ISSN 0006-2979, Biochemistry (Moscow), 2024, Vol. 89, No. 4, pp. 585-600 © Pleiades Publishing, Ltd., 2024.
585
REVIEW
Cohesin Complex:
Structure and Principles of Interaction with DNA
Arkadiy K. Golov
1,2,a
* and Alexey A. Gavrilov
1,b
*
1
Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia
2
Technion – Israel Institute of Technology, 3525433 Haifa, Israel
a
e-mail: golovstein@gmail.com
b
e-mail: aleksey.a.gavrilov@gmail.com
Received October 14, 2023
Revised February 19, 2024
Accepted February 23, 2024
Abstract— Accurate duplication and separation of long linear genomic DNA molecules is associated with a number
of purely mechanical problems. SMC complexes are key components of the cellular machinery that ensures decat-
enation of sister chromosomes and compaction of genomic DNA during division. Cohesin, one of the essential eu-
karyotic SMC complexes, has a typical ring structure with intersubunit pore through which DNA molecules can be
threaded. Capacity of cohesin for such topological entrapment of DNA is crucial for the phenomenon of post-rep-
licative association of sister chromatids better known as cohesion. Recently, it became apparent that cohesin and
other SMC complexes are, in fact, motor proteins with a very peculiar movement pattern leading to formation of
DNA loops. This specific process has been called loop extrusion. Extrusion underlies multiple functions of cohesin
beyond cohesion, but molecular mechanism of the process remains a mystery. In this review, we summarized the
data on molecular architecture of cohesin, effect of ATP hydrolysis cycle on this architecture, and known modes of
cohesin–DNA interactions. Many of the seemingly disparate facts presented here will probably be incorporated in
a unified mechanistic model of loop extrusion in the not-so-distant future.
DOI: 10.1134/S0006297924040011
Keywords: SMC complexes, cohesin, SMC subunits, kleisin, HAWK subunits, cohesion, topological entrapment, loop
extrusion, DNA gripping state
Abbreviations: HAWK,HEAT protein associated with Kleisin;
SMC,structural maintenance of chromosomes proteins.
* To whom correspondence should be addressed.
INTRODUCTION
Cohesin is a paneukaryotic protein complex be-
longing to the group of structural maintenance of
chromosomes proteins (SMC) participating in the pro-
cesses of individualization of sister chromatids, chro-
mosome decatenation, mitotic and meiotic cohesion,
establishment and maintenance of specific DNA fold-
ing in cells, repair of double-strand breaks, and sta-
bilization of stalled replication forks [1,2]. Similar to
other SMC complexes, cohesin, on the one hand, com-
prises a multisubunit ABC-ATPase, and, on the other
hand,– a non-sequence-specific DNA-binding complex.
Binding and hydrolysis of ATP are coupled with con-
formational changes in cohesin, as well as with changes
in affinity of different components of the complex to
DNA. The repeating binding/ATP hydrolysis cycles
result in the directional movements of the complex
along the DNA thread; hence, cohesin is a motor pro-
tein– DNA translocase.
Cohesin performs two different functions in the
eukaryotic cells: mediating sister chromatid cohe-
sion and so-called chromatin loop extrusion (Fig. 1a).
The process of extrusion starts with the capture of a
small DNA loop followed by its processive enlargement
by pulling DNA flanking regions inside [3-6]. An active
SMC complex is located at the basis of growing loops,
and their size could reach up to hundreds of thou-
sands of base pairs (Fig. 1a (2)). Extrusion is coupled
with ATP hydrolysis and represents a universal bio-
chemical activity of all SMC complexes[1]. Most likely,
extrusion appeared at the dawn of cellular evolution
as a way of post-replicative separation of the massive
molecules of genomic DNA(Fig.1b); in this process the
GOLOV, GAVRILOV586
BIOCHEMISTRY (Moscow) Vol. 89 No. 4 2024
Fig. 1. Sister chromatid cohesion and DNA loop extrusion is mediated by SMC complexes. a)Two basic activities of cohesin:
cohesion(1) and extrusion (2). b)Extrusion mediated by SMC complexes, and activity of type II DNA topoisomerases ensure
post-replicative individualization of sister genomes in all cells, prokaryotic and eukaryotic.
