efforts that have received institutional and external funding and have taken active roles in many institutional initiatives.

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L E A D I NG SCIENTIFI C C O LL A BOR ATIONS

Researchers within the Structural BIology department participate in several multidisciplinary collaborations.

Collaborative Research Consortium on the Biology and Biophysics of RNP Granules Founded in 2017 to increase our understanding of biomolecular condensate

Crystallization trays set up to grow protein crystals

has over 50 scientists with expertise in protein biochemistry, NMR spectroscopy, structural biology, bioinformatics and other computational approaches.

Fusion Oncoproteins in Childhood Cancers This NCI-funded consortium aims to determine the mechanisms behind NUP98-

Alex’s Lemonade Stand Foundation Crazy 8

rearranged acute leukemia and develop

University at Buffalo, Princeton University

Dr. Babu is a member of a team at St. Jude

of Pathology and Chemical Biology and

and Washington University in St. Louis. It

that investigates the use of small-molecule

Therapeutics, along with researchers

was renewed in 2022, under the leadership

degraders to target aberrant transcription

from Dana Farber Cancer Institute and

of Dr. Mittag, to explore the structure and

factors that drive acute leukemias and

Memorial Sloan Kettering Cancer Institute,

dynamics of condensates and how they

medulloblastoma. Led by Charles Mullighan,

investigate those mechanisms through

relate to biological functions and pathology.

MD, of the Pathology department and

experimental modeling and investigation

with members from Chemical Biology and

of chromatin biology, phase separation

Therapeutics, Developmental Neurobiology,

and drug development.

formation, this consortium includes researchers from St. Jude and from the

Blue-Sky Initiative “Seeing the Invisible in Protein Kinases” The initiative is led by Dr. Kalodimos in collaboration with Dr. Babu to systematically characterize the conformational landscape of the human kinome and identify rare conformational states. Approved in 2021, it has received institutional funding over six

new therapeutic modalities. Dr. Kriwacki and investigators from the departments

and Tumor Cell Biology, the team utilizes computational frameworks developed by Dr. Babu to analyze cancer dependency datasets from pediatric cancer cell lines and to identify zinc finger transcription factors that represent key vulnerabilities in those cancers.

years. The “Blue-Sky Kinases” team currently

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PR OM OTI N G CH A NGE S AC RO SS ST. J UDE

Members of the Structural Biology department understand the importance

Data Science Team

Biomedical Science Symposium

Data Science Task Force

of removing barriers between disciplines and demographics.

They have passionately engaged with their peers to enact positive change within the institution to build bridges.

Some initatives include:

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Women in Leadership and Learning

Women in STEM Task Force

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Vikas Trivedi, PhD, Scientist; Asaf Elazar, PhD, Postdoc; Katarina Nemec, PhD, Lead Researcher; and Georgi Kanev, PhD, Sr. Computational Research Scientist

CENTER OF EXCELLENCE FOR DATA-DRIVEN DISCOVERY

The Center of Excellence for Data-Driven Discovery (C3D) is part of St. Jude Children’s Research Hospital’s efforts to become a leader in applying data science to biological discovery. C3D was founded in 2020 to address the challenges of integrating and deriving actionable insights from vast and diverse biological datasets.

Its mission is to pioneer data science approaches to discover new biology, emphasizing mechanisms of human and catastrophic pediatric diseases.

This mission perfectly aligns with those of the Department of Structural Biology and St. Jude and will be achieved by bringing together investigators with diverse fields of interest but common use of data science approaches.

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Scan to learn more about the Structural Biology Center of Excellence.

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Mohammad Zuhaib Qayyum, PhD, Scientist

Katarina Nemec, PhD, Lead Researcher

C U LT U R E

Mentorship

it also offers career development

The Structural Biology department offers

opportunities. Within the Technology

mentorship programs for early- and mid-

Centers, staff members hold workshops and

career researchers, from the High School

hands-on training opportunities. Finally,

and College Research Immersion program

the annual Structural and Computational

all the way to assistant faculty members.

