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Too young to win a prize in Stockholm this December? We don’t think so.
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Page 1: Tooyoungtowinaprize inStockholmthisDecember? Wedon’tthinkso. · 2018-10-09 · Once a protein crystallizes, investigators take it to one of a few government-funded synchrotron facilities

Too young to win a prizein Stockholm this December?

We don’t think so.

Page 2: Tooyoungtowinaprize inStockholmthisDecember? Wedon’tthinkso. · 2018-10-09 · Once a protein crystallizes, investigators take it to one of a few government-funded synchrotron facilities

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Duolink image credit: Caroline Welsch, Gustave Roussy Comprehensive Cancer Centre

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Page 3: Tooyoungtowinaprize inStockholmthisDecember? Wedon’tthinkso. · 2018-10-09 · Once a protein crystallizes, investigators take it to one of a few government-funded synchrotron facilities

Dear Colleagues:

On behalf of the AAAS Board of Directors, it is my

honor to invite you to join us in Boston for the 2017

AAAS Annual Meeting, February 16-20.

The AAAS Annual Meeting is the most widely recognized

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The 2017 meeting theme—Serving Society Through Science Policy—focuses on how to

inform policies with the best available scientifc evidence.

We look forward to seeing you in Boston. Registration and housing open in August.

Barbara Schaal

AAAS President

Dean of the Faculty of Arts and Sciences

Mary-Dell Chilton Distinguished Professor of Biology

Washington University in St. Louis

SERVING SOCIETY THROUGH

SCIENCE POLICY

aaas.org/meetings

A M E R I C A N A S S O C I A T I O N F O R T H E A D V A N C E M E N T O F S C I E N C E

Page 4: Tooyoungtowinaprize inStockholmthisDecember? Wedon’tthinkso. · 2018-10-09 · Once a protein crystallizes, investigators take it to one of a few government-funded synchrotron facilities

Don’t miss the debut of

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age:Eraxion/iStockPhoto

Page 5: Tooyoungtowinaprize inStockholmthisDecember? Wedon’tthinkso. · 2018-10-09 · Once a protein crystallizes, investigators take it to one of a few government-funded synchrotron facilities

306 sciencemag.org/custom-publishing SCIENCE

LIFE SCIENCE TECHNOLOGIES

PROTEOMICS

Produced by the Science/AAAS Custom Publishing Office

Within a single generation, researchers discovered

that DNA was the genetic material encoding

RNA, which in turn encodes proteins, and these

proteins carry out the principal enzymatic reac-

tions of life. They established that the sequences of proteins

ultimately determine their 3D structures, which determine their

%&'(���'���������������%���������' ���������%��� ������

sequence genomes, predict the protein structures they encode,

and build accurate models of all of life.

Half a century later, a few problems persist. One of the

toughest is the challenge of getting from an amino acid se-

quence to a 3D protein structure. Though the former ostensi-

bly determines the latter, the exact rules of the peptide-folding

process remain largely inscrutable. Nonetheless, computa-

tional biologists continue to chip away at the problem, pro-

ducing an evolving series of tools that can predict some class-

es of protein structures quite accurately. In the meantime, the

classic technique of X-ray crystallography has become more

accessible to nonspecialists, and a revolutionary series of

developments in electron microscopy is revealing structures

that previously eluded understanding.

Advancing crystallography ��������'�����'�������� �(�������(&����������%����������

principles, X-ray crystallographers attack the problem from

the opposite direction, purifying and crystallizing a protein

' ����'����&��'�������� ����(���������%������������

technique can be tedious, often requiring thousands of ex-

periments to determine the conditions that will yield usable

protein crystals. Today, though, biologists can let robots do

much of the work.