SMC complexes cooperate with the typeII topoisomer-
ases. Cohesion of sister chromatids mediated by cohes-
in rings (Fig. 1a (1)), most likely, does not depend on
the extrusion activity of the complex [7, 8], although
ATP hydrolysis is also required for the loading of co-
hesin rings onto DNA [7,9].
Information on the protein structure is important
for understanding their activity and even more im-
portant for understanding activity of motor proteins.
In this review the data on cohesin structure as well as
current understanding of its interactions with DNA,
conformational changes, and how interactions with
DNA and binding/ hydrolysis of ATP control these con-
formational changes are presented. Detailed data on
the biological role of the cohesin-dependent extrusion,
as well as molecular mechanism of this process are
presented in the second part of this review published
in the same issue of this journal[10].
ANNULAR CORE COHESIN TRIMER COMPLEX
All eukaryotic genomes encode at least four SMC
complexes from three different classes: two variants
of cohesin (mitotic and meiotic), condensin I, and
SMC5/6 complex[3,4] (table). Trimer composed of two
SMC subunits and one kleisin subunit forms an invari-
ant basis of SMC complexes [2, 3,11]. SMC proteins[12]
and kleisins[13] represent two unrelated protein fam-
ilies. Different classes of SMC complexes are separat-
ed by hundreds of millions of years of evolution and
lost their homology in the larger part of their amino
acid sequences, while similarity within the short func-
tionally important motifs was retained, as well as their
common basic structure [14]. Nevertheless, a signifi-
cant degree of conservation has been observed within
the six main subfamilies of eukaryotic SMC proteins
(SMC1-6) and three subfamilies of eukaryotic kleisins
(kleisinsα-γ). The especially high degree of conserva-
tion is observed within the SMC1- and SMC3-subfam-
ilies. For example, the human and mouse SMC3 are
practically identical.
In the case of cohesin (here and further we con-
sider the better described mitotic variant of the com-
plex) the pair of SMC proteins is represented by the
SMC1 (Smc1)–SMC3 (Smc3)
1
heterodimer and the klei-
sin subunit– by the RAD21 protein (Scc1). SMC proteins
are rod-like molecules with length of about 50nm with
two globular domains at the ends connected via rela-
tively labile fibrillar structure (Fig.2a)[16-18]. Within
the rod-like structure of the SMC protein 1200-1300aa
long polypeptide chain is folded back on itself so that
1
Names of human proteins are used in the main text and names of homologous Saccharomyces cerevisiae proteins are given
in parenthesis (at first mention).
COHESIN COMPLEX STRUCTURE 587
BIOCHEMISTRY (Moscow) Vol. 89 No. 4 2024
Subunit composition of paneukaryotic SMC complexes
Complex →
Meiotic cohesin Mitotic cohesin CondensinI SMC5/6 complex
↓ Subunit
ν-SMC SMC3 (Smc3) SMC3 (Smc3) SMC2 (Smc2) SMC6 (Smc6)
κ-SMC SMC1 (Smc1) SMC1α (Smc1) SMC4 (Smc4) SMC5 (Smc5)
Kleisin REC8 (Rec8) RAD21 (Scc1) CAP-H (Brn1) NSE4A/B (Nse4)
HAWK
A
PDS5A/B (Pds5) NIPBL (Scc2) and PDS5A/B (Pds5) CAP-D2 (Ycs4) –
HAWK
B
STAG3 (Scc3) STAG1/2 (Scc3) CAP-G (Ycg1) –
KITE
A
– – – NSE5 (Nse5)
KITE
B
– – – NSE6 (Nse6)
Note. HAWK-subunits are present only in cohesins and condensins, while prokaryotic SMC complexes and SMC5/6 complex have
auxiliary subunits in their composition belonging to the group of KITE-proteins[15]. Names of the human subunits are present-
ed as well as names of homologous subunits of Saccharomyces cerevisiae (in parenthesis).