Biology Symposium invites internal and

These mentorship initiatives aim to provide

external researchers of all career levels

burgeoning scientists with the skills and

to present on topics at the forefront of

resources they will need to succeed in

structural biology.

their careers, including CV development, leadership opportunities, advice for

Support

navigating publishing processes and

The Structural Biology department features

much more.

an administrative/core team that provides researchers with support on different

Scientific Events

aspects of the scientific endeavor. This team

The Structural Biology department

Recognizing that innovative ideas don’t

plays a crucial role in the research process

is committed to fostering a sense of

form in a vacuum, the Structural Biology

by overseeing the necessary administrative

department has strived to provide

functions that allow investigators to focus

opportunities for all personnel to

on their work. These functions include

exchange ideas.

but are not limited to designing and

community among its members through targeted mentorship, exchanging knowledge and ideas at scientific events and providing structural support to the research enterprise.

outfitting laboratory spaces, managing the The weekly departmental seminar series

department’s budgetary plans, developing

invites internal and external speakers to

illustrations and animations of complex

present the latest developments within the

biological processes and concepts, providing

field and garner feedback on unpublished

manuscript support and assisting with grant

work. The annual departmental retreat is

applications and project proposals.

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A researcher inserts a sample into a cryo-electron microscope.

RESOURCES A N D S PA C E

In spring 2023, the department relocated to a new 67,000 sq ft space on the 6th and 7th floors of the I4ARC building. Combined with the expanded Plaza Level area of the DTRC (to expand the Cryo-EM Center), totaling almost 78,000 sq ft, the move aims to accommodate several incoming faculty members in the next few years.

The I4ARC location strategically houses shared equipment and working areas, with over 2,400 sq ft of shared space, including dedicated zones for specialized cell and tissue culture work. Major instrumentation for shared use includes equipment for biophysical studies (e.g., spectroscopy, microcalorimeter, light scattering), molecular biology and biochemistry (cell lysis, centrifugation, chromatography, imaging systems).

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Scan to learn more about the Structural Biology Resources and Space

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Youlin Xia, PhD, Lead Scientist and director of the Biomolecular Nuclear Magnetic Resonance Center, loading a sample into the NMR spectrometer

The Technology Core Centers within the Structural Biology department provide investigators access to cutting-edge equipment and methodologies. These stateof-the-art facilities, coupled with dedicated expert staff, enable St. Jude researchers to tackle challenging biological problems with multidisciplinary approaches.

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A view of the state-of-the-art Biomolecular NMR Center

44 peer-reviewed

publications since 2017, including co-authorships and with the director as the corresponding author.

2

17

60+ fully trained users.

B I O MO L ECU L A R NM R C ENTER The Biomolecular NMR Center was established in 2017 with the mission to provide all St. Jude scientists with access to state-of-the-art instrumentation and expert scientific support for solution NMR studies of proteins and other biomolecules. The Center enables St. Jude researchers to perform cutting-edge NMR studies that probe protein structure and dynamics, monitor protein-ligand interactions and characterize small molecule-protein interactions to support drug discovery.

Staff members are available to consult on NMR experiment design, support analysis and provide user training.

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By early 2024, the Center will have 13 NMR spectrometers, including the world’s first 1.1GHz instrument, installed in 2019.

“The NMR Center is very well maintained and organized. Everything was very easy and convenient to set up. The facility is doing a great job.”

– Giri Sekar, PhD

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In-house X-ray diffraction laboratory

Approximately

75,000

nanoliter crystallization trials are dispensed yearly, resulting in the crystallization of roughly B I O MO L ECU L A R X- R AY CRYSTA L LO G R A P HY C ENTER The Biomolecular X-Ray Crystallography Center is designed to facilitate studies of protein and macromolecular structure and function, which serve as a foundation for drug discovery efforts at St. Jude. Its staff members facilitate a collaborative environment through their commitment to training and supporting researchers at every level, assisting with project planning, experimental design, crystallization, data collection, structure determination, structure interpretation and manuscript preparation.

50 proteins annually.

Regularly achieves 2.2-Å-resolution or better for mid-size protein systems. The highest resolution obtained at the Center for a protein to date was 1.0 Å.

“I hold the X-Ray Crystallography Center in the highest regard. It provides an essential service for my lab’s structurebased drug design efforts, enabling many projects. The highly skilled center staff are approachable, always supportive of my trainees and seamlessly help troubleshoot issues as they arise.”

– Richard Lee, PhD

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Georgi Kanev, PhD, Sr. Computational Research Scientist

Involved in

20+ full

scientific collaborations.