ìRobots enable one to set up much smaller crystallization

drops, so that you need smaller amounts of sample to screen

large numbers of conditions,î says Cynthia Wolberger, a pro-

fessor of biophysical chemistry at Johns Hopkins School of

Medicine��'���������������' ���'&%(�&�����'��������

������(����������������� ����(���(����%��������'��(������

lization conditions, such as the TTP Labtech mosquito and

the Formulatrix Rock Imager. Meanwhile, rapid cloning and

protein expression platforms let researchers produce multiple

���'����%��������'������' ��'����������(���������������

Crystallographers have also improved their ability to study

membrane proteins, which have been notoriously hard to

(������������������'������ ��������' �������'���'����(���(�

proportions, researchers can form a cubic liquid crystal ame-

'������������ ����(���'����������� ��� &������'���''�����

quantities of protein. ìThis is a huge advance,î says Martin

!�����������%�������%����(���������' ����&'��������Trin-

ity College��'�"&���'��#���' ��!������ ��������& �����%�

G-protein coupled receptors and other critical membrane pro-

teins ìreally underwent an explosion as a result of this cubic

phase methodology.î

Once a protein crystallizes, investigators take it to one of

a few government-funded synchrotron facilities to have it

bombarded with X-rays and to collect their data. That process

has also gotten easier in recent years. ìWe rarely go [to the

synchrotron] anymore; we ship our crystals there,î says Wol-

berger, adding that ìitís all been set up with great software

and robotics so you can operate it from anywhere.î

Improvements in synchrotron data collection systems now

enable analyses that would have been impossible just a few

years ago. A process called ìraster scanningî allows research-

�����������'��(������$' ������������'���%�(������$�����' �

����������������� ����(���'��'�������������&� ����������

be unusable. Automated, high-speed data collection also per-

mits scanning many more crystals. For example, Wolberger

and her colleagues recently analyzed over a thousand crystals

to gather enough information for a structure, an approach that

would have been impractical with manual exposures.

GenomicsóOctober 7 NeurotechniquesóNovember 4 Cell AnalysisóNovember 25

Upcoming Features

"������� �'(����'��������� ��%���������(���������'�%�� �'��

still remains a mystery. Yet innovations in X-ray crystallogra-

phy, electron microscopy, and data analysis (think robots and

Google) are yielding answers about protein structures faster

than ever before. By Alan Dove

Structural biology shapes up

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Page 6: Tooyoungtowinaprize inStockholmthisDecember? Wedon’tthinkso. · 2018-10-09 · Once a protein crystallizes, investigators take it to one of a few government-funded synchrotron facilities

307SCIENCE sciencemag.org/custom-publishing

LIFE SCIENCE TECHNOLOGIES Produced by the Science/AAAS Custom Publishing Office

PROTEOMICS

ìHit and runîThe X-ray beams themselves have improved too, with newer

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reason not to try to do that; in my lab we do that as a matter of

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Page 7: Tooyoungtowinaprize inStockholmthisDecember? Wedon’tthinkso. · 2018-10-09 · Once a protein crystallizes, investigators take it to one of a few government-funded synchrotron facilities

308 sciencemag.org/custom-publishing SCIENCE

LIFE SCIENCE TECHNOLOGIES

PROTEOMICS

Produced by the Science/AAAS Custom Publishing Office

DOI: 10.1126/science.opms.p1600107

Alan Dove is a science writer and editor based in Massachusetts.

FEATURED PARTICIPANTS

Centre for Integrative Systems Biology and Bioinformaticswww.imperial.ac.uk/integrative-systems-biology

Computation Institute,University of Chicagowww.ci.uchicago.edu

Direct Electronwww.directelectron.com

FEIwww.fei.com

Formulatrixwww.formulatrix.com

Gatanwww.gatan.com

Hampton Researchwww.hamptonresearch.com

Johns Hopkins Schoolof Medicinewww.hopkinsmedicine.org

MiTeGenwww.mitegen.com

Molecular Dimensionswww.moleculardimensions.com

Trinity College Dublinwww.tcd.ie

some protein samples we can do pretty well, since now we

have much more data, so we can apply or develop much more

sophisticated techniques to model the sequenceñstructure

relationship,î says Jinbo Xu, a senior fellow of the Computa-

tion Institute at the University of Chicago. Xu is the principal

investigator behind RaptorX, another online portal for predicting

secondary and tertiary protein structures.

In addition to template-based modeling, some researchers

are now exploring a technique called ìcontact prediction.î

This approach searches through vast troves of sequence data

to identify evolutionarily conserved amino acid interactions,

then uses those correlations to predict a novel sequenceís

folding patterns. ìThatís certainly proving very useful for

membrane-bound proteins where there are very few crystal

structures available,î says Sternberg, but he adds that ìyou

still need quite a large number of aligned sequencesî for con-

tact prediction to work.