Fig. 2. Subunit structure of cohesin complex. a) Folding and main structural features of SMC proteins. b)General structure
of three-part cohesin ring and interaction of HAWK-subunits with it. c) General structure of hook-shaped HAWK-subunits
inSMCcomplexes.
one of the terminal globular domains is formed as a
result of interactions of N- and C-ends, and another is
formed by the uninterrupted sequence located approx-
imately in the middle of the linear sequence [17, 19].
The first of the globular domains was termed head
domain, and the second – hinge domain; polypeptide
chain of the SMC protein makes a 180° turn within the
latter. Fibrillar structure connecting two globular do-
mains comprises an intramolecular coiled-coil struc-
ture termed arm domain.
Stable dimerization of the SMC proteins is achieved
via homotypic interactions between the hinge domains
[17, 18]. Coiled-coil arm domains are directed to the
same direction away from the interacting hinge do-
mains; hence, the SMC1–SMC3 dimer in the absence
of ATP comprises a V-shaped structure with dimerized
GOLOV, GAVRILOV588
BIOCHEMISTRY (Moscow) Vol. 89 No. 4 2024
Fig. 3. Diversity of cohesin conformational states. a)O-, E-, and J-configurations of cohesin head domains and transitions be-
tween them, RAD21-subunit is not shown for better clarity. S-K-ring and subcompartments (E-S, E-K, and J-K) formed as a result
of head domains engagement are shown in pictograms. b)Major conformational states of cohesin detected using microscopy.
hinge domains at one pole and pair of separated head
domains at another pole [17,20].
The RAD21-kleisin subunit has length of approx-
imately 500-700 aa with two structured domains at
N- and C-ends, and extended mostly disordered region
between them [13]. The N-terminal domain of kleisin
interacts with the region connecting the head and arm
domains of SMC3 subunit, while the C-terminal do-
main– with the head domain of SMC1(Fig.2b)[21].
Molecules of the three core subunits of cohesin
form a closed annular structure through stable inter-
actions between the termini[17,22]. Elongated shape
of each of the core subunits results in formation of co-
hesin conformations in which it assumes an expanded
topologically closed intersubunit compartment called
S-K-ring(Fig.3a). Opening of the S-K-ring, also called
S-K-compartment, allows passage of globular parti-
cles with diameter of up to around 10 nm through
it[23,24]. It was shown that one or two DNA threads
can be entrapped within the S-K-compartment, thus
the ring-shaped complex can be put on the DNA as a
bead on a string. Inthe G2-phase of cell cycle such to-
pological interactions of cohesin molecules with the
pairs of sister chromatids mediate cohesion [7].
Hinge domains of the SMC proteins comprise
compact structures consisting of two (N- and C-termi-
nal) subdomains of α/β-class; each of the subdomains
contains a small β-sheet [17, 18]. The N-terminal sub-
domain interacts with the C-terminal subdomain of its
dimerization partner with merger of their β-sheets.
Hence, two separate surfaces are involved in the in-
teraction between two hinge domains of the dimer.
Dueto the fact that the two hinge subdomains are sep-
arated by a small groove, the dimerized hinge domains
look like a toroidal structure with the 2-fold rotation-
al pseudosymmetry (Fig.2b). Small channel inside the
hinge domain dimer contains functionally important
positively charged amino acids, which are assumed to
be able to participate in electrostatic interactions of
the complex with DNA. Asymmetry in the heterodimer
of cohesin SMC subunits allows distinguishing two in-
teraction surfaces of the hinge domains. One of them,
which is at a larger distance from the head domains
is commonly known as a northern one, and another–
asa southern (Fig.2b).
The arm domain of each SMC protein compris-
es a pair of antiparallel coiled-coils each consisting
of 300-400 aa. Coiled-coils of the arm domains have
a number of defects in which one or both antiparal-
lel chains lose their regular α-helical structure [19].