COM P UTAT I ONA L STRU C T U R A L B IO LO GY CE N T ER Over 150 petabytes of biological data are available through various openaccess databases, including information on genomics and gene expression, protein and cellular data, biomolecular networks and clinical data. Since its establishment in 2020, the mission of the Computational Structural Biology Center (CSBC) has been to mine this vast amount of data to discover new biological insights and mechanisms, identify and characterize functional elements within disordered regions of human and pathogen proteins, identify new drug targets and develop new compounds to help guide therapeutic development at St. Jude.

8 peer-reviewed papers and 1 patent application involving CSBC member contributions, with several more being prepared and submitted.

“The CSBC is unique in that we’re not built around a single core technology, but by construction, we strive to bring cutting-edge technologies in computational biology to support the ongoing mission at St. Jude. We develop, adapt and tailor modern computational methods to harness the power of data-driven science in an age of everincreasing data abundance.”

– Duccio Malinverni, PhD

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Comprehensive cryo-EM training provided from sample vitrification, grid clipping (pictured), and imaging

Contributed to

18 peer-reviewed

publications, including

9 with staff members CRYO - EM C ENTER The Cryo-EM Center was established in 2018 to enable researchers across St. Jude to visualize intricate biological structures with electron imaging techniques in cryogenic conditions.

The Cryo-EM Center aims to establish itself as a leader in this rapidly evolving field and to help train the next generation of structural biologists.

Members of the Cryo-EM Center staff provide extensive support and individualized training to investigators at all levels and over the complete workflow for structure determination by single-particle cryo-EM — from sample preparation to data collection, image processing, 3D reconstruction and structure modeling. The team fosters a collaborative environment by hosting monthly meetings where cryo-EM users can present their work and receive feedback from the community.

as co-authors. In 2023, the center contributed to 5 publications so far, with several more under review.

Upgraded Krios system can now acquire up to 730 images per hour, a substantial increase from the 230 images per hour it could acquire in 2021.

“We have collaborated with the Cryo-EM Center to prepare grids, perform negativestain imaging to screen for suitable samples, acquire high-quality cryo-EM images, and process the data. The Center staff is supportive and dedicated, and I look forward to receive further training from them.”

– Zaigham Khan, PhD

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Ajay Singh Tanwar, PhD, Lead Researcher, Protein Technologies Center

PTC staff members co-authored

22 publications

by the end of 2022.

P ROT EI N TECH N O LO G I ES C ENTER Established in 2019, the Protein Technologies Center (PTC) serves researchers across the institution, focusing on biochemistry and the structure-function relationship of proteins and protein complexes. The PTC tackles challenging biological systems, such as membrane proteins and macromolecular assemblies, by employing semi-automated and multipronged approaches, from construct design to cloning, protein expression, purification and characterization.

The PTC also offers training and assistance to researchers at all levels with biophysical characterization and molecular interaction analyses.

200 project requests for biophysical characterization of protein samples in 2022.

“The PTC has been indispensable to our project, which aims to determine the ligand-bound structure of membrane transporters; this can only be accomplished by producing high-quality protein samples that are amenable to our assays and analysis. The PTC has excelled at this.

Second, the former is impossible without a staff that facilitates the process by being collegial, approachable and helpful in advising on approaches and tactics that can help advance our project.”

– John Schuetz, PhD

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Daniel Terry, PhD, Principal Scientific Computing Engineer

SI N G L E- MO L EC U LE I MAG I N G C ENTER The Single-Molecule Imaging Center (SMC) was founded in 2019 to facilitate investigations into biological systems, revealing their conformational dynamics during function and molecular mechanisms that can explain dysfunction in disease states. The goal of the SMC is to ensure that this cutting-edge technology is accessible to non-expert users through userfriendly instrumentation design and software interfaces, along with the assistance of its experienced staff.

The center is highly collaborative and encourages proposal submissions for potential collaborations.

226

Facilitated microscope sessions, generating

54

terabytes of data, in 2023.

“The ability to make biophysical measurements and get these types of quantitative insights is one of the advances of single-molecular imaging that never ceases to amaze me.”

– Scott Blanchard, PhD

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Structural Biology

Scan to learn more about the St. Jude Structural Biology Department.

SCEO 235506 9/23 ©2023 St Jude Children’s Research Hospital

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