Besides improving the underlying algorithms, computational

biologists have been working on making their system inter-

faces friendlier. ìWeíre very much following the sort of Google

approach of a very clean screen, not inundating the user with

many options, and really only delivering what the user wants,î

says Sternberg. It seems to be working. Sternberg estimates

that of the 44,000 unique users who accessed Phyre2 last year,

only a few hundred contacted him or Kelley for support.

Expanding options Xu and his colleagues have also embraced the user-friendly

model, with similar results. ìThe broader community is using

the tools, [and] the users of my server have very diverse back-

grounds,î he says. Researchers without structural biology train-

ing may not understand the limitations of the underlying algo-

rithms, so most of the major portals are designed to help users

interpret their results. RaptorX provides a quality evaluation

along with each protein model, scoring how likely the structure

"#$%�$��$������%�$�"�"����$� ���$����"��#$�$������$����$�����$

score, as well as individual scores for substructures down to the

amino acid level.

Because all of the major structure prediction tools are free

online, scientists can also hedge their bets by sending their

target sequences to all of them to see how the models dif-

fer. Another site, CAMEO,$�#�$%�#%#$��$�%�#$% �$�"�$����%$

protein-structure services. Each week, CAMEO sends a test

sequence to all of the participating servers, then calculates

benchmarks based on the systemsí speed, server reliability,

and other characteristics.

�"�$����%$%���#$�#�$ ��$�"#%"��%$#%����% #$��$����

��##�#$������"��$��$$��#��� ���#$#���"�$�$����#�$��%���$

emphasizes template-based modeling for particularly chal-

lenging proteins, while other portals are better suited for rapid

analysis of large numbers of relatively well-characterized

���%�"�$��"�"�#�$� ���$��$��#$$#�"%�$��$��"%"���$#���"��#�$

the ìPhyre Alarm,î for example, will send an email to research-

ers when new data allow the system to calculate an improved

model of their protein.

Regardless of the approach they choose, investigators seek-

ing protein structures should expect more good news. Survey-

ing the progress in all three techniques, Agard echoes the gen-

eral sentiment of structural biologists: ìItís a fabulous time in

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company, FEI, and sensors for them are made by it, Direct

Electron, and Gatan. Regardless of which vendors and instru-

ments one chooses, a complete cryo-EM system costs several

million dollars to buy, and several hundred thousand annually

to maintain and operate. ìOnly the richest labs or institutions

that are subsidizing this will be able to do this, and thatís not

a good situation in terms of national capabilities,î says Agard.

Germany, the United Kingdom, and China have all established

national-level funding for cryo-EM facilities, while the U.S. Na-

tional Institutes of Health is still deciding how to proceed.

Siri, what does the protein look like?Regardless of how fast X-ray crystallography and cryo-EM

develop, though, neither is likely to satisfy researchersí growing

desires for structural models. ìYou canít beat an experimentally

determined structure, [but] the challenge is the vast number of

�� ���������������� ������ ������ ����������������������

sible task of devising 3D structures for all the proteins,î says

Michael Sternberg, director of the Centre for Integrative

Systems Biology and Bioinformatics at Imperial College Lon-

don, United Kingdom.

To address that challenge, Sternberg and his colleague

Lawrence Kelley have focused on the decades-old dream of

molecular biologists: predicting protein structures directly from

sequence information. The teamís latest tool, Phyre2, uses

template-based modeling, a process that compares a se-

quence against a global database of previously solved protein

structures. Several other research groups have developed simi-

lar tools, which are accessible online to researchers worldwide.

These tools can yield impressive results, at least for pro-

tein families that are well-represented in the databases. ìOn

TTP Labtechwww.ttplabtech.com

University of California, Berkeleywww.berkeley.edu

University of California, San Franciscowww.ucsf.edu

University of Chicagowww.uchicago.edu

ADDITIONAL

RESOURCES

CAMEO

www.cameo3d.org

Phyre2

www.sbg.bio.ic.ac.uk/phyre2

RaptorX

raptorx.uchicago.edu

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