Two such breaks in the coiled-coil of the arm domain
have high degree of evolutionary conservation and,
most likely, play an important role in the activity of
SMCcomplexes. The first one, located around the mid-
dle of the arm domain a bit closer to the hinge domain
has been called ‘elbow’ (Fig. 2a). This region ensures
mechanical flexibility of the arm domains: simulta-
neous bending of the two ‘elbow’ regions could bring
the hinge domains into the close proximity of the head
domains (Fig. 3b). The second conserved break of the
coiled-coil is located close to the head domain at the
distance of approximately 50aa; it is commonly called
‘joint’(Fig.2a). ‘Joints’ in the SMC subunits are import-
ant hubs of interactions with the auxiliary subunits
COHESIN COMPLEX STRUCTURE 589
BIOCHEMISTRY (Moscow) Vol. 89 No. 4 2024
ofthe complex [25], they also participate in the move-
ments of the head domains relative each other [26].
Head domains of the SMC proteins comprise ABC-
type ATPases[16,27]. Similarly to other ABC-proteins,
cohesin is capable of hydrolyzing ATP only during
physical interaction between ATPase domains of two
SMC subunits (Fig. 3a) [28, 29]. Head domain of one
of the subunit of the dimer binds an ATP molecule,
and the head domain of the other is required for hy-
drolysis of the bound molecule. Each cycle of the co-
hesin-dependent ATP hydrolysis involves binding of
ATP by each of the head domains, and as a result two
ATP molecules are hydrolysed. Engagement of head
domains is terminated after nucleoside triphosphate
hydrolysis and is established again after binding of a
new pair of ATP molecules. Hence, in contrast to inter-
action of the hinge domains with each other, dimeriza-
tion of the head domains depends on the presence of
the substrate and has dynamic nature (Fig.3a).
From the structural point of view the ABC-ATPase
of the head domain is a globule with the core consisting
of an open β-cylinder with β-strands belonging to both
N- and C-terminal parts of the SMC protein[9, 16,28].
At one of the poles of the β-cylinder there are two con-
served catalytically significant sequences: Walker A mo-
tif (also known as a P-loop or phosphate-binding loop)
and Walker B motif. Both these motifs are typical not
only for all representatives of the ABC-ATPase super-
family, but also for the wider monophyletic protein
group called P-loop NTPases[27]. The Walker A motif,
located in the N-terminal part, is responsible for bind-
ing β- and γ-phosphate groups of ATP. The Walker B
motif is located in the C-terminal part and is responsi-
ble for coordination of Mg
2+
in the active center. Unlike
in the case of other P-loop NTPases, effective hydroly-
sis of the phosphate bond by the ABC-ATPases requires
spatial interaction between nucleotide triphosphate
bound by the Walker A and B motifs and the serine
residue within the so-called SGG-motif. The SGG-mo-
tif is also located in the head domain, but at the rela-
tively large distance from the ATP-binding β-cylinder,
hence, such interaction is impossible within the head
of SMC monomer, it could be realized only between
the ATP-binding site of one head domain and SGG-mo-
tif of another one during their dimerization (Fig. 3a).
That is why ATPase activity of cohesin can be realized
only during physical engagement of the head domains
of two SMC subunits of the complex.
The structured N- and C-terminal domains of
RAD21 interact with two head domains of two SMC
proteins asymmetrically (Fig.2b)[30]. The N-terminal
domain of RAD21 binds to the site on the arm coiled-
coil coming out of the head domain of SMC3 Part of
the arm domain that binds N-terminal domain of klei-
sin is located between the head domain and ‘joint’
and is called ‘neck’. Fragment of the neck site of the
SMC3 coiled-coil domain interacts with two N-terminal
α-helices of RAD21 with formation of four-α-helix bun-
dle[30,31]. The C-terminal globular domain of RAD21
has a winged-helix fold and interacts with the top of
the SMC1 head domain[32].
INTERACTIONS
OF THE REGULATORY HAWK-PROTEINS
WITH THE KLEISIN
The core cohesin trimer interacts with three
auxiliary subunits: STAG1/2
2
(Scc3), PDS5A/B (Pds5),
and NIPBL (Scc2). The auxiliary subunits participate
in the complex binding to DNA and regulation of its
activity [1-3]. The disordered central part of RAD21
represents the major binding site for the auxiliary sub-
units on the core trimer [33-35].
All three auxiliary subunits of cohesin belong to
the family of HAWK-proteins (HEAT proteins associat-
ed with kleisin) [15]. These α-helical hook-shaped pro-
teins (Fig. 2c) [33, 36] are composed of around 20tan-
dem HEAT-repeats[37]. Each repeat consists of 30-40aa
organized as a pair of interacting antiparallel amphip-
athic α-helices. α-Helices of each HEAT- repeat are ar-
ranged perpendicularly to the axis of the HAWK-sub-
unit hook. Inner concave surface of the HAWK hook
interacts with kleisin-subunit.
STAG1/2 binds to kleisin stably and, hence, is a
constitutive component of the complex [38]. NIPBL and
PDS5A/B interact with kleisin transiently; moreover,
these two subunits compete with each other for
the same binding site [35]. Hence, at each time point
the complex could contain one (STAG1/2) or two
(STAG1/2+ NIPBL or STAG1/2 + PDS5A/B) HAWK-sub-
units (Fig. 2b). Binding of NIPBL or PDS5A/B dramat-
ically changes activity of the cohesin complex [35].
NIPBL increases substantially ATPase activity of the
complex [39, 40]. This subunit is essential for the co-
hesin-dependent loop extrusion[40, 41]. PDS5A/B-sub-
unit supresses ATPase activity, and in its presence the
WAPL protein could be recruited to the cohesin ring,
which stimulates dissociation of the N-terminal part
of RAD21 from the SMC3 subunits[42, 43]. Acetylation
of the SMC3 subunit, as well as interaction of the com-
plex with other chromatin components such as insu-
lator protein CTCF, regulates binding of NIPBL and
PDS5A/B to the cohesin ring[25, 44-46].
2
Vertebrate genomes generally encode a pair of somatically expressed paralogs for both Scc3 and Pds5 HAWK-proteins:
STAG1/STAG2 and PDS5A/PDS5B. These paralogs in the majority of cases are structurally and functionally equivalent, hence,
here and further in the text the designations STAG1/2 and PDS5A/B are used.
GOLOV, GAVRILOV590
BIOCHEMISTRY (Moscow) Vol. 89 No. 4 2024
CONFORMATIONAL POLYMORPHISM
OF COHESIN COMPLEX
Activity of all proteins one way or another is asso-
ciated with ligand-dependent conformational changes.
SMC complexes demonstrate ability of radical confor-
mational rearrangements, which mediate their motor
activity.
Various microscopic techniques, X-ray crystallog-
raphy, as well as indirect approaches for elucidation of
structure such as Förster Resonance Energy Transfer
(FRET), chemical cross-linking, and analysis of stability
of DNA–protein complexes in various physicochemical
conditions facilitated discovery of a wide spectrum of
cohesin conformational states (Fig.3b)[3,4].
Entire variety of the known cohesin conforma-
tions could be described to a large degree by three
parameters: (1) engagement of head domains of the
two SMC subunits, (2) distance between the hinge and
head domains controlled by the degree of the elbow
bending, (3) distance between the arm coiled-coils of
two SMC subunit. For example, in both I-conformation
and folded conformation head domains are engaged,
and arm’s coiled coils interact along the entire length;
difference is in the fact that in the first conformation
arm domains are in the straightened state, while in
the second conformation – in the fully bended state.
O- and B-conformations differ from the previous pair
by the fact that interactions between the arm domains
are absent (Fig.3b).
Part of conformational rearrangements of cohes-
in is strictly coupled with ATP binding or hydrolysis,
while others occur spontaneously. It is likely though
that the direction of some spontaneous cohesin rear-
rangements could be controlled by the irreversible
processes of ATP binding and hydrolysis.
Dimerization of head domains and ATP hydro-
lysis. ATP binding induces tight interaction between
the two cohesin head domains, the so-called E-state
(engaged state) [9, 28, 47]. This short-lived structure
breaks down after ATP hydrolysis (Fig.3a). ATP hydro-
lysis is followed by the release of the products of hy-
drolysis and change in positioning of the head domain
relative to each. It was originally assumed that ATP
hydrolysis inevitably leads to a complete separation of
head domains in a structure known as an O-state (open
state). However, it has been later discovered that even
in the absence of ATP the structure called J-state (jux-
taposed state) can be formed in which two head do-
mains interact in such a way that the SGG-motifs of the
pair of SMC proteins are brought close to each other
[26, 48] (Fig. 3a). Considering that this interaction is
realized through the surfaces located at a relatively
large distance in the E-state, transitions from E-state
to J-state and back involve significant rotation of the
head domains relative to each other.
Additional conformational changes coupled
with binding and hydrolysis of ATP. ATP binding
and engagement of head domains in E-state is coupled
with several important conformational rearrangements:
local separation of arm domains, temporal dissocia-
tion of kleisin from SMC3, establishing of an addition-
al bridge between the two head domains formed by
NIPBL[25,44,49].
Coiled-coils of the arm domains that are adjacent
to the head domains are in fixed orientation relative
to each other in the J- and E-states. Despite the relative
flexibility of the arm domains, comparatively long re-
gions of the coiled coils adjacent to the head domains
are constitutively separated in the E-state [25, 44, 49].
At the same time, position of the head domains in the
J-state ensures close proximity of the coiled-coil re-
gions of SMC1 and SMC3[26, 48]. The available struc-
tural data indicate that the arm domains in the J-state
are in contact with each other over their entire length
(Fig.3a). Hence, while in the absence of ATP (in the so-
called apo-form) the arm domains could be either sep-
arated, or interact with each other to a certain degree,
binding of ATP results in separation of the coiled coils
at least in the regions directly adjacent to the head do-
mains.
During interaction of the head domains with each
other in the E- and J-state the united S-K-compartment
is divided into two compartments (SandK) confined by,
respectively, SMC dimer and kleisin subunit (Fig. 3a).
Depending on the nature of the interaction between
the head domains, the following subcompartments can
be distinguished: E-K, E-S, J-K, and J-S; due to the tight
contact between the coiled coils of the arm domain,
the latter does not have any opening.
Another change of cohesin conformation associat-
ed with ATP binding in the active center is short-term
opening of the so-called N-kleisin gates of the complex.
At the moment of formation of the E-state, the N-termi-
nal domain of RAD21 dissociates from its binding site
at the SMC3 subunit[47,49], which results in temporal
disruption of integrity of the E-K compartment.
ATP binding also causes changes in the pattern
of NIPBL interaction with other subunits. In addition
to its main binding site in the central part of kleisin,
NIPBL has additional ATP-regulated sites of interac-
tion with the SMC subunits. In the absence of ATP
NIPBL interacts with the dimer of hinge domains;
ATP binding results in dissociation of NIPBL from the
hinge domains and attachment to the head domain of
SMC3 [50]. This jump of NIPBL, likely, stimulates for-
mation of the E-state, in which NIPBL forms addition-
al contacts with the head domain of SMC1[25, 44,49].
Apair of conserved lysine residues in SMC3, K105/K106
(K112/K113– inSmc3 S. cerevisiae), plays an important
role in the interaction of NIPBL with the SMC3 head
domain, acetylation of these residues by acetyl trans-
COHESIN COMPLEX STRUCTURE 591
BIOCHEMISTRY (Moscow) Vol. 89 No. 4 2024
ferase ESCO2(Eco1) is a key factor of stabilization of
the cohesive binding. Following ATP hydrolysis NIPBL
loses its interaction with the head domains and re-
stores interaction with the hinge domain site [50].
Spontaneous changes of cohesin conformation.
Microscopic observations, as well as the FRET data
indicate that the arm domains of cohesin and oth-
er SMC complexes are rather labile structures most-
ly due to the possibility of bending at elbows [17, 19,
49-51]. Amplitude of this bending reaches up to 180°
which makes possible direct physical interaction of the
head and hinge domains in the completely bent state
(Fig.3b).
Discovery of the J-state and recognition of the fact
that transitions between the E- and J-states should be
accompanied by the significant changes in the mutual
position of the arm domains led to the suggestion of a
hypothesis according to which bending and straighten-
ing of the elbow domains should be strictly controlled
by the ATP hydrolysis cycle [19]. However, experi-
mental data obtained later indicate that bending and
straightening of the elbows occur spontaneously [50].
The most important consequence of bending and
straightening of the elbows is the engagement of the
hinge domains with the head domains in the complete-
ly bent state. The possibility of temporal interaction be-
tween the head and hinge domains is a crucial premise
of many mechanistic models of SMC-dependent loop
extrusion[19, 50, 52, 53]. Despite the fact that bending
of the arm domains occurs spontaneously, there are
indication that there could be a ratchet mechanism
coupling bending and ATP hydrolysis. In particular, it
has been suggested that the complete bending of the
elbow domain could be required for the formation of
the E-state[25,44,49,50].
Another known spontaneous change of the cohes-
in architecture is reversible interaction of the coiled-
coils adjacent to the hinge domains. Such interaction
spreads from the hinge domain towards the elbows
and, likely, is associated with winding of the two
coiled-coil domains of the arm around each other [50].
It is hypothesized that this winding can be a necessary
prerequisite for the bending of the elbows.
INTERACTIONS BETWEEN DNA AND COHESIN
Binding to DNA is a key aspect of activity of SMC
complexes. There are two characteristic features of
interactions between SMC complexes and DNA: (1) as-
sociation between changes in affinity of different sites
to DNA and changes in complex conformation and
(2) ability of the complexes to entrap DNA topologically.
Unlike the classic electrostatic interactions typical
for the majority of DNA-binding proteins, topological
binding represents a qualitatively different mode of
non-covalent binding for which there is no need in
direct physical contact between the DNA and the pro-
tein [1, 44]. Topologically entrapped DNA is threaded
through the closed S-K-ring of the complex like a string
threaded through a bead (Fig. 4a). In this scenario
complex can be stably associated with DNA even in the
absence of electrostatic interactions.
Cohesin can also interact with DNA electrostat-
ically: several positively charged sites on the com-
plex surface mediate such interactions (Fig.5)[3, 50].
An important feature of the electrostatic interactions
of cohesin with DNA is cooperativity: small individu-
al sites dispersed over the different subunits are not
generally capable to form stable contacts with DNA on
their own, sufficient affinity is achieved only by the
composite surfaces formed by several DNA-binding
sites from different subunits coming together. Such
composite surfaces are assembled in some cohesin con-
formations and disassembled in others. Thedynamical-
ly assembled DNA-binding sites are crucial elements of
the machinery that couples the processes of ATP hydro-
lysis, structural changes of the complex, and its move-
ment along the DNA thread during loop extrusion.
Topological entrapment of DNA within cohesin.
Cohesin, same as almost all other SMC complexes, is
capable of binding DNA topologically
3
. Three observa-
tions underlie the ring hypothesis according to which
cohesin could entrap DNA topologically inside the
three- part S-K-ring [22, 54]: (1) complex structure sug-
gesting existence of the extended topologically closed
compartment [17, 55]; (2) capability of the complex to
establish extremely stable interactions with chromatin
during the G2-phase[56, 57], and (3) immediate desta-
bilization of these interactions upon proteolysis of the
kleisin subunit in anaphase [21, 58]. After more than
a decade of accumulation of indirect clues, this hy-
pothesis was finally confirmed with the experiments
including covalent cross-linking of the cohesin rings
invivo[7,30,48].
A number of experimental approaches have been
suggested for confirming topological nature of protein
and protein complexes binding to DNA. Topological
nature of interaction may be indicated by the follow-
ing experimental observations: (i) stability of binding
in the high ionic strength buffers[39,56] (Fig.4b(1));
(ii) sensitivity of the interaction to proteolytic cleavage
3
In certain conformations cohesin can form, in addition to S-K ring, other non-covalently closed compartments in which DNA
strand can be entrapped. Such structures include NIPBL-SMC3-subcompartment, E-S-, E-K-, and J-K-subcompartments. Integ-
rity of such subcompartments, unlike integrity of the S-K-ring, is usually very quickly disrupted. In the text term ‘topological
binding’ refers to the DNA entrapment within the stable S-K-ring.